Question: flowQ loading error after installing ImageMagick
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6.7 years ago by
Guest User12k
Guest User12k wrote:
Hi All, I'm having a problem that has been mentioned here before but I'm not sure how to fix it. I tried to load flowQ and got: Error : .onAttach failed in attachNamespace() for 'flowQ', details: call: mysys("convert -list configure", intern = TRUE, ignore.stderr = TRUE) error: error in running command In addition: Warning messages: 1: replacing previous import ???plot??? when loading ???graphics??? 2: replacing previous import ???as??? when loading ???methods??? Error: package/namespace load failed for ???flowQ???. I have installed ImageMagick using Macports as has been suggested and I have also run convert -list configure, which gave the following: Path: /opt/local/lib/ImageMagick-6.8.0/config/configure.xml Name Value ---------------------------------------------------------------------- --------- CC /usr/bin/gcc-4.2 -std=gnu99 -std=gnu99 CFLAGS -D_THREAD_SAFE -D_THREAD_SAFE -pthread -fopenmp -pipe -O2 -arch x86_64 -Wall -D_THREAD_SAFE -pthread CODER_PATH /opt/local/lib/ImageMagick-6.8.0/modules-Q16/coders CONFIGURE ./configure '--prefix=/opt/local' '--enable-shared' '--enable-static' '--disable-ltdl-install' '--disable-silent-rules' '--with-frozenpaths' '--without-openexr' '--disable-hdri' '--with-dps' '--with-bzlib' '--with-fontconfig' '--with-gslib' '--with-jpeg' '--with-lcms' '--with-png' '--with-tiff' '--with-webp' '--with-zlib' '--with-modules' '--with-xml' '--with-x' '--without-perl' '--without- fpx' '--without-jbig' '--without-jp2' '--without-wmf' '--without-gvc' '--without-rsvg' '--without-lqr' '--without-pango' '--with-gs-font- dir=/opt/local/share/fonts/urw-fonts' '--with-quantum-depth=16' 'CC=/usr/bin/gcc-4.2' 'CFLAGS=-pipe -O2 -arch x86_64' 'LDFLAGS=-L/opt/local/lib -arch x86_64' 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/g++-4.2' 'CXXFLAGS=-pipe -O2 -arch x86_64' CONFIGURE_PATH /opt/local/etc/ImageMagick/ COPYRIGHT Copyright (C) 1999-2012 ImageMagick Studio LLC CPPFLAGS -I/opt/local/include/ImageMagick CXX /usr/bin/g++-4.2 CXXFLAGS -pipe -O2 -arch x86_64 -D_THREAD_SAFE -pthread DEFS -DHAVE_CONFIG_H DELEGATES bzlib fftw fontconfig freetype gs jpeg jng lcms2 lzma png tiff x11 xml zlib DISTCHECK_CONFIG_FLAGS 'CC=/usr/bin/gcc-4.2' 'CFLAGS=-pipe -O2 -arch x86_64' 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/g++-4.2' 'LDFLAGS=-L/opt/local/lib -arch x86_64' --disable-deprecated --with- quantum-depth=16 --with-umem=no --with-autotrace=no --with-fpx=no --with-fontpath= --with-gs-font-dir=/opt/local/share/fonts/urw-fonts --with-gvc=no --with-jp2=no --with-lqr=no --with-openexr=no --with- pango=no --with-rsvg=no --with-wmf=no --with-perl=no DOCUMENTATION_PATH /opt/local/share/doc/ImageMagick-6.8.0 EXEC-PREFIX /opt/local EXECUTABLE_PATH /opt/local/bin FEATURES OpenCL OpenMP FILTER_PATH /opt/local/lib/ImageMagick-6.8.0/modules-Q16/filters HOST x86_64-apple-darwin10.8.0 INCLUDE_PATH /opt/local/include/ImageMagick LDFLAGS -L/opt/local/lib -L/opt/local/lib -arch x86_64 -L/opt/local/lib -L/opt/local/lib LIB_VERSION 0x680 LIB_VERSION_NUMBER 6,8,0,7 LIBRARY_PATH /opt/local/lib/ImageMagick-6.8.0 LIBS -lMagickCore -llcms2 -lfreetype -lfftw3 -L/opt/local/lib -lfontconfig -lXext -lSM -lICE -lX11 -lXt -L/opt/local/lib -llzma -lbz2 -lz -lltdl -lm -lgomp -lclparser -Wl,-framework,OpenCL -L/System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries -lm -lpthread NAME ImageMagick PCFLAGS -fopenmp PREFIX /opt/local QuantumDepth 16 RELEASE_DATE 2013-03-04 SHARE_PATH /opt/local/share/ImageMagick-6.8.0 SVN_REVISION 10029 TARGET_CPU x86_64 TARGET_OS darwin10.8.0 TARGET_VENDOR apple VERSION 6.8.0 WEBSITE http://www.imagemagick.org Path: [built-in] Name Value ---------------------------------------------------------------------- --------- NAME ImageMagick Any help would be appreciated. Thanks -- output of sessionInfo(): R version 2.15.2 (2012-10-26) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] tools stats graphics grDevices utils datasets methods base other attached packages: [1] latticeExtra_0.6-24 RColorBrewer_1.0-5 parody_1.16.0 bioDist_1.30.0 [5] KernSmooth_2.23-8 mvoutlier_1.9.9 sgeostat_1.0-25 robCompositions_1.6.3 [9] car_2.0-16 nnet_7.3-5 compositions_1.20-1 energy_1.4-0 [13] MASS_7.3-23 boot_1.3-7 tensorA_0.36 rgl_0.93.928 [17] flowViz_1.22.0 flowCore_1.24.2 rrcov_1.3-02 pcaPP_1.9-48 [21] mvtnorm_0.9-9994 robustbase_0.9-5 Biobase_2.18.0 lattice_0.20-13 [25] outliers_0.14 BiocGenerics_0.4.0 BiocInstaller_1.8.3 loaded via a namespace (and not attached): [1] annotate_1.36.0 AnnotationDbi_1.20.5 DBI_0.2-5 feature_1.2.8 [5] flowQ_1.18.0 geneplotter_1.36.0 graph_1.36.2 grid_2.15.2 [9] hexbin_1.26.1 IDPmisc_1.1.17 IRanges_1.16.6 ks_1.8.11 [13] parallel_2.15.2 RSQLite_0.11.2 stats4_2.15.2 XML_3.95-0.1 [17] xtable_1.7-1 -- Sent via the guest posting facility at bioconductor.org.
flowq • 979 views
ADD COMMENTlink modified 6.7 years ago by Dan Tenenbaum8.2k • written 6.7 years ago by Guest User12k
Answer: flowQ loading error after installing ImageMagick
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gravatar for Dan Tenenbaum
6.7 years ago by
Dan Tenenbaum8.2k
United States
Dan Tenenbaum8.2k wrote:
On Mon, Mar 4, 2013 at 2:09 PM, Chandra Jack [guest] <guest at="" bioconductor.org=""> wrote: > > Hi All, > > I'm having a problem that has been mentioned here before but I'm not sure how to fix it. I tried to load flowQ and got: > > Error : .onAttach failed in attachNamespace() for 'flowQ', details: > call: mysys("convert -list configure", intern = TRUE, ignore.stderr = TRUE) > error: error in running command Is the 'convert' command in your PATH? What is the output of the R command: Sys.which("convert") ? If it does not output anything, then the convert command is not in your PATH. I'm not sure where the convert command ended up, but I'm guessing it's in /opt/local/bin, so I think you need to edit your ~/.bashrc file and add the following line: PATH=$PATH:/opt/local/bin Then, start a new terminal window to make sure this setting is enabled, and try again. Dan > In addition: Warning messages: > 1: replacing previous import ???plot??? when loading ???graphics??? > 2: replacing previous import ???as??? when loading ???methods??? > Error: package/namespace load failed for ???flowQ???. > > I have installed ImageMagick using Macports as has been suggested and I have also run > convert -list configure, which gave the following: > Path: /opt/local/lib/ImageMagick-6.8.0/config/configure.xml > > Name Value > -------------------------------------------------------------------- ----------- > CC /usr/bin/gcc-4.2 -std=gnu99 -std=gnu99 > CFLAGS -D_THREAD_SAFE -D_THREAD_SAFE -pthread -fopenmp -pipe -O2 -arch x86_64 -Wall -D_THREAD_SAFE -pthread > CODER_PATH /opt/local/lib/ImageMagick-6.8.0/modules-Q16/coders > CONFIGURE ./configure '--prefix=/opt/local' '--enable-shared' '--enable-static' '--disable-ltdl-install' '--disable-silent-rules' '--with-frozenpaths' '--without-openexr' '--disable-hdri' '--with-dps' '--with-bzlib' '--with-fontconfig' '--with-gslib' '--with-jpeg' '--with-lcms' '--with-png' '--with-tiff' '--with-webp' '--with-zlib' '--with-modules' '--with-xml' '--with-x' '--without-perl' '--without- fpx' '--without-jbig' '--without-jp2' '--without-wmf' '--without-gvc' '--without-rsvg' '--without-lqr' '--without-pango' '--with-gs-font- dir=/opt/local/share/fonts/urw-fonts' '--with-quantum-depth=16' 'CC=/usr/bin/gcc-4.2' 'CFLAGS=-pipe -O2 -arch x86_64' 'LDFLAGS=-L/opt/local/lib -arch x86_64' 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/g++-4.2' 'CXXFLAGS=-pipe -O2 -arch x86_64' > CONFIGURE_PATH /opt/local/etc/ImageMagick/ > COPYRIGHT Copyright (C) 1999-2012 ImageMagick Studio LLC > CPPFLAGS -I/opt/local/include/ImageMagick > CXX /usr/bin/g++-4.2 > CXXFLAGS -pipe -O2 -arch x86_64 -D_THREAD_SAFE -pthread > DEFS -DHAVE_CONFIG_H > DELEGATES bzlib fftw fontconfig freetype gs jpeg jng lcms2 lzma png tiff x11 xml zlib > DISTCHECK_CONFIG_FLAGS 'CC=/usr/bin/gcc-4.2' 'CFLAGS=-pipe -O2 -arch x86_64' 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/g++-4.2' 'LDFLAGS=-L/opt/local/lib -arch x86_64' --disable-deprecated --with- quantum-depth=16 --with-umem=no --with-autotrace=no --with-fpx=no --with-fontpath= --with-gs-font-dir=/opt/local/share/fonts/urw-fonts --with-gvc=no --with-jp2=no --with-lqr=no --with-openexr=no --with- pango=no --with-rsvg=no --with-wmf=no --with-perl=no > DOCUMENTATION_PATH /opt/local/share/doc/ImageMagick-6.8.0 > EXEC-PREFIX /opt/local > EXECUTABLE_PATH /opt/local/bin > FEATURES OpenCL OpenMP > FILTER_PATH /opt/local/lib/ImageMagick-6.8.0/modules-Q16/filters > HOST x86_64-apple-darwin10.8.0 > INCLUDE_PATH /opt/local/include/ImageMagick > LDFLAGS -L/opt/local/lib -L/opt/local/lib -arch x86_64 -L/opt/local/lib -L/opt/local/lib > LIB_VERSION 0x680 > LIB_VERSION_NUMBER 6,8,0,7 > LIBRARY_PATH /opt/local/lib/ImageMagick-6.8.0 > LIBS -lMagickCore -llcms2 -lfreetype -lfftw3 -L/opt/local/lib -lfontconfig -lXext -lSM -lICE -lX11 -lXt -L/opt/local/lib -llzma -lbz2 -lz -lltdl -lm -lgomp -lclparser -Wl,-framework,OpenCL -L/System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries -lm -lpthread > NAME ImageMagick > PCFLAGS -fopenmp > PREFIX /opt/local > QuantumDepth 16 > RELEASE_DATE 2013-03-04 > SHARE_PATH /opt/local/share/ImageMagick-6.8.0 > SVN_REVISION 10029 > TARGET_CPU x86_64 > TARGET_OS darwin10.8.0 > TARGET_VENDOR apple > VERSION 6.8.0 > WEBSITE http://www.imagemagick.org > > Path: [built-in] > > Name Value > -------------------------------------------------------------------- ----------- > NAME ImageMagick > > Any help would be appreciated. Thanks > > -- output of sessionInfo(): > > R version 2.15.2 (2012-10-26) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] tools stats graphics grDevices utils datasets methods base > > other attached packages: > [1] latticeExtra_0.6-24 RColorBrewer_1.0-5 parody_1.16.0 bioDist_1.30.0 > [5] KernSmooth_2.23-8 mvoutlier_1.9.9 sgeostat_1.0-25 robCompositions_1.6.3 > [9] car_2.0-16 nnet_7.3-5 compositions_1.20-1 energy_1.4-0 > [13] MASS_7.3-23 boot_1.3-7 tensorA_0.36 rgl_0.93.928 > [17] flowViz_1.22.0 flowCore_1.24.2 rrcov_1.3-02 pcaPP_1.9-48 > [21] mvtnorm_0.9-9994 robustbase_0.9-5 Biobase_2.18.0 lattice_0.20-13 > [25] outliers_0.14 BiocGenerics_0.4.0 BiocInstaller_1.8.3 > > loaded via a namespace (and not attached): > [1] annotate_1.36.0 AnnotationDbi_1.20.5 DBI_0.2-5 feature_1.2.8 > [5] flowQ_1.18.0 geneplotter_1.36.0 graph_1.36.2 grid_2.15.2 > [9] hexbin_1.26.1 IDPmisc_1.1.17 IRanges_1.16.6 ks_1.8.11 > [13] parallel_2.15.2 RSQLite_0.11.2 stats4_2.15.2 XML_3.95-0.1 > [17] xtable_1.7-1 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 6.7 years ago by Dan Tenenbaum8.2k
The convert command isn't in my PATH but adding the newIt doesn't seem to be working. I don't have a .bashrc file but I have a .bash_profile. The original file was: # Setting PATH for EPD-7.1-2 # The orginal version is saved in .bash_profile.pysave PATH="/Library/Frameworks/EPD64.framework/Versions/Current/bin:${PATH} " export PATH MKL_NUM_THREADS=1 export MKL_NUM_THREADS # Setting PATH for Python 2.7 # The orginal version is saved in .bash_profile.pysave PATH="/Library/Frameworks/Python.framework/Versions/2.7/bin:${PATH}" export PATH ## # Your previous /Users/chanj/.bash_profile file was backed up as /Users/chanj/.bash_profile.macports-saved_2013-03-04_at_14:30:35 ## # MacPorts Installer addition on 2013-03-04_at_14:30:35: adding an appropriate PATH variable for use with MacPorts. export PATH=/opt/local/bin:/opt/local/sbin:$PATH # Finished adapting your PATH environment variable for use with MacPorts. I added PATH=$PATH:/opt/local/bin after the export line, resaved the text edit file and quit the terminal. When I checked Terminal again the file was updated but R couldn't find the command still. I also tried adding it before the export line, replacing the part after the export line with it, adding quotation marks but nothing seemed to work. I went in and found the convert command file and it is in opt/local/bin. I tried Sys.which with another file that was in the same location and R output "/usr/bin/clear" . Could it be related to the backup file that was created before I changed it? Thanks On Mar 4, 2013, at 4:15 PM, Dan Tenenbaum wrote: > On Mon, Mar 4, 2013 at 2:09 PM, Chandra Jack [guest] > <guest at="" bioconductor.org=""> wrote: >> >> Hi All, >> >> I'm having a problem that has been mentioned here before but I'm not sure how to fix it. I tried to load flowQ and got: >> >> Error : .onAttach failed in attachNamespace() for 'flowQ', details: >> call: mysys("convert -list configure", intern = TRUE, ignore.stderr = TRUE) >> error: error in running command > > Is the 'convert' command in your PATH? > > What is the output of the R command: > Sys.which("convert") > ? > > If it does not output anything, then the convert command is not in your PATH. > > I'm not sure where the convert command ended up, but I'm guessing it's > in /opt/local/bin, > so I think you need to edit your ~/.bashrc > file and add the following line: > > PATH=$PATH:/opt/local/bin > > Then, start a new terminal window to make sure this setting is > enabled, and try again. > > Dan > > >> In addition: Warning messages: >> 1: replacing previous import ???plot??? when loading ???graphics??? >> 2: replacing previous import ???as??? when loading ???methods??? >> Error: package/namespace load failed for ???flowQ???. >> >> I have installed ImageMagick using Macports as has been suggested and I have also run >> convert -list configure, which gave the following: >> Path: /opt/local/lib/ImageMagick-6.8.0/config/configure.xml >> >> Name Value >> ------------------------------------------------------------------- ------------ >> CC /usr/bin/gcc-4.2 -std=gnu99 -std=gnu99 >> CFLAGS -D_THREAD_SAFE -D_THREAD_SAFE -pthread -fopenmp -pipe -O2 -arch x86_64 -Wall -D_THREAD_SAFE -pthread >> CODER_PATH /opt/local/lib/ImageMagick-6.8.0/modules-Q16/coders >> CONFIGURE ./configure '--prefix=/opt/local' '--enable-shared' '--enable-static' '--disable-ltdl-install' '--disable-silent-rules' '--with-frozenpaths' '--without-openexr' '--disable-hdri' '--with-dps' '--with-bzlib' '--with-fontconfig' '--with-gslib' '--with-jpeg' '--with-lcms' '--with-png' '--with-tiff' '--with-webp' '--with-zlib' '--with-modules' '--with-xml' '--with-x' '--without-perl' '--without- fpx' '--without-jbig' '--without-jp2' '--without-wmf' '--without-gvc' '--without-rsvg' '--without-lqr' '--without-pango' '--with-gs-font- dir=/opt/local/share/fonts/urw-fonts' '--with-quantum-depth=16' 'CC=/usr/bin/gcc-4.2' 'CFLAGS=-pipe -O2 -arch x86_64' 'LDFLAGS=-L/opt/local/lib -arch x86_64' 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/g++-4.2' 'CXXFLAGS=-pipe -O2 -arch x86_64' >> CONFIGURE_PATH /opt/local/etc/ImageMagick/ >> COPYRIGHT Copyright (C) 1999-2012 ImageMagick Studio LLC >> CPPFLAGS -I/opt/local/include/ImageMagick >> CXX /usr/bin/g++-4.2 >> CXXFLAGS -pipe -O2 -arch x86_64 -D_THREAD_SAFE -pthread >> DEFS -DHAVE_CONFIG_H >> DELEGATES bzlib fftw fontconfig freetype gs jpeg jng lcms2 lzma png tiff x11 xml zlib >> DISTCHECK_CONFIG_FLAGS 'CC=/usr/bin/gcc-4.2' 'CFLAGS=-pipe -O2 -arch x86_64' 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/g++-4.2' 'LDFLAGS=-L/opt/local/lib -arch x86_64' --disable-deprecated --with- quantum-depth=16 --with-umem=no --with-autotrace=no --with-fpx=no --with-fontpath= --with-gs-font-dir=/opt/local/share/fonts/urw-fonts --with-gvc=no --with-jp2=no --with-lqr=no --with-openexr=no --with- pango=no --with-rsvg=no --with-wmf=no --with-perl=no >> DOCUMENTATION_PATH /opt/local/share/doc/ImageMagick-6.8.0 >> EXEC-PREFIX /opt/local >> EXECUTABLE_PATH /opt/local/bin >> FEATURES OpenCL OpenMP >> FILTER_PATH /opt/local/lib/ImageMagick-6.8.0/modules-Q16/filters >> HOST x86_64-apple-darwin10.8.0 >> INCLUDE_PATH /opt/local/include/ImageMagick >> LDFLAGS -L/opt/local/lib -L/opt/local/lib -arch x86_64 -L/opt/local/lib -L/opt/local/lib >> LIB_VERSION 0x680 >> LIB_VERSION_NUMBER 6,8,0,7 >> LIBRARY_PATH /opt/local/lib/ImageMagick-6.8.0 >> LIBS -lMagickCore -llcms2 -lfreetype -lfftw3 -L/opt/local/lib -lfontconfig -lXext -lSM -lICE -lX11 -lXt -L/opt/local/lib -llzma -lbz2 -lz -lltdl -lm -lgomp -lclparser -Wl,-framework,OpenCL -L/System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries -lm -lpthread >> NAME ImageMagick >> PCFLAGS -fopenmp >> PREFIX /opt/local >> QuantumDepth 16 >> RELEASE_DATE 2013-03-04 >> SHARE_PATH /opt/local/share/ImageMagick-6.8.0 >> SVN_REVISION 10029 >> TARGET_CPU x86_64 >> TARGET_OS darwin10.8.0 >> TARGET_VENDOR apple >> VERSION 6.8.0 >> WEBSITE http://www.imagemagick.org >> >> Path: [built-in] >> >> Name Value >> ------------------------------------------------------------------- ------------ >> NAME ImageMagick >> >> Any help would be appreciated. Thanks >> >> -- output of sessionInfo(): >> >> R version 2.15.2 (2012-10-26) >> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] tools stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] latticeExtra_0.6-24 RColorBrewer_1.0-5 parody_1.16.0 bioDist_1.30.0 >> [5] KernSmooth_2.23-8 mvoutlier_1.9.9 sgeostat_1.0-25 robCompositions_1.6.3 >> [9] car_2.0-16 nnet_7.3-5 compositions_1.20-1 energy_1.4-0 >> [13] MASS_7.3-23 boot_1.3-7 tensorA_0.36 rgl_0.93.928 >> [17] flowViz_1.22.0 flowCore_1.24.2 rrcov_1.3-02 pcaPP_1.9-48 >> [21] mvtnorm_0.9-9994 robustbase_0.9-5 Biobase_2.18.0 lattice_0.20-13 >> [25] outliers_0.14 BiocGenerics_0.4.0 BiocInstaller_1.8.3 >> >> loaded via a namespace (and not attached): >> [1] annotate_1.36.0 AnnotationDbi_1.20.5 DBI_0.2-5 feature_1.2.8 >> [5] flowQ_1.18.0 geneplotter_1.36.0 graph_1.36.2 grid_2.15.2 >> [9] hexbin_1.26.1 IDPmisc_1.1.17 IRanges_1.16.6 ks_1.8.11 >> [13] parallel_2.15.2 RSQLite_0.11.2 stats4_2.15.2 XML_3.95-0.1 >> [17] xtable_1.7-1 >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > Chandra Jack Postdoctoral Research Assoc. Dept. of Bioengineering Rice University chanj at rice.edu
ADD REPLYlink written 6.7 years ago by Chandra Jack90
On Mon, Mar 4, 2013 at 8:07 PM, Chandra Jack <chanj at="" rice.edu=""> wrote: > The convert command isn't in my PATH but adding the newIt doesn't seem to be working. I don't have a .bashrc file but I have a .bash_profile. The original file was: > # Setting PATH for EPD-7.1-2 > # The orginal version is saved in .bash_profile.pysave > PATH="/Library/Frameworks/EPD64.framework/Versions/Current/bin:${PAT H}" > export PATH > > MKL_NUM_THREADS=1 > export MKL_NUM_THREADS > > # Setting PATH for Python 2.7 > # The orginal version is saved in .bash_profile.pysave > PATH="/Library/Frameworks/Python.framework/Versions/2.7/bin:${PATH}" > export PATH > > ## > # Your previous /Users/chanj/.bash_profile file was backed up as /Users/chanj/.bash_profile.macports-saved_2013-03-04_at_14:30:35 > ## > > # MacPorts Installer addition on 2013-03-04_at_14:30:35: adding an appropriate PATH variable for use with MacPorts. > export PATH=/opt/local/bin:/opt/local/sbin:$PATH > # Finished adapting your PATH environment variable for use with MacPorts. > > I added PATH=$PATH:/opt/local/bin after the export line, resaved the text edit file and quit the terminal. When I checked Terminal again the file was updated but R couldn't find the command still. Sorry, it needs to say: export PATH=$PATH:/opt/local/bin I forgot the 'export' before. > > I also tried adding it before the export line, replacing the part after the export line with it, adding quotation marks but nothing seemed to work. I went in and found the convert command file and it is in opt/local/bin. I tried Sys.which with another file that was in the same location and R output "/usr/bin/clear" . Could it be related to the backup file that was created before I changed it? No, that just means there is a 'clear' executable in two locations. Dan > > Thanks > > On Mar 4, 2013, at 4:15 PM, Dan Tenenbaum wrote: > >> On Mon, Mar 4, 2013 at 2:09 PM, Chandra Jack [guest] >> <guest at="" bioconductor.org=""> wrote: >>> >>> Hi All, >>> >>> I'm having a problem that has been mentioned here before but I'm not sure how to fix it. I tried to load flowQ and got: >>> >>> Error : .onAttach failed in attachNamespace() for 'flowQ', details: >>> call: mysys("convert -list configure", intern = TRUE, ignore.stderr = TRUE) >>> error: error in running command >> >> Is the 'convert' command in your PATH? >> >> What is the output of the R command: >> Sys.which("convert") >> ? >> >> If it does not output anything, then the convert command is not in your PATH. >> >> I'm not sure where the convert command ended up, but I'm guessing it's >> in /opt/local/bin, >> so I think you need to edit your ~/.bashrc >> file and add the following line: >> >> PATH=$PATH:/opt/local/bin >> >> Then, start a new terminal window to make sure this setting is >> enabled, and try again. >> >> Dan >> >> >>> In addition: Warning messages: >>> 1: replacing previous import ???plot??? when loading ???graphics??? >>> 2: replacing previous import ???as??? when loading ???methods??? >>> Error: package/namespace load failed for ???flowQ???. >>> >>> I have installed ImageMagick using Macports as has been suggested and I have also run >>> convert -list configure, which gave the following: >>> Path: /opt/local/lib/ImageMagick-6.8.0/config/configure.xml >>> >>> Name Value >>> ------------------------------------------------------------------ ------------- >>> CC /usr/bin/gcc-4.2 -std=gnu99 -std=gnu99 >>> CFLAGS -D_THREAD_SAFE -D_THREAD_SAFE -pthread -fopenmp -pipe -O2 -arch x86_64 -Wall -D_THREAD_SAFE -pthread >>> CODER_PATH /opt/local/lib/ImageMagick-6.8.0/modules-Q16/coders >>> CONFIGURE ./configure '--prefix=/opt/local' '--enable-shared' '--enable-static' '--disable-ltdl-install' '--disable-silent-rules' '--with-frozenpaths' '--without-openexr' '--disable-hdri' '--with-dps' '--with-bzlib' '--with-fontconfig' '--with-gslib' '--with-jpeg' '--with-lcms' '--with-png' '--with-tiff' '--with-webp' '--with-zlib' '--with-modules' '--with-xml' '--with-x' '--without-perl' '--without- fpx' '--without-jbig' '--without-jp2' '--without-wmf' '--without-gvc' '--without-rsvg' '--without-lqr' '--without-pango' '--with-gs-font- dir=/opt/local/share/fonts/urw-fonts' '--with-quantum-depth=16' 'CC=/usr/bin/gcc-4.2' 'CFLAGS=-pipe -O2 -arch x86_64' 'LDFLAGS=-L/opt/local/lib -arch x86_64' 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/g++-4.2' 'CXXFLAGS=-pipe -O2 -arch x86_64' >>> CONFIGURE_PATH /opt/local/etc/ImageMagick/ >>> COPYRIGHT Copyright (C) 1999-2012 ImageMagick Studio LLC >>> CPPFLAGS -I/opt/local/include/ImageMagick >>> CXX /usr/bin/g++-4.2 >>> CXXFLAGS -pipe -O2 -arch x86_64 -D_THREAD_SAFE -pthread >>> DEFS -DHAVE_CONFIG_H >>> DELEGATES bzlib fftw fontconfig freetype gs jpeg jng lcms2 lzma png tiff x11 xml zlib >>> DISTCHECK_CONFIG_FLAGS 'CC=/usr/bin/gcc-4.2' 'CFLAGS=-pipe -O2 -arch x86_64' 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/g++-4.2' 'LDFLAGS=-L/opt/local/lib -arch x86_64' --disable-deprecated --with- quantum-depth=16 --with-umem=no --with-autotrace=no --with-fpx=no --with-fontpath= --with-gs-font-dir=/opt/local/share/fonts/urw-fonts --with-gvc=no --with-jp2=no --with-lqr=no --with-openexr=no --with- pango=no --with-rsvg=no --with-wmf=no --with-perl=no >>> DOCUMENTATION_PATH /opt/local/share/doc/ImageMagick-6.8.0 >>> EXEC-PREFIX /opt/local >>> EXECUTABLE_PATH /opt/local/bin >>> FEATURES OpenCL OpenMP >>> FILTER_PATH /opt/local/lib/ImageMagick-6.8.0/modules-Q16/filters >>> HOST x86_64-apple-darwin10.8.0 >>> INCLUDE_PATH /opt/local/include/ImageMagick >>> LDFLAGS -L/opt/local/lib -L/opt/local/lib -arch x86_64 -L/opt/local/lib -L/opt/local/lib >>> LIB_VERSION 0x680 >>> LIB_VERSION_NUMBER 6,8,0,7 >>> LIBRARY_PATH /opt/local/lib/ImageMagick-6.8.0 >>> LIBS -lMagickCore -llcms2 -lfreetype -lfftw3 -L/opt/local/lib -lfontconfig -lXext -lSM -lICE -lX11 -lXt -L/opt/local/lib -llzma -lbz2 -lz -lltdl -lm -lgomp -lclparser -Wl,-framework,OpenCL -L/System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries -lm -lpthread >>> NAME ImageMagick >>> PCFLAGS -fopenmp >>> PREFIX /opt/local >>> QuantumDepth 16 >>> RELEASE_DATE 2013-03-04 >>> SHARE_PATH /opt/local/share/ImageMagick-6.8.0 >>> SVN_REVISION 10029 >>> TARGET_CPU x86_64 >>> TARGET_OS darwin10.8.0 >>> TARGET_VENDOR apple >>> VERSION 6.8.0 >>> WEBSITE http://www.imagemagick.org >>> >>> Path: [built-in] >>> >>> Name Value >>> ------------------------------------------------------------------ ------------- >>> NAME ImageMagick >>> >>> Any help would be appreciated. Thanks >>> >>> -- output of sessionInfo(): >>> >>> R version 2.15.2 (2012-10-26) >>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >>> >>> locale: >>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>> >>> attached base packages: >>> [1] tools stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] latticeExtra_0.6-24 RColorBrewer_1.0-5 parody_1.16.0 bioDist_1.30.0 >>> [5] KernSmooth_2.23-8 mvoutlier_1.9.9 sgeostat_1.0-25 robCompositions_1.6.3 >>> [9] car_2.0-16 nnet_7.3-5 compositions_1.20-1 energy_1.4-0 >>> [13] MASS_7.3-23 boot_1.3-7 tensorA_0.36 rgl_0.93.928 >>> [17] flowViz_1.22.0 flowCore_1.24.2 rrcov_1.3-02 pcaPP_1.9-48 >>> [21] mvtnorm_0.9-9994 robustbase_0.9-5 Biobase_2.18.0 lattice_0.20-13 >>> [25] outliers_0.14 BiocGenerics_0.4.0 BiocInstaller_1.8.3 >>> >>> loaded via a namespace (and not attached): >>> [1] annotate_1.36.0 AnnotationDbi_1.20.5 DBI_0.2-5 feature_1.2.8 >>> [5] flowQ_1.18.0 geneplotter_1.36.0 graph_1.36.2 grid_2.15.2 >>> [9] hexbin_1.26.1 IDPmisc_1.1.17 IRanges_1.16.6 ks_1.8.11 >>> [13] parallel_2.15.2 RSQLite_0.11.2 stats4_2.15.2 XML_3.95-0.1 >>> [17] xtable_1.7-1 >>> >>> -- >>> Sent via the guest posting facility at bioconductor.org. >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > Chandra Jack > Postdoctoral Research Assoc. > Dept. of Bioengineering > Rice University > chanj at rice.edu > > >
ADD REPLYlink written 6.7 years ago by Dan Tenenbaum8.2k
I replaced the original export line with the one you wrote but it still didn't work. On Mar 4, 2013, at 10:18 PM, Dan Tenenbaum wrote: > On Mon, Mar 4, 2013 at 8:07 PM, Chandra Jack <chanj@rice.edu> wrote: >> The convert command isn't in my PATH but adding the newIt doesn't seem to be working. I don't have a .bashrc file but I have a .bash_profile. The original file was: >> # Setting PATH for EPD-7.1-2 >> # The orginal version is saved in .bash_profile.pysave >> PATH="/Library/Frameworks/EPD64.framework/Versions/Current/bin:${PA TH}" >> export PATH >> >> MKL_NUM_THREADS=1 >> export MKL_NUM_THREADS >> >> # Setting PATH for Python 2.7 >> # The orginal version is saved in .bash_profile.pysave >> PATH="/Library/Frameworks/Python.framework/Versions/2.7/bin:${PATH}" >> export PATH >> >> ## >> # Your previous /Users/chanj/.bash_profile file was backed up as /Users/chanj/.bash_profile.macports-saved_2013-03-04_at_14:30:35 >> ## >> >> # MacPorts Installer addition on 2013-03-04_at_14:30:35: adding an appropriate PATH variable for use with MacPorts. >> export PATH=/opt/local/bin:/opt/local/sbin:$PATH >> # Finished adapting your PATH environment variable for use with MacPorts. >> >> I added PATH=$PATH:/opt/local/bin after the export line, resaved the text edit file and quit the terminal. When I checked Terminal again the file was updated but R couldn't find the command still. > > Sorry, it needs to say: > > export PATH=$PATH:/opt/local/bin > > I forgot the 'export' before. > > > > > >> >> I also tried adding it before the export line, replacing the part after the export line with it, adding quotation marks but nothing seemed to work. I went in and found the convert command file and it is in opt/local/bin. I tried Sys.which with another file that was in the same location and R output "/usr/bin/clear" . Could it be related to the backup file that was created before I changed it? > > No, that just means there is a 'clear' executable in two locations. > Dan > > >> >> Thanks >> >> On Mar 4, 2013, at 4:15 PM, Dan Tenenbaum wrote: >> >>> On Mon, Mar 4, 2013 at 2:09 PM, Chandra Jack [guest] >>> <guest@bioconductor.org> wrote: >>>> >>>> Hi All, >>>> >>>> I'm having a problem that has been mentioned here before but I'm not sure how to fix it. I tried to load flowQ and got: >>>> >>>> Error : .onAttach failed in attachNamespace() for 'flowQ', details: >>>> call: mysys("convert -list configure", intern = TRUE, ignore.stderr = TRUE) >>>> error: error in running command >>> >>> Is the 'convert' command in your PATH? >>> >>> What is the output of the R command: >>> Sys.which("convert") >>> ? >>> >>> If it does not output anything, then the convert command is not in your PATH. >>> >>> I'm not sure where the convert command ended up, but I'm guessing it's >>> in /opt/local/bin, >>> so I think you need to edit your ~/.bashrc >>> file and add the following line: >>> >>> PATH=$PATH:/opt/local/bin >>> >>> Then, start a new terminal window to make sure this setting is >>> enabled, and try again. >>> >>> Dan >>> >>> >>>> In addition: Warning messages: >>>> 1: replacing previous import ‘plot’ when loading ‘graphics’ >>>> 2: replacing previous import ‘as’ when loading ‘methods’ >>>> Error: package/namespace load failed for ‘flowQ’. >>>> >>>> I have installed ImageMagick using Macports as has been suggested and I have also run >>>> convert -list configure, which gave the following: >>>> Path: /opt/local/lib/ImageMagick-6.8.0/config/configure.xml >>>> >>>> Name Value >>>> ----------------------------------------------------------------- -------------- >>>> CC /usr/bin/gcc-4.2 -std=gnu99 -std=gnu99 >>>> CFLAGS -D_THREAD_SAFE -D_THREAD_SAFE -pthread -fopenmp -pipe -O2 -arch x86_64 -Wall -D_THREAD_SAFE -pthread >>>> CODER_PATH /opt/local/lib/ImageMagick-6.8.0/modules-Q16/coders >>>> CONFIGURE ./configure '--prefix=/opt/local' '--enable- shared' '--enable-static' '--disable-ltdl-install' '--disable-silent- rules' '--with-frozenpaths' '--without-openexr' '--disable-hdri' '--with-dps' '--with-bzlib' '--with-fontconfig' '--with-gslib' '--with-jpeg' '--with-lcms' '--with-png' '--with-tiff' '--with-webp' '--with-zlib' '--with-modules' '--with-xml' '--with-x' '--without- perl' '--without-fpx' '--without-jbig' '--without-jp2' '--without-wmf' '--without-gvc' '--without-rsvg' '--without-lqr' '--without-pango' '--with-gs-font-dir=/opt/local/share/fonts/urw-fonts' '--with-quantum- depth=16' 'CC=/usr/bin/gcc-4.2' 'CFLAGS=-pipe -O2 -arch x86_64' 'LDFLAGS=-L/opt/local/lib -arch x86_64' 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/g++-4.2' 'CXXFLAGS=-pipe -O2 -arch x86_64' >>>> CONFIGURE_PATH /opt/local/etc/ImageMagick/ >>>> COPYRIGHT Copyright (C) 1999-2012 ImageMagick Studio LLC >>>> CPPFLAGS -I/opt/local/include/ImageMagick >>>> CXX /usr/bin/g++-4.2 >>>> CXXFLAGS -pipe -O2 -arch x86_64 -D_THREAD_SAFE -pthread >>>> DEFS -DHAVE_CONFIG_H >>>> DELEGATES bzlib fftw fontconfig freetype gs jpeg jng lcms2 lzma png tiff x11 xml zlib >>>> DISTCHECK_CONFIG_FLAGS 'CC=/usr/bin/gcc-4.2' 'CFLAGS=-pipe -O2 -arch x86_64' 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/g++-4.2' 'LDFLAGS=-L/opt/local/lib -arch x86_64' --disable-deprecated --with- quantum-depth=16 --with-umem=no --with-autotrace=no --with-fpx=no --with-fontpath= --with-gs-font-dir=/opt/local/share/fonts/urw-fonts --with-gvc=no --with-jp2=no --with-lqr=no --with-openexr=no --with- pango=no --with-rsvg=no --with-wmf=no --with-perl=no >>>> DOCUMENTATION_PATH /opt/local/share/doc/ImageMagick-6.8.0 >>>> EXEC-PREFIX /opt/local >>>> EXECUTABLE_PATH /opt/local/bin >>>> FEATURES OpenCL OpenMP >>>> FILTER_PATH /opt/local/lib/ImageMagick-6.8.0/modules-Q16/filters >>>> HOST x86_64-apple-darwin10.8.0 >>>> INCLUDE_PATH /opt/local/include/ImageMagick >>>> LDFLAGS -L/opt/local/lib -L/opt/local/lib -arch x86_64 -L/opt/local/lib -L/opt/local/lib >>>> LIB_VERSION 0x680 >>>> LIB_VERSION_NUMBER 6,8,0,7 >>>> LIBRARY_PATH /opt/local/lib/ImageMagick-6.8.0 >>>> LIBS -lMagickCore -llcms2 -lfreetype -lfftw3 -L/opt/local/lib -lfontconfig -lXext -lSM -lICE -lX11 -lXt -L/opt/local/lib -llzma -lbz2 -lz -lltdl -lm -lgomp -lclparser -Wl,-framework,OpenCL -L/System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries -lm -lpthread >>>> NAME ImageMagick >>>> PCFLAGS -fopenmp >>>> PREFIX /opt/local >>>> QuantumDepth 16 >>>> RELEASE_DATE 2013-03-04 >>>> SHARE_PATH /opt/local/share/ImageMagick-6.8.0 >>>> SVN_REVISION 10029 >>>> TARGET_CPU x86_64 >>>> TARGET_OS darwin10.8.0 >>>> TARGET_VENDOR apple >>>> VERSION 6.8.0 >>>> WEBSITE http://www.imagemagick.org >>>> >>>> Path: [built-in] >>>> >>>> Name Value >>>> ----------------------------------------------------------------- -------------- >>>> NAME ImageMagick >>>> >>>> Any help would be appreciated. Thanks >>>> >>>> -- output of sessionInfo(): >>>> >>>> R version 2.15.2 (2012-10-26) >>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >>>> >>>> locale: >>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>>> >>>> attached base packages: >>>> [1] tools stats graphics grDevices utils datasets methods base >>>> >>>> other attached packages: >>>> [1] latticeExtra_0.6-24 RColorBrewer_1.0-5 parody_1.16.0 bioDist_1.30.0 >>>> [5] KernSmooth_2.23-8 mvoutlier_1.9.9 sgeostat_1.0-25 robCompositions_1.6.3 >>>> [9] car_2.0-16 nnet_7.3-5 compositions_1.20-1 energy_1.4-0 >>>> [13] MASS_7.3-23 boot_1.3-7 tensorA_0.36 rgl_0.93.928 >>>> [17] flowViz_1.22.0 flowCore_1.24.2 rrcov_1.3-02 pcaPP_1.9-48 >>>> [21] mvtnorm_0.9-9994 robustbase_0.9-5 Biobase_2.18.0 lattice_0.20-13 >>>> [25] outliers_0.14 BiocGenerics_0.4.0 BiocInstaller_1.8.3 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] annotate_1.36.0 AnnotationDbi_1.20.5 DBI_0.2-5 feature_1.2.8 >>>> [5] flowQ_1.18.0 geneplotter_1.36.0 graph_1.36.2 grid_2.15.2 >>>> [9] hexbin_1.26.1 IDPmisc_1.1.17 IRanges_1.16.6 ks_1.8.11 >>>> [13] parallel_2.15.2 RSQLite_0.11.2 stats4_2.15.2 XML_3.95-0.1 >>>> [17] xtable_1.7-1 >>>> >>>> -- >>>> Sent via the guest posting facility at bioconductor.org. >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor@r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> Chandra Jack >> Postdoctoral Research Assoc. >> Dept. of Bioengineering >> Rice University >> chanj@rice.edu >> >> >> > Chandra Jack Postdoctoral Research Assoc. Dept. of Bioengineering Rice University chanj@rice.edu [[alternative HTML version deleted]]
ADD REPLYlink written 6.7 years ago by Chandra Jack90
On Mon, Mar 4, 2013 at 9:30 PM, Chandra Jack <chanj at="" rice.edu=""> wrote: > I replaced the original export line with the one you wrote but it still > didn't work. > OK, at a terminal prompt, please enter the following commands and send me the output they produce: source ~/.bash_profile echo $PATH which convert thanks, Dan > On Mar 4, 2013, at 10:18 PM, Dan Tenenbaum wrote: > > On Mon, Mar 4, 2013 at 8:07 PM, Chandra Jack <chanj at="" rice.edu=""> wrote: > > The convert command isn't in my PATH but adding the newIt doesn't seem to be > working. I don't have a .bashrc file but I have a .bash_profile. The > original file was: > > # Setting PATH for EPD-7.1-2 > > # The orginal version is saved in .bash_profile.pysave > > PATH="/Library/Frameworks/EPD64.framework/Versions/Current/bin:${PAT H}" > > export PATH > > > MKL_NUM_THREADS=1 > > export MKL_NUM_THREADS > > > # Setting PATH for Python 2.7 > > # The orginal version is saved in .bash_profile.pysave > > PATH="/Library/Frameworks/Python.framework/Versions/2.7/bin:${PATH}" > > export PATH > > > ## > > # Your previous /Users/chanj/.bash_profile file was backed up as > /Users/chanj/.bash_profile.macports-saved_2013-03-04_at_14:30:35 > > ## > > > # MacPorts Installer addition on 2013-03-04_at_14:30:35: adding an > appropriate PATH variable for use with MacPorts. > > export PATH=/opt/local/bin:/opt/local/sbin:$PATH > > # Finished adapting your PATH environment variable for use with MacPorts. > > > I added PATH=$PATH:/opt/local/bin after the export line, resaved the text > edit file and quit the terminal. When I checked Terminal again the file was > updated but R couldn't find the command still. > > > Sorry, it needs to say: > > export PATH=$PATH:/opt/local/bin > > I forgot the 'export' before. > > > > > > > I also tried adding it before the export line, replacing the part after the > export line with it, adding quotation marks but nothing seemed to work. I > went in and found the convert command file and it is in opt/local/bin. I > tried Sys.which with another file that was in the same location and R output > "/usr/bin/clear" . Could it be related to the backup file that was created > before I changed it? > > > No, that just means there is a 'clear' executable in two locations. > Dan > > > > Thanks > > > On Mar 4, 2013, at 4:15 PM, Dan Tenenbaum wrote: > > > On Mon, Mar 4, 2013 at 2:09 PM, Chandra Jack [guest] > > <guest at="" bioconductor.org=""> wrote: > > > Hi All, > > > I'm having a problem that has been mentioned here before but I'm not sure > how to fix it. I tried to load flowQ and got: > > > Error : .onAttach failed in attachNamespace() for 'flowQ', details: > > call: mysys("convert -list configure", intern = TRUE, ignore.stderr = TRUE) > > error: error in running command > > > Is the 'convert' command in your PATH? > > > What is the output of the R command: > > Sys.which("convert") > > ? > > > If it does not output anything, then the convert command is not in your > PATH. > > > I'm not sure where the convert command ended up, but I'm guessing it's > > in /opt/local/bin, > > so I think you need to edit your ~/.bashrc > > file and add the following line: > > > PATH=$PATH:/opt/local/bin > > > Then, start a new terminal window to make sure this setting is > > enabled, and try again. > > > Dan > > > > In addition: Warning messages: > > 1: replacing previous import ???plot??? when loading ???graphics??? > > 2: replacing previous import ???as??? when loading ???methods??? > > Error: package/namespace load failed for ???flowQ???. > > > I have installed ImageMagick using Macports as has been suggested and I have > also run > > convert -list configure, which gave the following: > > Path: /opt/local/lib/ImageMagick-6.8.0/config/configure.xml > > > Name Value > > -------------------------------------------------------------------- ----------- > > CC /usr/bin/gcc-4.2 -std=gnu99 -std=gnu99 > > CFLAGS -D_THREAD_SAFE -D_THREAD_SAFE -pthread -fopenmp -pipe -O2 > -arch x86_64 -Wall -D_THREAD_SAFE -pthread > > CODER_PATH /opt/local/lib/ImageMagick-6.8.0/modules-Q16/coders > > CONFIGURE ./configure '--prefix=/opt/local' '--enable-shared' > '--enable-static' '--disable-ltdl-install' '--disable-silent-rules' > '--with-frozenpaths' '--without-openexr' '--disable-hdri' '--with- dps' > '--with-bzlib' '--with-fontconfig' '--with-gslib' '--with-jpeg' > '--with-lcms' '--with-png' '--with-tiff' '--with-webp' '--with-zlib' > '--with-modules' '--with-xml' '--with-x' '--without-perl' '--without-fpx' > '--without-jbig' '--without-jp2' '--without-wmf' '--without-gvc' > '--without-rsvg' '--without-lqr' '--without-pango' > '--with-gs-font-dir=/opt/local/share/fonts/urw-fonts' > '--with-quantum-depth=16' 'CC=/usr/bin/gcc-4.2' 'CFLAGS=-pipe -O2 -arch > x86_64' 'LDFLAGS=-L/opt/local/lib -arch x86_64' > 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/g++-4.2' 'CXXFLAGS=-pipe -O2 > -arch x86_64' > > CONFIGURE_PATH /opt/local/etc/ImageMagick/ > > COPYRIGHT Copyright (C) 1999-2012 ImageMagick Studio LLC > > CPPFLAGS -I/opt/local/include/ImageMagick > > CXX /usr/bin/g++-4.2 > > CXXFLAGS -pipe -O2 -arch x86_64 -D_THREAD_SAFE -pthread > > DEFS -DHAVE_CONFIG_H > > DELEGATES bzlib fftw fontconfig freetype gs jpeg jng lcms2 lzma png tiff > x11 xml zlib > > DISTCHECK_CONFIG_FLAGS 'CC=/usr/bin/gcc-4.2' 'CFLAGS=-pipe -O2 -arch x86_64' > 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/g++-4.2' > 'LDFLAGS=-L/opt/local/lib -arch x86_64' --disable-deprecated > --with-quantum-depth=16 --with-umem=no --with-autotrace=no --with- fpx=no > --with-fontpath= --with-gs-font-dir=/opt/local/share/fonts/urw-fonts > --with-gvc=no --with-jp2=no --with-lqr=no --with-openexr=no --with- pango=no > --with-rsvg=no --with-wmf=no --with-perl=no > > DOCUMENTATION_PATH /opt/local/share/doc/ImageMagick-6.8.0 > > EXEC-PREFIX /opt/local > > EXECUTABLE_PATH /opt/local/bin > > FEATURES OpenCL OpenMP > > FILTER_PATH /opt/local/lib/ImageMagick-6.8.0/modules-Q16/filters > > HOST x86_64-apple-darwin10.8.0 > > INCLUDE_PATH /opt/local/include/ImageMagick > > LDFLAGS -L/opt/local/lib -L/opt/local/lib -arch x86_64 > -L/opt/local/lib -L/opt/local/lib > > LIB_VERSION 0x680 > > LIB_VERSION_NUMBER 6,8,0,7 > > LIBRARY_PATH /opt/local/lib/ImageMagick-6.8.0 > > LIBS -lMagickCore -llcms2 -lfreetype -lfftw3 -L/opt/local/lib > -lfontconfig -lXext -lSM -lICE -lX11 -lXt -L/opt/local/lib -llzma -lbz2 -lz > -lltdl -lm -lgomp -lclparser -Wl,-framework,OpenCL > -L/System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries -lm > -lpthread > > NAME ImageMagick > > PCFLAGS -fopenmp > > PREFIX /opt/local > > QuantumDepth 16 > > RELEASE_DATE 2013-03-04 > > SHARE_PATH /opt/local/share/ImageMagick-6.8.0 > > SVN_REVISION 10029 > > TARGET_CPU x86_64 > > TARGET_OS darwin10.8.0 > > TARGET_VENDOR apple > > VERSION 6.8.0 > > WEBSITE http://www.imagemagick.org > > > Path: [built-in] > > > Name Value > > -------------------------------------------------------------------- ----------- > > NAME ImageMagick > > > Any help would be appreciated. Thanks > > > -- output of sessionInfo(): > > > R version 2.15.2 (2012-10-26) > > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > > locale: > > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > > attached base packages: > > [1] tools stats graphics grDevices utils datasets methods > base > > > other attached packages: > > [1] latticeExtra_0.6-24 RColorBrewer_1.0-5 parody_1.16.0 > bioDist_1.30.0 > > [5] KernSmooth_2.23-8 mvoutlier_1.9.9 sgeostat_1.0-25 > robCompositions_1.6.3 > > [9] car_2.0-16 nnet_7.3-5 compositions_1.20-1 > energy_1.4-0 > > [13] MASS_7.3-23 boot_1.3-7 tensorA_0.36 > rgl_0.93.928 > > [17] flowViz_1.22.0 flowCore_1.24.2 rrcov_1.3-02 > pcaPP_1.9-48 > > [21] mvtnorm_0.9-9994 robustbase_0.9-5 Biobase_2.18.0 > lattice_0.20-13 > > [25] outliers_0.14 BiocGenerics_0.4.0 BiocInstaller_1.8.3 > > > loaded via a namespace (and not attached): > > [1] annotate_1.36.0 AnnotationDbi_1.20.5 DBI_0.2-5 > feature_1.2.8 > > [5] flowQ_1.18.0 geneplotter_1.36.0 graph_1.36.2 > grid_2.15.2 > > [9] hexbin_1.26.1 IDPmisc_1.1.17 IRanges_1.16.6 ks_1.8.11 > > [13] parallel_2.15.2 RSQLite_0.11.2 stats4_2.15.2 > XML_3.95-0.1 > > [17] xtable_1.7-1 > > > -- > > Sent via the guest posting facility at bioconductor.org. > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > Chandra Jack > > Postdoctoral Research Assoc. > > Dept. of Bioengineering > > Rice University > > chanj at rice.edu > > > > > > > Chandra Jack > Postdoctoral Research Assoc. > Dept. of Bioengineering > Rice University > chanj at rice.edu > > >
ADD REPLYlink written 6.7 years ago by Dan Tenenbaum8.2k
Thank you so much for your help. Chandra-Jacks-MacBook:~ chanj$ source ~/.bash_profile Chandra-Jacks-MacBook:~ chanj$ echo $PATH /Library/Frameworks/Python.framework/Versions/2.7/bin:/Library/Framewo rks/EPD64.framework/Versions/Current/bin:/Library/Frameworks/Python.fr amework/Versions/2.7/bin:/Library/Frameworks/EPD64.framework/Versions/ Current/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin: /opt/local/bin:/opt/local/bin Chandra-Jacks-MacBook:~ chanj$ which convert /opt/local/bin/convert On Mar 4, 2013, at 11:45 PM, Dan Tenenbaum wrote: > On Mon, Mar 4, 2013 at 9:30 PM, Chandra Jack <chanj at="" rice.edu=""> wrote: >> I replaced the original export line with the one you wrote but it still >> didn't work. >> > > OK, at a terminal prompt, please enter the following commands and send > me the output they produce: > > source ~/.bash_profile > echo $PATH > which convert > > > > thanks, > Dan > > > >> On Mar 4, 2013, at 10:18 PM, Dan Tenenbaum wrote: >> >> On Mon, Mar 4, 2013 at 8:07 PM, Chandra Jack <chanj at="" rice.edu=""> wrote: >> >> The convert command isn't in my PATH but adding the newIt doesn't seem to be >> working. I don't have a .bashrc file but I have a .bash_profile. The >> original file was: >> >> # Setting PATH for EPD-7.1-2 >> >> # The orginal version is saved in .bash_profile.pysave >> >> PATH="/Library/Frameworks/EPD64.framework/Versions/Current/bin:${PA TH}" >> >> export PATH >> >> >> MKL_NUM_THREADS=1 >> >> export MKL_NUM_THREADS >> >> >> # Setting PATH for Python 2.7 >> >> # The orginal version is saved in .bash_profile.pysave >> >> PATH="/Library/Frameworks/Python.framework/Versions/2.7/bin:${PATH}" >> >> export PATH >> >> >> ## >> >> # Your previous /Users/chanj/.bash_profile file was backed up as >> /Users/chanj/.bash_profile.macports-saved_2013-03-04_at_14:30:35 >> >> ## >> >> >> # MacPorts Installer addition on 2013-03-04_at_14:30:35: adding an >> appropriate PATH variable for use with MacPorts. >> >> export PATH=/opt/local/bin:/opt/local/sbin:$PATH >> >> # Finished adapting your PATH environment variable for use with MacPorts. >> >> >> I added PATH=$PATH:/opt/local/bin after the export line, resaved the text >> edit file and quit the terminal. When I checked Terminal again the file was >> updated but R couldn't find the command still. >> >> >> Sorry, it needs to say: >> >> export PATH=$PATH:/opt/local/bin >> >> I forgot the 'export' before. >> >> >> >> >> >> >> I also tried adding it before the export line, replacing the part after the >> export line with it, adding quotation marks but nothing seemed to work. I >> went in and found the convert command file and it is in opt/local/bin. I >> tried Sys.which with another file that was in the same location and R output >> "/usr/bin/clear" . Could it be related to the backup file that was created >> before I changed it? >> >> >> No, that just means there is a 'clear' executable in two locations. >> Dan >> >> >> >> Thanks >> >> >> On Mar 4, 2013, at 4:15 PM, Dan Tenenbaum wrote: >> >> >> On Mon, Mar 4, 2013 at 2:09 PM, Chandra Jack [guest] >> >> <guest at="" bioconductor.org=""> wrote: >> >> >> Hi All, >> >> >> I'm having a problem that has been mentioned here before but I'm not sure >> how to fix it. I tried to load flowQ and got: >> >> >> Error : .onAttach failed in attachNamespace() for 'flowQ', details: >> >> call: mysys("convert -list configure", intern = TRUE, ignore.stderr = TRUE) >> >> error: error in running command >> >> >> Is the 'convert' command in your PATH? >> >> >> What is the output of the R command: >> >> Sys.which("convert") >> >> ? >> >> >> If it does not output anything, then the convert command is not in your >> PATH. >> >> >> I'm not sure where the convert command ended up, but I'm guessing it's >> >> in /opt/local/bin, >> >> so I think you need to edit your ~/.bashrc >> >> file and add the following line: >> >> >> PATH=$PATH:/opt/local/bin >> >> >> Then, start a new terminal window to make sure this setting is >> >> enabled, and try again. >> >> >> Dan >> >> >> >> In addition: Warning messages: >> >> 1: replacing previous import ???plot??? when loading ???graphics??? >> >> 2: replacing previous import ???as??? when loading ???methods??? >> >> Error: package/namespace load failed for ???flowQ???. >> >> >> I have installed ImageMagick using Macports as has been suggested and I have >> also run >> >> convert -list configure, which gave the following: >> >> Path: /opt/local/lib/ImageMagick-6.8.0/config/configure.xml >> >> >> Name Value >> >> ------------------------------------------------------------------- ------------ >> >> CC /usr/bin/gcc-4.2 -std=gnu99 -std=gnu99 >> >> CFLAGS -D_THREAD_SAFE -D_THREAD_SAFE -pthread -fopenmp -pipe -O2 >> -arch x86_64 -Wall -D_THREAD_SAFE -pthread >> >> CODER_PATH /opt/local/lib/ImageMagick-6.8.0/modules-Q16/coders >> >> CONFIGURE ./configure '--prefix=/opt/local' '--enable-shared' >> '--enable-static' '--disable-ltdl-install' '--disable-silent-rules' >> '--with-frozenpaths' '--without-openexr' '--disable-hdri' '--with- dps' >> '--with-bzlib' '--with-fontconfig' '--with-gslib' '--with-jpeg' >> '--with-lcms' '--with-png' '--with-tiff' '--with-webp' '--with- zlib' >> '--with-modules' '--with-xml' '--with-x' '--without-perl' '--without-fpx' >> '--without-jbig' '--without-jp2' '--without-wmf' '--without-gvc' >> '--without-rsvg' '--without-lqr' '--without-pango' >> '--with-gs-font-dir=/opt/local/share/fonts/urw-fonts' >> '--with-quantum-depth=16' 'CC=/usr/bin/gcc-4.2' 'CFLAGS=-pipe -O2 -arch >> x86_64' 'LDFLAGS=-L/opt/local/lib -arch x86_64' >> 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/g++-4.2' 'CXXFLAGS=-pipe -O2 >> -arch x86_64' >> >> CONFIGURE_PATH /opt/local/etc/ImageMagick/ >> >> COPYRIGHT Copyright (C) 1999-2012 ImageMagick Studio LLC >> >> CPPFLAGS -I/opt/local/include/ImageMagick >> >> CXX /usr/bin/g++-4.2 >> >> CXXFLAGS -pipe -O2 -arch x86_64 -D_THREAD_SAFE -pthread >> >> DEFS -DHAVE_CONFIG_H >> >> DELEGATES bzlib fftw fontconfig freetype gs jpeg jng lcms2 lzma png tiff >> x11 xml zlib >> >> DISTCHECK_CONFIG_FLAGS 'CC=/usr/bin/gcc-4.2' 'CFLAGS=-pipe -O2 -arch x86_64' >> 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/g++-4.2' >> 'LDFLAGS=-L/opt/local/lib -arch x86_64' --disable-deprecated >> --with-quantum-depth=16 --with-umem=no --with-autotrace=no --with- fpx=no >> --with-fontpath= --with-gs-font-dir=/opt/local/share/fonts/urw- fonts >> --with-gvc=no --with-jp2=no --with-lqr=no --with-openexr=no --with- pango=no >> --with-rsvg=no --with-wmf=no --with-perl=no >> >> DOCUMENTATION_PATH /opt/local/share/doc/ImageMagick-6.8.0 >> >> EXEC-PREFIX /opt/local >> >> EXECUTABLE_PATH /opt/local/bin >> >> FEATURES OpenCL OpenMP >> >> FILTER_PATH /opt/local/lib/ImageMagick-6.8.0/modules-Q16/filters >> >> HOST x86_64-apple-darwin10.8.0 >> >> INCLUDE_PATH /opt/local/include/ImageMagick >> >> LDFLAGS -L/opt/local/lib -L/opt/local/lib -arch x86_64 >> -L/opt/local/lib -L/opt/local/lib >> >> LIB_VERSION 0x680 >> >> LIB_VERSION_NUMBER 6,8,0,7 >> >> LIBRARY_PATH /opt/local/lib/ImageMagick-6.8.0 >> >> LIBS -lMagickCore -llcms2 -lfreetype -lfftw3 -L/opt/local/lib >> -lfontconfig -lXext -lSM -lICE -lX11 -lXt -L/opt/local/lib -llzma -lbz2 -lz >> -lltdl -lm -lgomp -lclparser -Wl,-framework,OpenCL >> -L/System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries -lm >> -lpthread >> >> NAME ImageMagick >> >> PCFLAGS -fopenmp >> >> PREFIX /opt/local >> >> QuantumDepth 16 >> >> RELEASE_DATE 2013-03-04 >> >> SHARE_PATH /opt/local/share/ImageMagick-6.8.0 >> >> SVN_REVISION 10029 >> >> TARGET_CPU x86_64 >> >> TARGET_OS darwin10.8.0 >> >> TARGET_VENDOR apple >> >> VERSION 6.8.0 >> >> WEBSITE http://www.imagemagick.org >> >> >> Path: [built-in] >> >> >> Name Value >> >> ------------------------------------------------------------------- ------------ >> >> NAME ImageMagick >> >> >> Any help would be appreciated. Thanks >> >> >> -- output of sessionInfo(): >> >> >> R version 2.15.2 (2012-10-26) >> >> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >> >> >> locale: >> >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> >> attached base packages: >> >> [1] tools stats graphics grDevices utils datasets methods >> base >> >> >> other attached packages: >> >> [1] latticeExtra_0.6-24 RColorBrewer_1.0-5 parody_1.16.0 >> bioDist_1.30.0 >> >> [5] KernSmooth_2.23-8 mvoutlier_1.9.9 sgeostat_1.0-25 >> robCompositions_1.6.3 >> >> [9] car_2.0-16 nnet_7.3-5 compositions_1.20-1 >> energy_1.4-0 >> >> [13] MASS_7.3-23 boot_1.3-7 tensorA_0.36 >> rgl_0.93.928 >> >> [17] flowViz_1.22.0 flowCore_1.24.2 rrcov_1.3-02 >> pcaPP_1.9-48 >> >> [21] mvtnorm_0.9-9994 robustbase_0.9-5 Biobase_2.18.0 >> lattice_0.20-13 >> >> [25] outliers_0.14 BiocGenerics_0.4.0 BiocInstaller_1.8.3 >> >> >> loaded via a namespace (and not attached): >> >> [1] annotate_1.36.0 AnnotationDbi_1.20.5 DBI_0.2-5 >> feature_1.2.8 >> >> [5] flowQ_1.18.0 geneplotter_1.36.0 graph_1.36.2 >> grid_2.15.2 >> >> [9] hexbin_1.26.1 IDPmisc_1.1.17 IRanges_1.16.6 ks_1.8.11 >> >> [13] parallel_2.15.2 RSQLite_0.11.2 stats4_2.15.2 >> XML_3.95-0.1 >> >> [17] xtable_1.7-1 >> >> >> -- >> >> Sent via the guest posting facility at bioconductor.org. >> >> >> _______________________________________________ >> >> Bioconductor mailing list >> >> Bioconductor at r-project.org >> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> >> Chandra Jack >> >> Postdoctoral Research Assoc. >> >> Dept. of Bioengineering >> >> Rice University >> >> chanj at rice.edu >> >> >> >> >> >> >> Chandra Jack >> Postdoctoral Research Assoc. >> Dept. of Bioengineering >> Rice University >> chanj at rice.edu >> >> >> > Chandra Jack Postdoctoral Research Assoc. Dept. of Bioengineering Rice University chanj at rice.edu
ADD REPLYlink written 6.7 years ago by Chandra Jack90
On Mon, Mar 4, 2013 at 9:53 PM, Chandra Jack <chanj at="" rice.edu=""> wrote: > Thank you so much for your help. > > Chandra-Jacks-MacBook:~ chanj$ source ~/.bash_profile > Chandra-Jacks-MacBook:~ chanj$ echo $PATH > /Library/Frameworks/Python.framework/Versions/2.7/bin:/Library/Frame works/EPD64.framework/Versions/Current/bin:/Library/Frameworks/Python. framework/Versions/2.7/bin:/Library/Frameworks/EPD64.framework/Version s/Current/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bi n:/opt/local/bin:/opt/local/bin > Chandra-Jacks-MacBook:~ chanj$ which convert > /opt/local/bin/convert > It looks like convert is in your PATH. What happens if you type convert at the terminal prompt? What if you go into R and type system("convert") ? Dan > On Mar 4, 2013, at 11:45 PM, Dan Tenenbaum wrote: > >> On Mon, Mar 4, 2013 at 9:30 PM, Chandra Jack <chanj at="" rice.edu=""> wrote: >>> I replaced the original export line with the one you wrote but it still >>> didn't work. >>> >> >> OK, at a terminal prompt, please enter the following commands and send >> me the output they produce: >> >> source ~/.bash_profile >> echo $PATH >> which convert >> >> >> >> thanks, >> Dan >> >> >> >>> On Mar 4, 2013, at 10:18 PM, Dan Tenenbaum wrote: >>> >>> On Mon, Mar 4, 2013 at 8:07 PM, Chandra Jack <chanj at="" rice.edu=""> wrote: >>> >>> The convert command isn't in my PATH but adding the newIt doesn't seem to be >>> working. I don't have a .bashrc file but I have a .bash_profile. The >>> original file was: >>> >>> # Setting PATH for EPD-7.1-2 >>> >>> # The orginal version is saved in .bash_profile.pysave >>> >>> PATH="/Library/Frameworks/EPD64.framework/Versions/Current/bin:${P ATH}" >>> >>> export PATH >>> >>> >>> MKL_NUM_THREADS=1 >>> >>> export MKL_NUM_THREADS >>> >>> >>> # Setting PATH for Python 2.7 >>> >>> # The orginal version is saved in .bash_profile.pysave >>> >>> PATH="/Library/Frameworks/Python.framework/Versions/2.7/bin:${PATH}" >>> >>> export PATH >>> >>> >>> ## >>> >>> # Your previous /Users/chanj/.bash_profile file was backed up as >>> /Users/chanj/.bash_profile.macports-saved_2013-03-04_at_14:30:35 >>> >>> ## >>> >>> >>> # MacPorts Installer addition on 2013-03-04_at_14:30:35: adding an >>> appropriate PATH variable for use with MacPorts. >>> >>> export PATH=/opt/local/bin:/opt/local/sbin:$PATH >>> >>> # Finished adapting your PATH environment variable for use with MacPorts. >>> >>> >>> I added PATH=$PATH:/opt/local/bin after the export line, resaved the text >>> edit file and quit the terminal. When I checked Terminal again the file was >>> updated but R couldn't find the command still. >>> >>> >>> Sorry, it needs to say: >>> >>> export PATH=$PATH:/opt/local/bin >>> >>> I forgot the 'export' before. >>> >>> >>> >>> >>> >>> >>> I also tried adding it before the export line, replacing the part after the >>> export line with it, adding quotation marks but nothing seemed to work. I >>> went in and found the convert command file and it is in opt/local/bin. I >>> tried Sys.which with another file that was in the same location and R output >>> "/usr/bin/clear" . Could it be related to the backup file that was created >>> before I changed it? >>> >>> >>> No, that just means there is a 'clear' executable in two locations. >>> Dan >>> >>> >>> >>> Thanks >>> >>> >>> On Mar 4, 2013, at 4:15 PM, Dan Tenenbaum wrote: >>> >>> >>> On Mon, Mar 4, 2013 at 2:09 PM, Chandra Jack [guest] >>> >>> <guest at="" bioconductor.org=""> wrote: >>> >>> >>> Hi All, >>> >>> >>> I'm having a problem that has been mentioned here before but I'm not sure >>> how to fix it. I tried to load flowQ and got: >>> >>> >>> Error : .onAttach failed in attachNamespace() for 'flowQ', details: >>> >>> call: mysys("convert -list configure", intern = TRUE, ignore.stderr = TRUE) >>> >>> error: error in running command >>> >>> >>> Is the 'convert' command in your PATH? >>> >>> >>> What is the output of the R command: >>> >>> Sys.which("convert") >>> >>> ? >>> >>> >>> If it does not output anything, then the convert command is not in your >>> PATH. >>> >>> >>> I'm not sure where the convert command ended up, but I'm guessing it's >>> >>> in /opt/local/bin, >>> >>> so I think you need to edit your ~/.bashrc >>> >>> file and add the following line: >>> >>> >>> PATH=$PATH:/opt/local/bin >>> >>> >>> Then, start a new terminal window to make sure this setting is >>> >>> enabled, and try again. >>> >>> >>> Dan >>> >>> >>> >>> In addition: Warning messages: >>> >>> 1: replacing previous import ???plot??? when loading ???graphics??? >>> >>> 2: replacing previous import ???as??? when loading ???methods??? >>> >>> Error: package/namespace load failed for ???flowQ???. >>> >>> >>> I have installed ImageMagick using Macports as has been suggested and I have >>> also run >>> >>> convert -list configure, which gave the following: >>> >>> Path: /opt/local/lib/ImageMagick-6.8.0/config/configure.xml >>> >>> >>> Name Value >>> >>> ------------------------------------------------------------------ ------------- >>> >>> CC /usr/bin/gcc-4.2 -std=gnu99 -std=gnu99 >>> >>> CFLAGS -D_THREAD_SAFE -D_THREAD_SAFE -pthread -fopenmp -pipe -O2 >>> -arch x86_64 -Wall -D_THREAD_SAFE -pthread >>> >>> CODER_PATH /opt/local/lib/ImageMagick-6.8.0/modules-Q16/coders >>> >>> CONFIGURE ./configure '--prefix=/opt/local' '--enable-shared' >>> '--enable-static' '--disable-ltdl-install' '--disable-silent- rules' >>> '--with-frozenpaths' '--without-openexr' '--disable-hdri' '--with- dps' >>> '--with-bzlib' '--with-fontconfig' '--with-gslib' '--with-jpeg' >>> '--with-lcms' '--with-png' '--with-tiff' '--with-webp' '--with- zlib' >>> '--with-modules' '--with-xml' '--with-x' '--without-perl' '--without-fpx' >>> '--without-jbig' '--without-jp2' '--without-wmf' '--without-gvc' >>> '--without-rsvg' '--without-lqr' '--without-pango' >>> '--with-gs-font-dir=/opt/local/share/fonts/urw-fonts' >>> '--with-quantum-depth=16' 'CC=/usr/bin/gcc-4.2' 'CFLAGS=-pipe -O2 -arch >>> x86_64' 'LDFLAGS=-L/opt/local/lib -arch x86_64' >>> 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/g++-4.2' 'CXXFLAGS=-pipe -O2 >>> -arch x86_64' >>> >>> CONFIGURE_PATH /opt/local/etc/ImageMagick/ >>> >>> COPYRIGHT Copyright (C) 1999-2012 ImageMagick Studio LLC >>> >>> CPPFLAGS -I/opt/local/include/ImageMagick >>> >>> CXX /usr/bin/g++-4.2 >>> >>> CXXFLAGS -pipe -O2 -arch x86_64 -D_THREAD_SAFE -pthread >>> >>> DEFS -DHAVE_CONFIG_H >>> >>> DELEGATES bzlib fftw fontconfig freetype gs jpeg jng lcms2 lzma png tiff >>> x11 xml zlib >>> >>> DISTCHECK_CONFIG_FLAGS 'CC=/usr/bin/gcc-4.2' 'CFLAGS=-pipe -O2 -arch x86_64' >>> 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/g++-4.2' >>> 'LDFLAGS=-L/opt/local/lib -arch x86_64' --disable-deprecated >>> --with-quantum-depth=16 --with-umem=no --with-autotrace=no --with- fpx=no >>> --with-fontpath= --with-gs-font-dir=/opt/local/share/fonts/urw- fonts >>> --with-gvc=no --with-jp2=no --with-lqr=no --with-openexr=no --with-pango=no >>> --with-rsvg=no --with-wmf=no --with-perl=no >>> >>> DOCUMENTATION_PATH /opt/local/share/doc/ImageMagick-6.8.0 >>> >>> EXEC-PREFIX /opt/local >>> >>> EXECUTABLE_PATH /opt/local/bin >>> >>> FEATURES OpenCL OpenMP >>> >>> FILTER_PATH /opt/local/lib/ImageMagick-6.8.0/modules-Q16/filters >>> >>> HOST x86_64-apple-darwin10.8.0 >>> >>> INCLUDE_PATH /opt/local/include/ImageMagick >>> >>> LDFLAGS -L/opt/local/lib -L/opt/local/lib -arch x86_64 >>> -L/opt/local/lib -L/opt/local/lib >>> >>> LIB_VERSION 0x680 >>> >>> LIB_VERSION_NUMBER 6,8,0,7 >>> >>> LIBRARY_PATH /opt/local/lib/ImageMagick-6.8.0 >>> >>> LIBS -lMagickCore -llcms2 -lfreetype -lfftw3 -L/opt/local/lib >>> -lfontconfig -lXext -lSM -lICE -lX11 -lXt -L/opt/local/lib -llzma -lbz2 -lz >>> -lltdl -lm -lgomp -lclparser -Wl,-framework,OpenCL >>> -L/System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries -lm >>> -lpthread >>> >>> NAME ImageMagick >>> >>> PCFLAGS -fopenmp >>> >>> PREFIX /opt/local >>> >>> QuantumDepth 16 >>> >>> RELEASE_DATE 2013-03-04 >>> >>> SHARE_PATH /opt/local/share/ImageMagick-6.8.0 >>> >>> SVN_REVISION 10029 >>> >>> TARGET_CPU x86_64 >>> >>> TARGET_OS darwin10.8.0 >>> >>> TARGET_VENDOR apple >>> >>> VERSION 6.8.0 >>> >>> WEBSITE http://www.imagemagick.org >>> >>> >>> Path: [built-in] >>> >>> >>> Name Value >>> >>> ------------------------------------------------------------------ ------------- >>> >>> NAME ImageMagick >>> >>> >>> Any help would be appreciated. Thanks >>> >>> >>> -- output of sessionInfo(): >>> >>> >>> R version 2.15.2 (2012-10-26) >>> >>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >>> >>> >>> locale: >>> >>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>> >>> >>> attached base packages: >>> >>> [1] tools stats graphics grDevices utils datasets methods >>> base >>> >>> >>> other attached packages: >>> >>> [1] latticeExtra_0.6-24 RColorBrewer_1.0-5 parody_1.16.0 >>> bioDist_1.30.0 >>> >>> [5] KernSmooth_2.23-8 mvoutlier_1.9.9 sgeostat_1.0-25 >>> robCompositions_1.6.3 >>> >>> [9] car_2.0-16 nnet_7.3-5 compositions_1.20-1 >>> energy_1.4-0 >>> >>> [13] MASS_7.3-23 boot_1.3-7 tensorA_0.36 >>> rgl_0.93.928 >>> >>> [17] flowViz_1.22.0 flowCore_1.24.2 rrcov_1.3-02 >>> pcaPP_1.9-48 >>> >>> [21] mvtnorm_0.9-9994 robustbase_0.9-5 Biobase_2.18.0 >>> lattice_0.20-13 >>> >>> [25] outliers_0.14 BiocGenerics_0.4.0 BiocInstaller_1.8.3 >>> >>> >>> loaded via a namespace (and not attached): >>> >>> [1] annotate_1.36.0 AnnotationDbi_1.20.5 DBI_0.2-5 >>> feature_1.2.8 >>> >>> [5] flowQ_1.18.0 geneplotter_1.36.0 graph_1.36.2 >>> grid_2.15.2 >>> >>> [9] hexbin_1.26.1 IDPmisc_1.1.17 IRanges_1.16.6 ks_1.8.11 >>> >>> [13] parallel_2.15.2 RSQLite_0.11.2 stats4_2.15.2 >>> XML_3.95-0.1 >>> >>> [17] xtable_1.7-1 >>> >>> >>> -- >>> >>> Sent via the guest posting facility at bioconductor.org. >>> >>> >>> _______________________________________________ >>> >>> Bioconductor mailing list >>> >>> Bioconductor at r-project.org >>> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >>> >>> Chandra Jack >>> >>> Postdoctoral Research Assoc. >>> >>> Dept. of Bioengineering >>> >>> Rice University >>> >>> chanj at rice.edu >>> >>> >>> >>> >>> >>> >>> Chandra Jack >>> Postdoctoral Research Assoc. >>> Dept. of Bioengineering >>> Rice University >>> chanj at rice.edu >>> >>> >>> >> > > Chandra Jack > Postdoctoral Research Assoc. > Dept. of Bioengineering > Rice University > chanj at rice.edu > > >
ADD REPLYlink written 6.7 years ago by Dan Tenenbaum8.2k
On Mar 4, 2013, at 11:57 PM, Dan Tenenbaum wrote: > On Mon, Mar 4, 2013 at 9:53 PM, Chandra Jack <chanj at="" rice.edu=""> wrote: >> Thank you so much for your help. >> >> Chandra-Jacks-MacBook:~ chanj$ source ~/.bash_profile >> Chandra-Jacks-MacBook:~ chanj$ echo $PATH >> /Library/Frameworks/Python.framework/Versions/2.7/bin:/Library/Fram eworks/EPD64.framework/Versions/Current/bin:/Library/Frameworks/Python .framework/Versions/2.7/bin:/Library/Frameworks/EPD64.framework/Versio ns/Current/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/b in:/opt/local/bin:/opt/local/bin >> Chandra-Jacks-MacBook:~ chanj$ which convert >> /opt/local/bin/convert >> > > It looks like convert is in your PATH. > > What happens if you type > convert > at the terminal prompt? I think it opens ImageMagick Chandra-Jacks-MacBook:~ chanj$ convert Version: ImageMagick 6.8.0-7 2013-03-04 Q16 http://www.imagemagick.org Copyright: Copyright (C) 1999-2012 ImageMagick Studio LLC Features: OpenMP OpenCL Usage: convert [options ...] file [ [options ...] file ...] [options ...] file Image Settings: -adjoin join images into a single multi-image file etc.... > > What if you go into R and type > system("convert") > ? > system("convert") /bin/sh: convert: command not found > Dan > >> On Mar 4, 2013, at 11:45 PM, Dan Tenenbaum wrote: >> >>> On Mon, Mar 4, 2013 at 9:30 PM, Chandra Jack <chanj at="" rice.edu=""> wrote: >>>> I replaced the original export line with the one you wrote but it still >>>> didn't work. >>>> >>> >>> OK, at a terminal prompt, please enter the following commands and send >>> me the output they produce: >>> >>> source ~/.bash_profile >>> echo $PATH >>> which convert >>> >>> >>> >>> thanks, >>> Dan >>> >>> >>> >>>> On Mar 4, 2013, at 10:18 PM, Dan Tenenbaum wrote: >>>> >>>> On Mon, Mar 4, 2013 at 8:07 PM, Chandra Jack <chanj at="" rice.edu=""> wrote: >>>> >>>> The convert command isn't in my PATH but adding the newIt doesn't seem to be >>>> working. I don't have a .bashrc file but I have a .bash_profile. The >>>> original file was: >>>> >>>> # Setting PATH for EPD-7.1-2 >>>> >>>> # The orginal version is saved in .bash_profile.pysave >>>> >>>> PATH="/Library/Frameworks/EPD64.framework/Versions/Current/bin:${ PATH}" >>>> >>>> export PATH >>>> >>>> >>>> MKL_NUM_THREADS=1 >>>> >>>> export MKL_NUM_THREADS >>>> >>>> >>>> # Setting PATH for Python 2.7 >>>> >>>> # The orginal version is saved in .bash_profile.pysave >>>> >>>> PATH="/Library/Frameworks/Python.framework/Versions/2.7/bin:${PATH}" >>>> >>>> export PATH >>>> >>>> >>>> ## >>>> >>>> # Your previous /Users/chanj/.bash_profile file was backed up as >>>> /Users/chanj/.bash_profile.macports-saved_2013-03-04_at_14:30:35 >>>> >>>> ## >>>> >>>> >>>> # MacPorts Installer addition on 2013-03-04_at_14:30:35: adding an >>>> appropriate PATH variable for use with MacPorts. >>>> >>>> export PATH=/opt/local/bin:/opt/local/sbin:$PATH >>>> >>>> # Finished adapting your PATH environment variable for use with MacPorts. >>>> >>>> >>>> I added PATH=$PATH:/opt/local/bin after the export line, resaved the text >>>> edit file and quit the terminal. When I checked Terminal again the file was >>>> updated but R couldn't find the command still. >>>> >>>> >>>> Sorry, it needs to say: >>>> >>>> export PATH=$PATH:/opt/local/bin >>>> >>>> I forgot the 'export' before. >>>> >>>> >>>> >>>> >>>> >>>> >>>> I also tried adding it before the export line, replacing the part after the >>>> export line with it, adding quotation marks but nothing seemed to work. I >>>> went in and found the convert command file and it is in opt/local/bin. I >>>> tried Sys.which with another file that was in the same location and R output >>>> "/usr/bin/clear" . Could it be related to the backup file that was created >>>> before I changed it? >>>> >>>> >>>> No, that just means there is a 'clear' executable in two locations. >>>> Dan >>>> >>>> >>>> >>>> Thanks >>>> >>>> >>>> On Mar 4, 2013, at 4:15 PM, Dan Tenenbaum wrote: >>>> >>>> >>>> On Mon, Mar 4, 2013 at 2:09 PM, Chandra Jack [guest] >>>> >>>> <guest at="" bioconductor.org=""> wrote: >>>> >>>> >>>> Hi All, >>>> >>>> >>>> I'm having a problem that has been mentioned here before but I'm not sure >>>> how to fix it. I tried to load flowQ and got: >>>> >>>> >>>> Error : .onAttach failed in attachNamespace() for 'flowQ', details: >>>> >>>> call: mysys("convert -list configure", intern = TRUE, ignore.stderr = TRUE) >>>> >>>> error: error in running command >>>> >>>> >>>> Is the 'convert' command in your PATH? >>>> >>>> >>>> What is the output of the R command: >>>> >>>> Sys.which("convert") >>>> >>>> ? >>>> >>>> >>>> If it does not output anything, then the convert command is not in your >>>> PATH. >>>> >>>> >>>> I'm not sure where the convert command ended up, but I'm guessing it's >>>> >>>> in /opt/local/bin, >>>> >>>> so I think you need to edit your ~/.bashrc >>>> >>>> file and add the following line: >>>> >>>> >>>> PATH=$PATH:/opt/local/bin >>>> >>>> >>>> Then, start a new terminal window to make sure this setting is >>>> >>>> enabled, and try again. >>>> >>>> >>>> Dan >>>> >>>> >>>> >>>> In addition: Warning messages: >>>> >>>> 1: replacing previous import ???plot??? when loading ???graphics??? >>>> >>>> 2: replacing previous import ???as??? when loading ???methods??? >>>> >>>> Error: package/namespace load failed for ???flowQ???. >>>> >>>> >>>> I have installed ImageMagick using Macports as has been suggested and I have >>>> also run >>>> >>>> convert -list configure, which gave the following: >>>> >>>> Path: /opt/local/lib/ImageMagick-6.8.0/config/configure.xml >>>> >>>> >>>> Name Value >>>> >>>> ----------------------------------------------------------------- -------------- >>>> >>>> CC /usr/bin/gcc-4.2 -std=gnu99 -std=gnu99 >>>> >>>> CFLAGS -D_THREAD_SAFE -D_THREAD_SAFE -pthread -fopenmp -pipe -O2 >>>> -arch x86_64 -Wall -D_THREAD_SAFE -pthread >>>> >>>> CODER_PATH /opt/local/lib/ImageMagick-6.8.0/modules-Q16/coders >>>> >>>> CONFIGURE ./configure '--prefix=/opt/local' '--enable- shared' >>>> '--enable-static' '--disable-ltdl-install' '--disable-silent- rules' >>>> '--with-frozenpaths' '--without-openexr' '--disable-hdri' '--with-dps' >>>> '--with-bzlib' '--with-fontconfig' '--with-gslib' '--with-jpeg' >>>> '--with-lcms' '--with-png' '--with-tiff' '--with-webp' '--with- zlib' >>>> '--with-modules' '--with-xml' '--with-x' '--without-perl' '--without-fpx' >>>> '--without-jbig' '--without-jp2' '--without-wmf' '--without-gvc' >>>> '--without-rsvg' '--without-lqr' '--without-pango' >>>> '--with-gs-font-dir=/opt/local/share/fonts/urw-fonts' >>>> '--with-quantum-depth=16' 'CC=/usr/bin/gcc-4.2' 'CFLAGS=-pipe -O2 -arch >>>> x86_64' 'LDFLAGS=-L/opt/local/lib -arch x86_64' >>>> 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/g++-4.2' 'CXXFLAGS=-pipe -O2 >>>> -arch x86_64' >>>> >>>> CONFIGURE_PATH /opt/local/etc/ImageMagick/ >>>> >>>> COPYRIGHT Copyright (C) 1999-2012 ImageMagick Studio LLC >>>> >>>> CPPFLAGS -I/opt/local/include/ImageMagick >>>> >>>> CXX /usr/bin/g++-4.2 >>>> >>>> CXXFLAGS -pipe -O2 -arch x86_64 -D_THREAD_SAFE -pthread >>>> >>>> DEFS -DHAVE_CONFIG_H >>>> >>>> DELEGATES bzlib fftw fontconfig freetype gs jpeg jng lcms2 lzma png tiff >>>> x11 xml zlib >>>> >>>> DISTCHECK_CONFIG_FLAGS 'CC=/usr/bin/gcc-4.2' 'CFLAGS=-pipe -O2 -arch x86_64' >>>> 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/g++-4.2' >>>> 'LDFLAGS=-L/opt/local/lib -arch x86_64' --disable-deprecated >>>> --with-quantum-depth=16 --with-umem=no --with-autotrace=no --with-fpx=no >>>> --with-fontpath= --with-gs-font-dir=/opt/local/share/fonts/urw- fonts >>>> --with-gvc=no --with-jp2=no --with-lqr=no --with-openexr=no --with-pango=no >>>> --with-rsvg=no --with-wmf=no --with-perl=no >>>> >>>> DOCUMENTATION_PATH /opt/local/share/doc/ImageMagick-6.8.0 >>>> >>>> EXEC-PREFIX /opt/local >>>> >>>> EXECUTABLE_PATH /opt/local/bin >>>> >>>> FEATURES OpenCL OpenMP >>>> >>>> FILTER_PATH /opt/local/lib/ImageMagick-6.8.0/modules-Q16/filters >>>> >>>> HOST x86_64-apple-darwin10.8.0 >>>> >>>> INCLUDE_PATH /opt/local/include/ImageMagick >>>> >>>> LDFLAGS -L/opt/local/lib -L/opt/local/lib -arch x86_64 >>>> -L/opt/local/lib -L/opt/local/lib >>>> >>>> LIB_VERSION 0x680 >>>> >>>> LIB_VERSION_NUMBER 6,8,0,7 >>>> >>>> LIBRARY_PATH /opt/local/lib/ImageMagick-6.8.0 >>>> >>>> LIBS -lMagickCore -llcms2 -lfreetype -lfftw3 -L/opt/local/lib >>>> -lfontconfig -lXext -lSM -lICE -lX11 -lXt -L/opt/local/lib -llzma -lbz2 -lz >>>> -lltdl -lm -lgomp -lclparser -Wl,-framework,OpenCL >>>> -L/System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries -lm >>>> -lpthread >>>> >>>> NAME ImageMagick >>>> >>>> PCFLAGS -fopenmp >>>> >>>> PREFIX /opt/local >>>> >>>> QuantumDepth 16 >>>> >>>> RELEASE_DATE 2013-03-04 >>>> >>>> SHARE_PATH /opt/local/share/ImageMagick-6.8.0 >>>> >>>> SVN_REVISION 10029 >>>> >>>> TARGET_CPU x86_64 >>>> >>>> TARGET_OS darwin10.8.0 >>>> >>>> TARGET_VENDOR apple >>>> >>>> VERSION 6.8.0 >>>> >>>> WEBSITE http://www.imagemagick.org >>>> >>>> >>>> Path: [built-in] >>>> >>>> >>>> Name Value >>>> >>>> ----------------------------------------------------------------- -------------- >>>> >>>> NAME ImageMagick >>>> >>>> >>>> Any help would be appreciated. Thanks >>>> >>>> >>>> -- output of sessionInfo(): >>>> >>>> >>>> R version 2.15.2 (2012-10-26) >>>> >>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >>>> >>>> >>>> locale: >>>> >>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>>> >>>> >>>> attached base packages: >>>> >>>> [1] tools stats graphics grDevices utils datasets methods >>>> base >>>> >>>> >>>> other attached packages: >>>> >>>> [1] latticeExtra_0.6-24 RColorBrewer_1.0-5 parody_1.16.0 >>>> bioDist_1.30.0 >>>> >>>> [5] KernSmooth_2.23-8 mvoutlier_1.9.9 sgeostat_1.0-25 >>>> robCompositions_1.6.3 >>>> >>>> [9] car_2.0-16 nnet_7.3-5 compositions_1.20-1 >>>> energy_1.4-0 >>>> >>>> [13] MASS_7.3-23 boot_1.3-7 tensorA_0.36 >>>> rgl_0.93.928 >>>> >>>> [17] flowViz_1.22.0 flowCore_1.24.2 rrcov_1.3-02 >>>> pcaPP_1.9-48 >>>> >>>> [21] mvtnorm_0.9-9994 robustbase_0.9-5 Biobase_2.18.0 >>>> lattice_0.20-13 >>>> >>>> [25] outliers_0.14 BiocGenerics_0.4.0 BiocInstaller_1.8.3 >>>> >>>> >>>> loaded via a namespace (and not attached): >>>> >>>> [1] annotate_1.36.0 AnnotationDbi_1.20.5 DBI_0.2-5 >>>> feature_1.2.8 >>>> >>>> [5] flowQ_1.18.0 geneplotter_1.36.0 graph_1.36.2 >>>> grid_2.15.2 >>>> >>>> [9] hexbin_1.26.1 IDPmisc_1.1.17 IRanges_1.16.6 ks_1.8.11 >>>> >>>> [13] parallel_2.15.2 RSQLite_0.11.2 stats4_2.15.2 >>>> XML_3.95-0.1 >>>> >>>> [17] xtable_1.7-1 >>>> >>>> >>>> -- >>>> >>>> Sent via the guest posting facility at bioconductor.org. >>>> >>>> >>>> _______________________________________________ >>>> >>>> Bioconductor mailing list >>>> >>>> Bioconductor at r-project.org >>>> >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>>> >>>> >>>> Chandra Jack >>>> >>>> Postdoctoral Research Assoc. >>>> >>>> Dept. of Bioengineering >>>> >>>> Rice University >>>> >>>> chanj at rice.edu >>>> >>>> >>>> >>>> >>>> >>>> >>>> Chandra Jack >>>> Postdoctoral Research Assoc. >>>> Dept. of Bioengineering >>>> Rice University >>>> chanj at rice.edu >>>> >>>> >>>> >>> >> >> Chandra Jack >> Postdoctoral Research Assoc. >> Dept. of Bioengineering >> Rice University >> chanj at rice.edu >> >> >> > Chandra Jack Postdoctoral Research Assoc. Dept. of Bioengineering Rice University chanj at rice.edu
ADD REPLYlink written 6.7 years ago by Chandra Jack90
On Mon, Mar 4, 2013 at 10:06 PM, Chandra Jack <chanj at="" rice.edu=""> wrote: > > On Mar 4, 2013, at 11:57 PM, Dan Tenenbaum wrote: > >> On Mon, Mar 4, 2013 at 9:53 PM, Chandra Jack <chanj at="" rice.edu=""> wrote: >>> Thank you so much for your help. >>> >>> Chandra-Jacks-MacBook:~ chanj$ source ~/.bash_profile >>> Chandra-Jacks-MacBook:~ chanj$ echo $PATH >>> /Library/Frameworks/Python.framework/Versions/2.7/bin:/Library/Fra meworks/EPD64.framework/Versions/Current/bin:/Library/Frameworks/Pytho n.framework/Versions/2.7/bin:/Library/Frameworks/EPD64.framework/Versi ons/Current/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/ bin:/opt/local/bin:/opt/local/bin >>> Chandra-Jacks-MacBook:~ chanj$ which convert >>> /opt/local/bin/convert >>> >> >> It looks like convert is in your PATH. >> >> What happens if you type >> convert >> at the terminal prompt? > > I think it opens ImageMagick > Chandra-Jacks-MacBook:~ chanj$ convert > Version: ImageMagick 6.8.0-7 2013-03-04 Q16 http://www.imagemagick.org > Copyright: Copyright (C) 1999-2012 ImageMagick Studio LLC > Features: OpenMP OpenCL > > Usage: convert [options ...] file [ [options ...] file ...] [options ...] file > > Image Settings: > -adjoin join images into a single multi-image file > > etc.... > > > >> >> What if you go into R and type >> system("convert") >> ? >> > system("convert") > /bin/sh: convert: command not found > This means convert is in your path but R can't see it. Did you restart R after editing .bash_profile? Dan >> Dan >> >>> On Mar 4, 2013, at 11:45 PM, Dan Tenenbaum wrote: >>> >>>> On Mon, Mar 4, 2013 at 9:30 PM, Chandra Jack <chanj at="" rice.edu=""> wrote: >>>>> I replaced the original export line with the one you wrote but it still >>>>> didn't work. >>>>> >>>> >>>> OK, at a terminal prompt, please enter the following commands and send >>>> me the output they produce: >>>> >>>> source ~/.bash_profile >>>> echo $PATH >>>> which convert >>>> >>>> >>>> >>>> thanks, >>>> Dan >>>> >>>> >>>> >>>>> On Mar 4, 2013, at 10:18 PM, Dan Tenenbaum wrote: >>>>> >>>>> On Mon, Mar 4, 2013 at 8:07 PM, Chandra Jack <chanj at="" rice.edu=""> wrote: >>>>> >>>>> The convert command isn't in my PATH but adding the newIt doesn't seem to be >>>>> working. I don't have a .bashrc file but I have a .bash_profile. The >>>>> original file was: >>>>> >>>>> # Setting PATH for EPD-7.1-2 >>>>> >>>>> # The orginal version is saved in .bash_profile.pysave >>>>> >>>>> PATH="/Library/Frameworks/EPD64.framework/Versions/Current/bin:$ {PATH}" >>>>> >>>>> export PATH >>>>> >>>>> >>>>> MKL_NUM_THREADS=1 >>>>> >>>>> export MKL_NUM_THREADS >>>>> >>>>> >>>>> # Setting PATH for Python 2.7 >>>>> >>>>> # The orginal version is saved in .bash_profile.pysave >>>>> >>>>> PATH="/Library/Frameworks/Python.framework/Versions/2.7/bin:${PATH}" >>>>> >>>>> export PATH >>>>> >>>>> >>>>> ## >>>>> >>>>> # Your previous /Users/chanj/.bash_profile file was backed up as >>>>> /Users/chanj/.bash_profile.macports-saved_2013-03-04_at_14:30:35 >>>>> >>>>> ## >>>>> >>>>> >>>>> # MacPorts Installer addition on 2013-03-04_at_14:30:35: adding an >>>>> appropriate PATH variable for use with MacPorts. >>>>> >>>>> export PATH=/opt/local/bin:/opt/local/sbin:$PATH >>>>> >>>>> # Finished adapting your PATH environment variable for use with MacPorts. >>>>> >>>>> >>>>> I added PATH=$PATH:/opt/local/bin after the export line, resaved the text >>>>> edit file and quit the terminal. When I checked Terminal again the file was >>>>> updated but R couldn't find the command still. >>>>> >>>>> >>>>> Sorry, it needs to say: >>>>> >>>>> export PATH=$PATH:/opt/local/bin >>>>> >>>>> I forgot the 'export' before. >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> I also tried adding it before the export line, replacing the part after the >>>>> export line with it, adding quotation marks but nothing seemed to work. I >>>>> went in and found the convert command file and it is in opt/local/bin. I >>>>> tried Sys.which with another file that was in the same location and R output >>>>> "/usr/bin/clear" . Could it be related to the backup file that was created >>>>> before I changed it? >>>>> >>>>> >>>>> No, that just means there is a 'clear' executable in two locations. >>>>> Dan >>>>> >>>>> >>>>> >>>>> Thanks >>>>> >>>>> >>>>> On Mar 4, 2013, at 4:15 PM, Dan Tenenbaum wrote: >>>>> >>>>> >>>>> On Mon, Mar 4, 2013 at 2:09 PM, Chandra Jack [guest] >>>>> >>>>> <guest at="" bioconductor.org=""> wrote: >>>>> >>>>> >>>>> Hi All, >>>>> >>>>> >>>>> I'm having a problem that has been mentioned here before but I'm not sure >>>>> how to fix it. I tried to load flowQ and got: >>>>> >>>>> >>>>> Error : .onAttach failed in attachNamespace() for 'flowQ', details: >>>>> >>>>> call: mysys("convert -list configure", intern = TRUE, ignore.stderr = TRUE) >>>>> >>>>> error: error in running command >>>>> >>>>> >>>>> Is the 'convert' command in your PATH? >>>>> >>>>> >>>>> What is the output of the R command: >>>>> >>>>> Sys.which("convert") >>>>> >>>>> ? >>>>> >>>>> >>>>> If it does not output anything, then the convert command is not in your >>>>> PATH. >>>>> >>>>> >>>>> I'm not sure where the convert command ended up, but I'm guessing it's >>>>> >>>>> in /opt/local/bin, >>>>> >>>>> so I think you need to edit your ~/.bashrc >>>>> >>>>> file and add the following line: >>>>> >>>>> >>>>> PATH=$PATH:/opt/local/bin >>>>> >>>>> >>>>> Then, start a new terminal window to make sure this setting is >>>>> >>>>> enabled, and try again. >>>>> >>>>> >>>>> Dan >>>>> >>>>> >>>>> >>>>> In addition: Warning messages: >>>>> >>>>> 1: replacing previous import ???plot??? when loading ???graphics??? >>>>> >>>>> 2: replacing previous import ???as??? when loading ???methods??? >>>>> >>>>> Error: package/namespace load failed for ???flowQ???. >>>>> >>>>> >>>>> I have installed ImageMagick using Macports as has been suggested and I have >>>>> also run >>>>> >>>>> convert -list configure, which gave the following: >>>>> >>>>> Path: /opt/local/lib/ImageMagick-6.8.0/config/configure.xml >>>>> >>>>> >>>>> Name Value >>>>> >>>>> ---------------------------------------------------------------- --------------- >>>>> >>>>> CC /usr/bin/gcc-4.2 -std=gnu99 -std=gnu99 >>>>> >>>>> CFLAGS -D_THREAD_SAFE -D_THREAD_SAFE -pthread -fopenmp -pipe -O2 >>>>> -arch x86_64 -Wall -D_THREAD_SAFE -pthread >>>>> >>>>> CODER_PATH /opt/local/lib/ImageMagick-6.8.0/modules-Q16/coders >>>>> >>>>> CONFIGURE ./configure '--prefix=/opt/local' '--enable- shared' >>>>> '--enable-static' '--disable-ltdl-install' '--disable-silent- rules' >>>>> '--with-frozenpaths' '--without-openexr' '--disable-hdri' '--with-dps' >>>>> '--with-bzlib' '--with-fontconfig' '--with-gslib' '--with-jpeg' >>>>> '--with-lcms' '--with-png' '--with-tiff' '--with-webp' '--with- zlib' >>>>> '--with-modules' '--with-xml' '--with-x' '--without-perl' '--without-fpx' >>>>> '--without-jbig' '--without-jp2' '--without-wmf' '--without-gvc' >>>>> '--without-rsvg' '--without-lqr' '--without-pango' >>>>> '--with-gs-font-dir=/opt/local/share/fonts/urw-fonts' >>>>> '--with-quantum-depth=16' 'CC=/usr/bin/gcc-4.2' 'CFLAGS=-pipe -O2 -arch >>>>> x86_64' 'LDFLAGS=-L/opt/local/lib -arch x86_64' >>>>> 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/g++-4.2' 'CXXFLAGS=-pipe -O2 >>>>> -arch x86_64' >>>>> >>>>> CONFIGURE_PATH /opt/local/etc/ImageMagick/ >>>>> >>>>> COPYRIGHT Copyright (C) 1999-2012 ImageMagick Studio LLC >>>>> >>>>> CPPFLAGS -I/opt/local/include/ImageMagick >>>>> >>>>> CXX /usr/bin/g++-4.2 >>>>> >>>>> CXXFLAGS -pipe -O2 -arch x86_64 -D_THREAD_SAFE -pthread >>>>> >>>>> DEFS -DHAVE_CONFIG_H >>>>> >>>>> DELEGATES bzlib fftw fontconfig freetype gs jpeg jng lcms2 lzma png tiff >>>>> x11 xml zlib >>>>> >>>>> DISTCHECK_CONFIG_FLAGS 'CC=/usr/bin/gcc-4.2' 'CFLAGS=-pipe -O2 -arch x86_64' >>>>> 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/g++-4.2' >>>>> 'LDFLAGS=-L/opt/local/lib -arch x86_64' --disable-deprecated >>>>> --with-quantum-depth=16 --with-umem=no --with-autotrace=no --with-fpx=no >>>>> --with-fontpath= --with-gs-font-dir=/opt/local/share/fonts/urw- fonts >>>>> --with-gvc=no --with-jp2=no --with-lqr=no --with-openexr=no --with-pango=no >>>>> --with-rsvg=no --with-wmf=no --with-perl=no >>>>> >>>>> DOCUMENTATION_PATH /opt/local/share/doc/ImageMagick-6.8.0 >>>>> >>>>> EXEC-PREFIX /opt/local >>>>> >>>>> EXECUTABLE_PATH /opt/local/bin >>>>> >>>>> FEATURES OpenCL OpenMP >>>>> >>>>> FILTER_PATH /opt/local/lib/ImageMagick-6.8.0/modules-Q16/filters >>>>> >>>>> HOST x86_64-apple-darwin10.8.0 >>>>> >>>>> INCLUDE_PATH /opt/local/include/ImageMagick >>>>> >>>>> LDFLAGS -L/opt/local/lib -L/opt/local/lib -arch x86_64 >>>>> -L/opt/local/lib -L/opt/local/lib >>>>> >>>>> LIB_VERSION 0x680 >>>>> >>>>> LIB_VERSION_NUMBER 6,8,0,7 >>>>> >>>>> LIBRARY_PATH /opt/local/lib/ImageMagick-6.8.0 >>>>> >>>>> LIBS -lMagickCore -llcms2 -lfreetype -lfftw3 -L/opt/local/lib >>>>> -lfontconfig -lXext -lSM -lICE -lX11 -lXt -L/opt/local/lib -llzma -lbz2 -lz >>>>> -lltdl -lm -lgomp -lclparser -Wl,-framework,OpenCL >>>>> -L/System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries -lm >>>>> -lpthread >>>>> >>>>> NAME ImageMagick >>>>> >>>>> PCFLAGS -fopenmp >>>>> >>>>> PREFIX /opt/local >>>>> >>>>> QuantumDepth 16 >>>>> >>>>> RELEASE_DATE 2013-03-04 >>>>> >>>>> SHARE_PATH /opt/local/share/ImageMagick-6.8.0 >>>>> >>>>> SVN_REVISION 10029 >>>>> >>>>> TARGET_CPU x86_64 >>>>> >>>>> TARGET_OS darwin10.8.0 >>>>> >>>>> TARGET_VENDOR apple >>>>> >>>>> VERSION 6.8.0 >>>>> >>>>> WEBSITE http://www.imagemagick.org >>>>> >>>>> >>>>> Path: [built-in] >>>>> >>>>> >>>>> Name Value >>>>> >>>>> ---------------------------------------------------------------- --------------- >>>>> >>>>> NAME ImageMagick >>>>> >>>>> >>>>> Any help would be appreciated. Thanks >>>>> >>>>> >>>>> -- output of sessionInfo(): >>>>> >>>>> >>>>> R version 2.15.2 (2012-10-26) >>>>> >>>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >>>>> >>>>> >>>>> locale: >>>>> >>>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>>>> >>>>> >>>>> attached base packages: >>>>> >>>>> [1] tools stats graphics grDevices utils datasets methods >>>>> base >>>>> >>>>> >>>>> other attached packages: >>>>> >>>>> [1] latticeExtra_0.6-24 RColorBrewer_1.0-5 parody_1.16.0 >>>>> bioDist_1.30.0 >>>>> >>>>> [5] KernSmooth_2.23-8 mvoutlier_1.9.9 sgeostat_1.0-25 >>>>> robCompositions_1.6.3 >>>>> >>>>> [9] car_2.0-16 nnet_7.3-5 compositions_1.20-1 >>>>> energy_1.4-0 >>>>> >>>>> [13] MASS_7.3-23 boot_1.3-7 tensorA_0.36 >>>>> rgl_0.93.928 >>>>> >>>>> [17] flowViz_1.22.0 flowCore_1.24.2 rrcov_1.3-02 >>>>> pcaPP_1.9-48 >>>>> >>>>> [21] mvtnorm_0.9-9994 robustbase_0.9-5 Biobase_2.18.0 >>>>> lattice_0.20-13 >>>>> >>>>> [25] outliers_0.14 BiocGenerics_0.4.0 BiocInstaller_1.8.3 >>>>> >>>>> >>>>> loaded via a namespace (and not attached): >>>>> >>>>> [1] annotate_1.36.0 AnnotationDbi_1.20.5 DBI_0.2-5 >>>>> feature_1.2.8 >>>>> >>>>> [5] flowQ_1.18.0 geneplotter_1.36.0 graph_1.36.2 >>>>> grid_2.15.2 >>>>> >>>>> [9] hexbin_1.26.1 IDPmisc_1.1.17 IRanges_1.16.6 ks_1.8.11 >>>>> >>>>> [13] parallel_2.15.2 RSQLite_0.11.2 stats4_2.15.2 >>>>> XML_3.95-0.1 >>>>> >>>>> [17] xtable_1.7-1 >>>>> >>>>> >>>>> -- >>>>> >>>>> Sent via the guest posting facility at bioconductor.org. >>>>> >>>>> >>>>> _______________________________________________ >>>>> >>>>> Bioconductor mailing list >>>>> >>>>> Bioconductor at r-project.org >>>>> >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> >>>>> Search the archives: >>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>> >>>>> >>>>> >>>>> Chandra Jack >>>>> >>>>> Postdoctoral Research Assoc. >>>>> >>>>> Dept. of Bioengineering >>>>> >>>>> Rice University >>>>> >>>>> chanj at rice.edu >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> Chandra Jack >>>>> Postdoctoral Research Assoc. >>>>> Dept. of Bioengineering >>>>> Rice University >>>>> chanj at rice.edu >>>>> >>>>> >>>>> >>>> >>> >>> Chandra Jack >>> Postdoctoral Research Assoc. >>> Dept. of Bioengineering >>> Rice University >>> chanj at rice.edu >>> >>> >>> >> > > Chandra Jack > Postdoctoral Research Assoc. > Dept. of Bioengineering > Rice University > chanj at rice.edu > > >
ADD REPLYlink written 6.7 years ago by Dan Tenenbaum8.2k
Yes. I've been restarting R after everytime I changed bash_profile. I also just tried reinstalling R but that didn't help either. On Mar 5, 2013, at 12:20 AM, Dan Tenenbaum wrote: > On Mon, Mar 4, 2013 at 10:06 PM, Chandra Jack <chanj@rice.edu> wrote: >> >> On Mar 4, 2013, at 11:57 PM, Dan Tenenbaum wrote: >> >>> On Mon, Mar 4, 2013 at 9:53 PM, Chandra Jack <chanj@rice.edu> wrote: >>>> Thank you so much for your help. >>>> >>>> Chandra-Jacks-MacBook:~ chanj$ source ~/.bash_profile >>>> Chandra-Jacks-MacBook:~ chanj$ echo $PATH >>>> /Library/Frameworks/Python.framework/Versions/2.7/bin:/Library/Fr ameworks/EPD64.framework/Versions/Current/bin:/Library/Frameworks/Pyth on.framework/Versions/2.7/bin:/Library/Frameworks/EPD64.framework/Vers ions/Current/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11 /bin:/opt/local/bin:/opt/local/bin >>>> Chandra-Jacks-MacBook:~ chanj$ which convert >>>> /opt/local/bin/convert >>>> >>> >>> It looks like convert is in your PATH. >>> >>> What happens if you type >>> convert >>> at the terminal prompt? >> >> I think it opens ImageMagick >> Chandra-Jacks-MacBook:~ chanj$ convert >> Version: ImageMagick 6.8.0-7 2013-03-04 Q16 http://www.imagemagick.org >> Copyright: Copyright (C) 1999-2012 ImageMagick Studio LLC >> Features: OpenMP OpenCL >> >> Usage: convert [options ...] file [ [options ...] file ...] [options ...] file >> >> Image Settings: >> -adjoin join images into a single multi-image file >> >> etc.... >> >> >> >>> >>> What if you go into R and type >>> system("convert") >>> ? >>> >> system("convert") >> /bin/sh: convert: command not found >> > > This means convert is in your path but R can't see it. Did you restart > R after editing .bash_profile? > > Dan > > >>> Dan >>> >>>> On Mar 4, 2013, at 11:45 PM, Dan Tenenbaum wrote: >>>> >>>>> On Mon, Mar 4, 2013 at 9:30 PM, Chandra Jack <chanj@rice.edu> wrote: >>>>>> I replaced the original export line with the one you wrote but it still >>>>>> didn't work. >>>>>> >>>>> >>>>> OK, at a terminal prompt, please enter the following commands and send >>>>> me the output they produce: >>>>> >>>>> source ~/.bash_profile >>>>> echo $PATH >>>>> which convert >>>>> >>>>> >>>>> >>>>> thanks, >>>>> Dan >>>>> >>>>> >>>>> >>>>>> On Mar 4, 2013, at 10:18 PM, Dan Tenenbaum wrote: >>>>>> >>>>>> On Mon, Mar 4, 2013 at 8:07 PM, Chandra Jack <chanj@rice.edu> wrote: >>>>>> >>>>>> The convert command isn't in my PATH but adding the newIt doesn't seem to be >>>>>> working. I don't have a .bashrc file but I have a .bash_profile. The >>>>>> original file was: >>>>>> >>>>>> # Setting PATH for EPD-7.1-2 >>>>>> >>>>>> # The orginal version is saved in .bash_profile.pysave >>>>>> >>>>>> PATH="/Library/Frameworks/EPD64.framework/Versions/Current/bin: ${PATH}" >>>>>> >>>>>> export PATH >>>>>> >>>>>> >>>>>> MKL_NUM_THREADS=1 >>>>>> >>>>>> export MKL_NUM_THREADS >>>>>> >>>>>> >>>>>> # Setting PATH for Python 2.7 >>>>>> >>>>>> # The orginal version is saved in .bash_profile.pysave >>>>>> >>>>>> PATH="/Library/Frameworks/Python.framework/Versions/2.7/bin:${PATH}" >>>>>> >>>>>> export PATH >>>>>> >>>>>> >>>>>> ## >>>>>> >>>>>> # Your previous /Users/chanj/.bash_profile file was backed up as >>>>>> /Users/chanj/.bash_profile.macports- saved_2013-03-04_at_14:30:35 >>>>>> >>>>>> ## >>>>>> >>>>>> >>>>>> # MacPorts Installer addition on 2013-03-04_at_14:30:35: adding an >>>>>> appropriate PATH variable for use with MacPorts. >>>>>> >>>>>> export PATH=/opt/local/bin:/opt/local/sbin:$PATH >>>>>> >>>>>> # Finished adapting your PATH environment variable for use with MacPorts. >>>>>> >>>>>> >>>>>> I added PATH=$PATH:/opt/local/bin after the export line, resaved the text >>>>>> edit file and quit the terminal. When I checked Terminal again the file was >>>>>> updated but R couldn't find the command still. >>>>>> >>>>>> >>>>>> Sorry, it needs to say: >>>>>> >>>>>> export PATH=$PATH:/opt/local/bin >>>>>> >>>>>> I forgot the 'export' before. >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> I also tried adding it before the export line, replacing the part after the >>>>>> export line with it, adding quotation marks but nothing seemed to work. I >>>>>> went in and found the convert command file and it is in opt/local/bin. I >>>>>> tried Sys.which with another file that was in the same location and R output >>>>>> "/usr/bin/clear" . Could it be related to the backup file that was created >>>>>> before I changed it? >>>>>> >>>>>> >>>>>> No, that just means there is a 'clear' executable in two locations. >>>>>> Dan >>>>>> >>>>>> >>>>>> >>>>>> Thanks >>>>>> >>>>>> >>>>>> On Mar 4, 2013, at 4:15 PM, Dan Tenenbaum wrote: >>>>>> >>>>>> >>>>>> On Mon, Mar 4, 2013 at 2:09 PM, Chandra Jack [guest] >>>>>> >>>>>> <guest@bioconductor.org> wrote: >>>>>> >>>>>> >>>>>> Hi All, >>>>>> >>>>>> >>>>>> I'm having a problem that has been mentioned here before but I'm not sure >>>>>> how to fix it. I tried to load flowQ and got: >>>>>> >>>>>> >>>>>> Error : .onAttach failed in attachNamespace() for 'flowQ', details: >>>>>> >>>>>> call: mysys("convert -list configure", intern = TRUE, ignore.stderr = TRUE) >>>>>> >>>>>> error: error in running command >>>>>> >>>>>> >>>>>> Is the 'convert' command in your PATH? >>>>>> >>>>>> >>>>>> What is the output of the R command: >>>>>> >>>>>> Sys.which("convert") >>>>>> >>>>>> ? >>>>>> >>>>>> >>>>>> If it does not output anything, then the convert command is not in your >>>>>> PATH. >>>>>> >>>>>> >>>>>> I'm not sure where the convert command ended up, but I'm guessing it's >>>>>> >>>>>> in /opt/local/bin, >>>>>> >>>>>> so I think you need to edit your ~/.bashrc >>>>>> >>>>>> file and add the following line: >>>>>> >>>>>> >>>>>> PATH=$PATH:/opt/local/bin >>>>>> >>>>>> >>>>>> Then, start a new terminal window to make sure this setting is >>>>>> >>>>>> enabled, and try again. >>>>>> >>>>>> >>>>>> Dan >>>>>> >>>>>> >>>>>> >>>>>> In addition: Warning messages: >>>>>> >>>>>> 1: replacing previous import ‘plot’ when loading ‘graphics’ >>>>>> >>>>>> 2: replacing previous import ‘as’ when loading ‘methods’ >>>>>> >>>>>> Error: package/namespace load failed for ‘flowQ’. >>>>>> >>>>>> >>>>>> I have installed ImageMagick using Macports as has been suggested and I have >>>>>> also run >>>>>> >>>>>> convert -list configure, which gave the following: >>>>>> >>>>>> Path: /opt/local/lib/ImageMagick-6.8.0/config/configure.xml >>>>>> >>>>>> >>>>>> Name Value >>>>>> >>>>>> --------------------------------------------------------------- ---------------- >>>>>> >>>>>> CC /usr/bin/gcc-4.2 -std=gnu99 -std=gnu99 >>>>>> >>>>>> CFLAGS -D_THREAD_SAFE -D_THREAD_SAFE -pthread -fopenmp -pipe -O2 >>>>>> -arch x86_64 -Wall -D_THREAD_SAFE -pthread >>>>>> >>>>>> CODER_PATH /opt/local/lib/ImageMagick-6.8.0/modules-Q16/coders >>>>>> >>>>>> CONFIGURE ./configure '--prefix=/opt/local' '--enable- shared' >>>>>> '--enable-static' '--disable-ltdl-install' '--disable-silent- rules' >>>>>> '--with-frozenpaths' '--without-openexr' '--disable-hdri' '--with-dps' >>>>>> '--with-bzlib' '--with-fontconfig' '--with-gslib' '--with-jpeg' >>>>>> '--with-lcms' '--with-png' '--with-tiff' '--with-webp' '--with- zlib' >>>>>> '--with-modules' '--with-xml' '--with-x' '--without-perl' '--without-fpx' >>>>>> '--without-jbig' '--without-jp2' '--without-wmf' '--without- gvc' >>>>>> '--without-rsvg' '--without-lqr' '--without-pango' >>>>>> '--with-gs-font-dir=/opt/local/share/fonts/urw-fonts' >>>>>> '--with-quantum-depth=16' 'CC=/usr/bin/gcc-4.2' 'CFLAGS=-pipe -O2 -arch >>>>>> x86_64' 'LDFLAGS=-L/opt/local/lib -arch x86_64' >>>>>> 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/g++-4.2' 'CXXFLAGS=-pipe -O2 >>>>>> -arch x86_64' >>>>>> >>>>>> CONFIGURE_PATH /opt/local/etc/ImageMagick/ >>>>>> >>>>>> COPYRIGHT Copyright (C) 1999-2012 ImageMagick Studio LLC >>>>>> >>>>>> CPPFLAGS -I/opt/local/include/ImageMagick >>>>>> >>>>>> CXX /usr/bin/g++-4.2 >>>>>> >>>>>> CXXFLAGS -pipe -O2 -arch x86_64 -D_THREAD_SAFE -pthread >>>>>> >>>>>> DEFS -DHAVE_CONFIG_H >>>>>> >>>>>> DELEGATES bzlib fftw fontconfig freetype gs jpeg jng lcms2 lzma png tiff >>>>>> x11 xml zlib >>>>>> >>>>>> DISTCHECK_CONFIG_FLAGS 'CC=/usr/bin/gcc-4.2' 'CFLAGS=-pipe -O2 -arch x86_64' >>>>>> 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/g++-4.2' >>>>>> 'LDFLAGS=-L/opt/local/lib -arch x86_64' --disable-deprecated >>>>>> --with-quantum-depth=16 --with-umem=no --with-autotrace=no --with-fpx=no >>>>>> --with-fontpath= --with-gs-font-dir=/opt/local/share/fonts/urw- fonts >>>>>> --with-gvc=no --with-jp2=no --with-lqr=no --with-openexr=no --with-pango=no >>>>>> --with-rsvg=no --with-wmf=no --with-perl=no >>>>>> >>>>>> DOCUMENTATION_PATH /opt/local/share/doc/ImageMagick-6.8.0 >>>>>> >>>>>> EXEC-PREFIX /opt/local >>>>>> >>>>>> EXECUTABLE_PATH /opt/local/bin >>>>>> >>>>>> FEATURES OpenCL OpenMP >>>>>> >>>>>> FILTER_PATH /opt/local/lib/ImageMagick-6.8.0/modules-Q16/filters >>>>>> >>>>>> HOST x86_64-apple-darwin10.8.0 >>>>>> >>>>>> INCLUDE_PATH /opt/local/include/ImageMagick >>>>>> >>>>>> LDFLAGS -L/opt/local/lib -L/opt/local/lib -arch x86_64 >>>>>> -L/opt/local/lib -L/opt/local/lib >>>>>> >>>>>> LIB_VERSION 0x680 >>>>>> >>>>>> LIB_VERSION_NUMBER 6,8,0,7 >>>>>> >>>>>> LIBRARY_PATH /opt/local/lib/ImageMagick-6.8.0 >>>>>> >>>>>> LIBS -lMagickCore -llcms2 -lfreetype -lfftw3 -L/opt/local/lib >>>>>> -lfontconfig -lXext -lSM -lICE -lX11 -lXt -L/opt/local/lib -llzma -lbz2 -lz >>>>>> -lltdl -lm -lgomp -lclparser -Wl,-framework,OpenCL >>>>>> -L/System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries -lm >>>>>> -lpthread >>>>>> >>>>>> NAME ImageMagick >>>>>> >>>>>> PCFLAGS -fopenmp >>>>>> >>>>>> PREFIX /opt/local >>>>>> >>>>>> QuantumDepth 16 >>>>>> >>>>>> RELEASE_DATE 2013-03-04 >>>>>> >>>>>> SHARE_PATH /opt/local/share/ImageMagick-6.8.0 >>>>>> >>>>>> SVN_REVISION 10029 >>>>>> >>>>>> TARGET_CPU x86_64 >>>>>> >>>>>> TARGET_OS darwin10.8.0 >>>>>> >>>>>> TARGET_VENDOR apple >>>>>> >>>>>> VERSION 6.8.0 >>>>>> >>>>>> WEBSITE http://www.imagemagick.org >>>>>> >>>>>> >>>>>> Path: [built-in] >>>>>> >>>>>> >>>>>> Name Value >>>>>> >>>>>> --------------------------------------------------------------- ---------------- >>>>>> >>>>>> NAME ImageMagick >>>>>> >>>>>> >>>>>> Any help would be appreciated. Thanks >>>>>> >>>>>> >>>>>> -- output of sessionInfo(): >>>>>> >>>>>> >>>>>> R version 2.15.2 (2012-10-26) >>>>>> >>>>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >>>>>> >>>>>> >>>>>> locale: >>>>>> >>>>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>>>>> >>>>>> >>>>>> attached base packages: >>>>>> >>>>>> [1] tools stats graphics grDevices utils datasets methods >>>>>> base >>>>>> >>>>>> >>>>>> other attached packages: >>>>>> >>>>>> [1] latticeExtra_0.6-24 RColorBrewer_1.0-5 parody_1.16.0 >>>>>> bioDist_1.30.0 >>>>>> >>>>>> [5] KernSmooth_2.23-8 mvoutlier_1.9.9 sgeostat_1.0-25 >>>>>> robCompositions_1.6.3 >>>>>> >>>>>> [9] car_2.0-16 nnet_7.3-5 compositions_1.20-1 >>>>>> energy_1.4-0 >>>>>> >>>>>> [13] MASS_7.3-23 boot_1.3-7 tensorA_0.36 >>>>>> rgl_0.93.928 >>>>>> >>>>>> [17] flowViz_1.22.0 flowCore_1.24.2 rrcov_1.3-02 >>>>>> pcaPP_1.9-48 >>>>>> >>>>>> [21] mvtnorm_0.9-9994 robustbase_0.9-5 Biobase_2.18.0 >>>>>> lattice_0.20-13 >>>>>> >>>>>> [25] outliers_0.14 BiocGenerics_0.4.0 BiocInstaller_1.8.3 >>>>>> >>>>>> >>>>>> loaded via a namespace (and not attached): >>>>>> >>>>>> [1] annotate_1.36.0 AnnotationDbi_1.20.5 DBI_0.2-5 >>>>>> feature_1.2.8 >>>>>> >>>>>> [5] flowQ_1.18.0 geneplotter_1.36.0 graph_1.36.2 >>>>>> grid_2.15.2 >>>>>> >>>>>> [9] hexbin_1.26.1 IDPmisc_1.1.17 IRanges_1.16.6 ks_1.8.11 >>>>>> >>>>>> [13] parallel_2.15.2 RSQLite_0.11.2 stats4_2.15.2 >>>>>> XML_3.95-0.1 >>>>>> >>>>>> [17] xtable_1.7-1 >>>>>> >>>>>> >>>>>> -- >>>>>> >>>>>> Sent via the guest posting facility at bioconductor.org. >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> >>>>>> Bioconductor mailing list >>>>>> >>>>>> Bioconductor@r-project.org >>>>>> >>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>> >>>>>> Search the archives: >>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>> >>>>>> >>>>>> >>>>>> Chandra Jack >>>>>> >>>>>> Postdoctoral Research Assoc. >>>>>> >>>>>> Dept. of Bioengineering >>>>>> >>>>>> Rice University >>>>>> >>>>>> chanj@rice.edu >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> Chandra Jack >>>>>> Postdoctoral Research Assoc. >>>>>> Dept. of Bioengineering >>>>>> Rice University >>>>>> chanj@rice.edu >>>>>> >>>>>> >>>>>> >>>>> >>>> >>>> Chandra Jack >>>> Postdoctoral Research Assoc. >>>> Dept. of Bioengineering >>>> Rice University >>>> chanj@rice.edu >>>> >>>> >>>> >>> >> >> Chandra Jack >> Postdoctoral Research Assoc. >> Dept. of Bioengineering >> Rice University >> chanj@rice.edu >> >> >> > Chandra Jack Postdoctoral Research Assoc. Dept. of Bioengineering Rice University chanj@rice.edu [[alternative HTML version deleted]]
ADD REPLYlink written 6.7 years ago by Chandra Jack90
>From your R error message, system is calling /bin/sh not /bin/bash (which should be the same program but i don't think sh reads the .bashrc config file). Maybe the convert command is not available from /bin/sh? On 5 March 2013 06:42, Chandra Jack <chanj@rice.edu> wrote: > Yes. I've been restarting R after everytime I changed bash_profile. I also > just tried reinstalling R but that didn't help either. > > On Mar 5, 2013, at 12:20 AM, Dan Tenenbaum wrote: > > > On Mon, Mar 4, 2013 at 10:06 PM, Chandra Jack <chanj@rice.edu> wrote: > >> > >> On Mar 4, 2013, at 11:57 PM, Dan Tenenbaum wrote: > >> > >>> On Mon, Mar 4, 2013 at 9:53 PM, Chandra Jack <chanj@rice.edu> wrote: > >>>> Thank you so much for your help. > >>>> > >>>> Chandra-Jacks-MacBook:~ chanj$ source ~/.bash_profile > >>>> Chandra-Jacks-MacBook:~ chanj$ echo $PATH > >>>> > /Library/Frameworks/Python.framework/Versions/2.7/bin:/Library/Frame works/EPD64.framework/Versions/Current/bin:/Library/Frameworks/Python. framework/Versions/2.7/bin:/Library/Frameworks/EPD64.framework/Version s/Current/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bi n:/opt/local/bin:/opt/local/bin > >>>> Chandra-Jacks-MacBook:~ chanj$ which convert > >>>> /opt/local/bin/convert > >>>> > >>> > >>> It looks like convert is in your PATH. > >>> > >>> What happens if you type > >>> convert > >>> at the terminal prompt? > >> > >> I think it opens ImageMagick > >> Chandra-Jacks-MacBook:~ chanj$ convert > >> Version: ImageMagick 6.8.0-7 2013-03-04 Q16 http://www.imagemagick.org > >> Copyright: Copyright (C) 1999-2012 ImageMagick Studio LLC > >> Features: OpenMP OpenCL > >> > >> Usage: convert [options ...] file [ [options ...] file ...] [options > ...] file > >> > >> Image Settings: > >> -adjoin join images into a single multi-image file > >> > >> etc.... > >> > >> > >> > >>> > >>> What if you go into R and type > >>> system("convert") > >>> ? > >>> > >> system("convert") > >> /bin/sh: convert: command not found > >> > > > > This means convert is in your path but R can't see it. Did you restart > > R after editing .bash_profile? > > > > Dan > > > > > >>> Dan > >>> > >>>> On Mar 4, 2013, at 11:45 PM, Dan Tenenbaum wrote: > >>>> > >>>>> On Mon, Mar 4, 2013 at 9:30 PM, Chandra Jack <chanj@rice.edu> wrote: > >>>>>> I replaced the original export line with the one you wrote but it > still > >>>>>> didn't work. > >>>>>> > >>>>> > >>>>> OK, at a terminal prompt, please enter the following commands and > send > >>>>> me the output they produce: > >>>>> > >>>>> source ~/.bash_profile > >>>>> echo $PATH > >>>>> which convert > >>>>> > >>>>> > >>>>> > >>>>> thanks, > >>>>> Dan > >>>>> > >>>>> > >>>>> > >>>>>> On Mar 4, 2013, at 10:18 PM, Dan Tenenbaum wrote: > >>>>>> > >>>>>> On Mon, Mar 4, 2013 at 8:07 PM, Chandra Jack <chanj@rice.edu> > wrote: > >>>>>> > >>>>>> The convert command isn't in my PATH but adding the newIt doesn't > seem to be > >>>>>> working. I don't have a .bashrc file but I have a .bash_profile. The > >>>>>> original file was: > >>>>>> > >>>>>> # Setting PATH for EPD-7.1-2 > >>>>>> > >>>>>> # The orginal version is saved in .bash_profile.pysave > >>>>>> > >>>>>> > PATH="/Library/Frameworks/EPD64.framework/Versions/Current/bin:${PAT H}" > >>>>>> > >>>>>> export PATH > >>>>>> > >>>>>> > >>>>>> MKL_NUM_THREADS=1 > >>>>>> > >>>>>> export MKL_NUM_THREADS > >>>>>> > >>>>>> > >>>>>> # Setting PATH for Python 2.7 > >>>>>> > >>>>>> # The orginal version is saved in .bash_profile.pysave > >>>>>> > >>>>>> PATH="/Library/Frameworks/Python.framework/Versions/2.7/bin:${PATH}" > >>>>>> > >>>>>> export PATH > >>>>>> > >>>>>> > >>>>>> ## > >>>>>> > >>>>>> # Your previous /Users/chanj/.bash_profile file was backed up as > >>>>>> /Users/chanj/.bash_profile.macports- saved_2013-03-04_at_14:30:35 > >>>>>> > >>>>>> ## > >>>>>> > >>>>>> > >>>>>> # MacPorts Installer addition on 2013-03-04_at_14:30:35: adding an > >>>>>> appropriate PATH variable for use with MacPorts. > >>>>>> > >>>>>> export PATH=/opt/local/bin:/opt/local/sbin:$PATH > >>>>>> > >>>>>> # Finished adapting your PATH environment variable for use with > MacPorts. > >>>>>> > >>>>>> > >>>>>> I added PATH=$PATH:/opt/local/bin after the export line, resaved > the text > >>>>>> edit file and quit the terminal. When I checked Terminal again the > file was > >>>>>> updated but R couldn't find the command still. > >>>>>> > >>>>>> > >>>>>> Sorry, it needs to say: > >>>>>> > >>>>>> export PATH=$PATH:/opt/local/bin > >>>>>> > >>>>>> I forgot the 'export' before. > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> I also tried adding it before the export line, replacing the part > after the > >>>>>> export line with it, adding quotation marks but nothing seemed to > work. I > >>>>>> went in and found the convert command file and it is in > opt/local/bin. I > >>>>>> tried Sys.which with another file that was in the same location and > R output > >>>>>> "/usr/bin/clear" . Could it be related to the backup file that was > created > >>>>>> before I changed it? > >>>>>> > >>>>>> > >>>>>> No, that just means there is a 'clear' executable in two locations. > >>>>>> Dan > >>>>>> > >>>>>> > >>>>>> > >>>>>> Thanks > >>>>>> > >>>>>> > >>>>>> On Mar 4, 2013, at 4:15 PM, Dan Tenenbaum wrote: > >>>>>> > >>>>>> > >>>>>> On Mon, Mar 4, 2013 at 2:09 PM, Chandra Jack [guest] > >>>>>> > >>>>>> <guest@bioconductor.org> wrote: > >>>>>> > >>>>>> > >>>>>> Hi All, > >>>>>> > >>>>>> > >>>>>> I'm having a problem that has been mentioned here before but I'm > not sure > >>>>>> how to fix it. I tried to load flowQ and got: > >>>>>> > >>>>>> > >>>>>> Error : .onAttach failed in attachNamespace() for 'flowQ', details: > >>>>>> > >>>>>> call: mysys("convert -list configure", intern = TRUE, ignore.stderr > = TRUE) > >>>>>> > >>>>>> error: error in running command > >>>>>> > >>>>>> > >>>>>> Is the 'convert' command in your PATH? > >>>>>> > >>>>>> > >>>>>> What is the output of the R command: > >>>>>> > >>>>>> Sys.which("convert") > >>>>>> > >>>>>> ? > >>>>>> > >>>>>> > >>>>>> If it does not output anything, then the convert command is not in > your > >>>>>> PATH. > >>>>>> > >>>>>> > >>>>>> I'm not sure where the convert command ended up, but I'm guessing > it's > >>>>>> > >>>>>> in /opt/local/bin, > >>>>>> > >>>>>> so I think you need to edit your ~/.bashrc > >>>>>> > >>>>>> file and add the following line: > >>>>>> > >>>>>> > >>>>>> PATH=$PATH:/opt/local/bin > >>>>>> > >>>>>> > >>>>>> Then, start a new terminal window to make sure this setting is > >>>>>> > >>>>>> enabled, and try again. > >>>>>> > >>>>>> > >>>>>> Dan > >>>>>> > >>>>>> > >>>>>> > >>>>>> In addition: Warning messages: > >>>>>> > >>>>>> 1: replacing previous import ‘plot’ when loading ‘graphics’ > >>>>>> > >>>>>> 2: replacing previous import ‘as’ when loading ‘methods’ > >>>>>> > >>>>>> Error: package/namespace load failed for ‘flowQ’. > >>>>>> > >>>>>> > >>>>>> I have installed ImageMagick using Macports as has been suggested > and I have > >>>>>> also run > >>>>>> > >>>>>> convert -list configure, which gave the following: > >>>>>> > >>>>>> Path: /opt/local/lib/ImageMagick-6.8.0/config/configure.xml > >>>>>> > >>>>>> > >>>>>> Name Value > >>>>>> > >>>>>> > -------------------------------------------------------------------- ----------- > >>>>>> > >>>>>> CC /usr/bin/gcc-4.2 -std=gnu99 -std=gnu99 > >>>>>> > >>>>>> CFLAGS -D_THREAD_SAFE -D_THREAD_SAFE -pthread -fopenmp -pipe > -O2 > >>>>>> -arch x86_64 -Wall -D_THREAD_SAFE -pthread > >>>>>> > >>>>>> CODER_PATH /opt/local/lib/ImageMagick-6.8.0/modules-Q16/coders > >>>>>> > >>>>>> CONFIGURE ./configure '--prefix=/opt/local' '--enable- shared' > >>>>>> '--enable-static' '--disable-ltdl-install' '--disable-silent- rules' > >>>>>> '--with-frozenpaths' '--without-openexr' '--disable-hdri' > '--with-dps' > >>>>>> '--with-bzlib' '--with-fontconfig' '--with-gslib' '--with- jpeg' > >>>>>> '--with-lcms' '--with-png' '--with-tiff' '--with-webp' '--with-zlib' > >>>>>> '--with-modules' '--with-xml' '--with-x' '--without-perl' > '--without-fpx' > >>>>>> '--without-jbig' '--without-jp2' '--without-wmf' '--without- gvc' > >>>>>> '--without-rsvg' '--without-lqr' '--without-pango' > >>>>>> '--with-gs-font-dir=/opt/local/share/fonts/urw-fonts' > >>>>>> '--with-quantum-depth=16' 'CC=/usr/bin/gcc-4.2' 'CFLAGS=-pipe -O2 > -arch > >>>>>> x86_64' 'LDFLAGS=-L/opt/local/lib -arch x86_64' > >>>>>> 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/g++-4.2' > 'CXXFLAGS=-pipe -O2 > >>>>>> -arch x86_64' > >>>>>> > >>>>>> CONFIGURE_PATH /opt/local/etc/ImageMagick/ > >>>>>> > >>>>>> COPYRIGHT Copyright (C) 1999-2012 ImageMagick Studio LLC > >>>>>> > >>>>>> CPPFLAGS -I/opt/local/include/ImageMagick > >>>>>> > >>>>>> CXX /usr/bin/g++-4.2 > >>>>>> > >>>>>> CXXFLAGS -pipe -O2 -arch x86_64 -D_THREAD_SAFE -pthread > >>>>>> > >>>>>> DEFS -DHAVE_CONFIG_H > >>>>>> > >>>>>> DELEGATES bzlib fftw fontconfig freetype gs jpeg jng lcms2 lzma > png tiff > >>>>>> x11 xml zlib > >>>>>> > >>>>>> DISTCHECK_CONFIG_FLAGS 'CC=/usr/bin/gcc-4.2' 'CFLAGS=-pipe -O2 > -arch x86_64' > >>>>>> 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/g++-4.2' > >>>>>> 'LDFLAGS=-L/opt/local/lib -arch x86_64' --disable-deprecated > >>>>>> --with-quantum-depth=16 --with-umem=no --with-autotrace=no > --with-fpx=no > >>>>>> --with-fontpath= --with-gs-font-dir=/opt/local/share/fonts /urw-fonts > >>>>>> --with-gvc=no --with-jp2=no --with-lqr=no --with-openexr=no > --with-pango=no > >>>>>> --with-rsvg=no --with-wmf=no --with-perl=no > >>>>>> > >>>>>> DOCUMENTATION_PATH /opt/local/share/doc/ImageMagick-6.8.0 > >>>>>> > >>>>>> EXEC-PREFIX /opt/local > >>>>>> > >>>>>> EXECUTABLE_PATH /opt/local/bin > >>>>>> > >>>>>> FEATURES OpenCL OpenMP > >>>>>> > >>>>>> FILTER_PATH /opt/local/lib/ImageMagick-6.8.0/modules-Q16/filters > >>>>>> > >>>>>> HOST x86_64-apple-darwin10.8.0 > >>>>>> > >>>>>> INCLUDE_PATH /opt/local/include/ImageMagick > >>>>>> > >>>>>> LDFLAGS -L/opt/local/lib -L/opt/local/lib -arch x86_64 > >>>>>> -L/opt/local/lib -L/opt/local/lib > >>>>>> > >>>>>> LIB_VERSION 0x680 > >>>>>> > >>>>>> LIB_VERSION_NUMBER 6,8,0,7 > >>>>>> > >>>>>> LIBRARY_PATH /opt/local/lib/ImageMagick-6.8.0 > >>>>>> > >>>>>> LIBS -lMagickCore -llcms2 -lfreetype -lfftw3 > -L/opt/local/lib > >>>>>> -lfontconfig -lXext -lSM -lICE -lX11 -lXt -L/opt/local/lib -llzma > -lbz2 -lz > >>>>>> -lltdl -lm -lgomp -lclparser -Wl,-framework,OpenCL > >>>>>> -L/System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries > -lm > >>>>>> -lpthread > >>>>>> > >>>>>> NAME ImageMagick > >>>>>> > >>>>>> PCFLAGS -fopenmp > >>>>>> > >>>>>> PREFIX /opt/local > >>>>>> > >>>>>> QuantumDepth 16 > >>>>>> > >>>>>> RELEASE_DATE 2013-03-04 > >>>>>> > >>>>>> SHARE_PATH /opt/local/share/ImageMagick-6.8.0 > >>>>>> > >>>>>> SVN_REVISION 10029 > >>>>>> > >>>>>> TARGET_CPU x86_64 > >>>>>> > >>>>>> TARGET_OS darwin10.8.0 > >>>>>> > >>>>>> TARGET_VENDOR apple > >>>>>> > >>>>>> VERSION 6.8.0 > >>>>>> > >>>>>> WEBSITE http://www.imagemagick.org > >>>>>> > >>>>>> > >>>>>> Path: [built-in] > >>>>>> > >>>>>> > >>>>>> Name Value > >>>>>> > >>>>>> > -------------------------------------------------------------------- ----------- > >>>>>> > >>>>>> NAME ImageMagick > >>>>>> > >>>>>> > >>>>>> Any help would be appreciated. Thanks > >>>>>> > >>>>>> > >>>>>> -- output of sessionInfo(): > >>>>>> > >>>>>> > >>>>>> R version 2.15.2 (2012-10-26) > >>>>>> > >>>>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > >>>>>> > >>>>>> > >>>>>> locale: > >>>>>> > >>>>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > >>>>>> > >>>>>> > >>>>>> attached base packages: > >>>>>> > >>>>>> [1] tools stats graphics grDevices utils datasets > methods > >>>>>> base > >>>>>> > >>>>>> > >>>>>> other attached packages: > >>>>>> > >>>>>> [1] latticeExtra_0.6-24 RColorBrewer_1.0-5 parody_1.16.0 > >>>>>> bioDist_1.30.0 > >>>>>> > >>>>>> [5] KernSmooth_2.23-8 mvoutlier_1.9.9 sgeostat_1.0-25 > >>>>>> robCompositions_1.6.3 > >>>>>> > >>>>>> [9] car_2.0-16 nnet_7.3-5 compositions_1.20-1 > >>>>>> energy_1.4-0 > >>>>>> > >>>>>> [13] MASS_7.3-23 boot_1.3-7 tensorA_0.36 > >>>>>> rgl_0.93.928 > >>>>>> > >>>>>> [17] flowViz_1.22.0 flowCore_1.24.2 rrcov_1.3-02 > >>>>>> pcaPP_1.9-48 > >>>>>> > >>>>>> [21] mvtnorm_0.9-9994 robustbase_0.9-5 Biobase_2.18.0 > >>>>>> lattice_0.20-13 > >>>>>> > >>>>>> [25] outliers_0.14 BiocGenerics_0.4.0 BiocInstaller_1.8.3 > >>>>>> > >>>>>> > >>>>>> loaded via a namespace (and not attached): > >>>>>> > >>>>>> [1] annotate_1.36.0 AnnotationDbi_1.20.5 DBI_0.2-5 > >>>>>> feature_1.2.8 > >>>>>> > >>>>>> [5] flowQ_1.18.0 geneplotter_1.36.0 graph_1.36.2 > >>>>>> grid_2.15.2 > >>>>>> > >>>>>> [9] hexbin_1.26.1 IDPmisc_1.1.17 IRanges_1.16.6 > ks_1.8.11 > >>>>>> > >>>>>> [13] parallel_2.15.2 RSQLite_0.11.2 stats4_2.15.2 > >>>>>> XML_3.95-0.1 > >>>>>> > >>>>>> [17] xtable_1.7-1 > >>>>>> > >>>>>> > >>>>>> -- > >>>>>> > >>>>>> Sent via the guest posting facility at bioconductor.org. > >>>>>> > >>>>>> > >>>>>> _______________________________________________ > >>>>>> > >>>>>> Bioconductor mailing list > >>>>>> > >>>>>> Bioconductor@r-project.org > >>>>>> > >>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor > >>>>>> > >>>>>> Search the archives: > >>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor > >>>>>> > >>>>>> > >>>>>> > >>>>>> Chandra Jack > >>>>>> > >>>>>> Postdoctoral Research Assoc. > >>>>>> > >>>>>> Dept. of Bioengineering > >>>>>> > >>>>>> Rice University > >>>>>> > >>>>>> chanj@rice.edu > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> Chandra Jack > >>>>>> Postdoctoral Research Assoc. > >>>>>> Dept. of Bioengineering > >>>>>> Rice University > >>>>>> chanj@rice.edu > >>>>>> > >>>>>> > >>>>>> > >>>>> > >>>> > >>>> Chandra Jack > >>>> Postdoctoral Research Assoc. > >>>> Dept. of Bioengineering > >>>> Rice University > >>>> chanj@rice.edu > >>>> > >>>> > >>>> > >>> > >> > >> Chandra Jack > >> Postdoctoral Research Assoc. > >> Dept. of Bioengineering > >> Rice University > >> chanj@rice.edu > >> > >> > >> > > > > Chandra Jack > Postdoctoral Research Assoc. > Dept. of Bioengineering > Rice University > chanj@rice.edu > > > > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD REPLYlink written 6.7 years ago by Nikolas30
On Tue, Mar 5, 2013 at 12:21 AM, Nikolas Pontikos <n.pontikos at="" gmail.com=""> wrote: > From your R error message, system is calling /bin/sh not /bin/bash (which > should be the same program but i don't think sh reads the .bashrc config > file). > Maybe the convert command is not available from /bin/sh? In that case the file to be edited is ~/.profile Dan > > > On 5 March 2013 06:42, Chandra Jack <chanj at="" rice.edu=""> wrote: >> >> Yes. I've been restarting R after everytime I changed bash_profile. I also >> just tried reinstalling R but that didn't help either. >> >> On Mar 5, 2013, at 12:20 AM, Dan Tenenbaum wrote: >> >> > On Mon, Mar 4, 2013 at 10:06 PM, Chandra Jack <chanj at="" rice.edu=""> wrote: >> >> >> >> On Mar 4, 2013, at 11:57 PM, Dan Tenenbaum wrote: >> >> >> >>> On Mon, Mar 4, 2013 at 9:53 PM, Chandra Jack <chanj at="" rice.edu=""> wrote: >> >>>> Thank you so much for your help. >> >>>> >> >>>> Chandra-Jacks-MacBook:~ chanj$ source ~/.bash_profile >> >>>> Chandra-Jacks-MacBook:~ chanj$ echo $PATH >> >>>> >> >>>> /Library/Frameworks/Python.framework/Versions/2.7/bin:/Library /Frameworks/EPD64.framework/Versions/Current/bin:/Library/Frameworks/P ython.framework/Versions/2.7/bin:/Library/Frameworks/EPD64.framework/V ersions/Current/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/ X11/bin:/opt/local/bin:/opt/local/bin >> >>>> Chandra-Jacks-MacBook:~ chanj$ which convert >> >>>> /opt/local/bin/convert >> >>>> >> >>> >> >>> It looks like convert is in your PATH. >> >>> >> >>> What happens if you type >> >>> convert >> >>> at the terminal prompt? >> >> >> >> I think it opens ImageMagick >> >> Chandra-Jacks-MacBook:~ chanj$ convert >> >> Version: ImageMagick 6.8.0-7 2013-03-04 Q16 http://www.imagemagick.org >> >> Copyright: Copyright (C) 1999-2012 ImageMagick Studio LLC >> >> Features: OpenMP OpenCL >> >> >> >> Usage: convert [options ...] file [ [options ...] file ...] [options >> >> ...] file >> >> >> >> Image Settings: >> >> -adjoin join images into a single multi-image file >> >> >> >> etc.... >> >> >> >> >> >> >> >>> >> >>> What if you go into R and type >> >>> system("convert") >> >>> ? >> >>> >> >> system("convert") >> >> /bin/sh: convert: command not found >> >> >> > >> > This means convert is in your path but R can't see it. Did you restart >> > R after editing .bash_profile? >> > >> > Dan >> > >> > >> >>> Dan >> >>> >> >>>> On Mar 4, 2013, at 11:45 PM, Dan Tenenbaum wrote: >> >>>> >> >>>>> On Mon, Mar 4, 2013 at 9:30 PM, Chandra Jack <chanj at="" rice.edu=""> wrote: >> >>>>>> I replaced the original export line with the one you wrote but it >> >>>>>> still >> >>>>>> didn't work. >> >>>>>> >> >>>>> >> >>>>> OK, at a terminal prompt, please enter the following commands and >> >>>>> send >> >>>>> me the output they produce: >> >>>>> >> >>>>> source ~/.bash_profile >> >>>>> echo $PATH >> >>>>> which convert >> >>>>> >> >>>>> >> >>>>> >> >>>>> thanks, >> >>>>> Dan >> >>>>> >> >>>>> >> >>>>> >> >>>>>> On Mar 4, 2013, at 10:18 PM, Dan Tenenbaum wrote: >> >>>>>> >> >>>>>> On Mon, Mar 4, 2013 at 8:07 PM, Chandra Jack <chanj at="" rice.edu=""> >> >>>>>> wrote: >> >>>>>> >> >>>>>> The convert command isn't in my PATH but adding the newIt doesn't >> >>>>>> seem to be >> >>>>>> working. I don't have a .bashrc file but I have a .bash_profile. >> >>>>>> The >> >>>>>> original file was: >> >>>>>> >> >>>>>> # Setting PATH for EPD-7.1-2 >> >>>>>> >> >>>>>> # The orginal version is saved in .bash_profile.pysave >> >>>>>> >> >>>>>> >> >>>>>> PATH="/Library/Frameworks/EPD64.framework/Versions/Current/b in:${PATH}" >> >>>>>> >> >>>>>> export PATH >> >>>>>> >> >>>>>> >> >>>>>> MKL_NUM_THREADS=1 >> >>>>>> >> >>>>>> export MKL_NUM_THREADS >> >>>>>> >> >>>>>> >> >>>>>> # Setting PATH for Python 2.7 >> >>>>>> >> >>>>>> # The orginal version is saved in .bash_profile.pysave >> >>>>>> >> >>>>>> >> >>>>>> PATH="/Library/Frameworks/Python.framework/Versions/2.7/bin:${PATH}" >> >>>>>> >> >>>>>> export PATH >> >>>>>> >> >>>>>> >> >>>>>> ## >> >>>>>> >> >>>>>> # Your previous /Users/chanj/.bash_profile file was backed up as >> >>>>>> /Users/chanj/.bash_profile.macports- saved_2013-03-04_at_14:30:35 >> >>>>>> >> >>>>>> ## >> >>>>>> >> >>>>>> >> >>>>>> # MacPorts Installer addition on 2013-03-04_at_14:30:35: adding an >> >>>>>> appropriate PATH variable for use with MacPorts. >> >>>>>> >> >>>>>> export PATH=/opt/local/bin:/opt/local/sbin:$PATH >> >>>>>> >> >>>>>> # Finished adapting your PATH environment variable for use with >> >>>>>> MacPorts. >> >>>>>> >> >>>>>> >> >>>>>> I added PATH=$PATH:/opt/local/bin after the export line, resaved >> >>>>>> the text >> >>>>>> edit file and quit the terminal. When I checked Terminal again the >> >>>>>> file was >> >>>>>> updated but R couldn't find the command still. >> >>>>>> >> >>>>>> >> >>>>>> Sorry, it needs to say: >> >>>>>> >> >>>>>> export PATH=$PATH:/opt/local/bin >> >>>>>> >> >>>>>> I forgot the 'export' before. >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> I also tried adding it before the export line, replacing the part >> >>>>>> after the >> >>>>>> export line with it, adding quotation marks but nothing seemed to >> >>>>>> work. I >> >>>>>> went in and found the convert command file and it is in >> >>>>>> opt/local/bin. I >> >>>>>> tried Sys.which with another file that was in the same location and >> >>>>>> R output >> >>>>>> "/usr/bin/clear" . Could it be related to the backup file that was >> >>>>>> created >> >>>>>> before I changed it? >> >>>>>> >> >>>>>> >> >>>>>> No, that just means there is a 'clear' executable in two locations. >> >>>>>> Dan >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> Thanks >> >>>>>> >> >>>>>> >> >>>>>> On Mar 4, 2013, at 4:15 PM, Dan Tenenbaum wrote: >> >>>>>> >> >>>>>> >> >>>>>> On Mon, Mar 4, 2013 at 2:09 PM, Chandra Jack [guest] >> >>>>>> >> >>>>>> <guest at="" bioconductor.org=""> wrote: >> >>>>>> >> >>>>>> >> >>>>>> Hi All, >> >>>>>> >> >>>>>> >> >>>>>> I'm having a problem that has been mentioned here before but I'm >> >>>>>> not sure >> >>>>>> how to fix it. I tried to load flowQ and got: >> >>>>>> >> >>>>>> >> >>>>>> Error : .onAttach failed in attachNamespace() for 'flowQ', details: >> >>>>>> >> >>>>>> call: mysys("convert -list configure", intern = TRUE, ignore.stderr >> >>>>>> = TRUE) >> >>>>>> >> >>>>>> error: error in running command >> >>>>>> >> >>>>>> >> >>>>>> Is the 'convert' command in your PATH? >> >>>>>> >> >>>>>> >> >>>>>> What is the output of the R command: >> >>>>>> >> >>>>>> Sys.which("convert") >> >>>>>> >> >>>>>> ? >> >>>>>> >> >>>>>> >> >>>>>> If it does not output anything, then the convert command is not in >> >>>>>> your >> >>>>>> PATH. >> >>>>>> >> >>>>>> >> >>>>>> I'm not sure where the convert command ended up, but I'm guessing >> >>>>>> it's >> >>>>>> >> >>>>>> in /opt/local/bin, >> >>>>>> >> >>>>>> so I think you need to edit your ~/.bashrc >> >>>>>> >> >>>>>> file and add the following line: >> >>>>>> >> >>>>>> >> >>>>>> PATH=$PATH:/opt/local/bin >> >>>>>> >> >>>>>> >> >>>>>> Then, start a new terminal window to make sure this setting is >> >>>>>> >> >>>>>> enabled, and try again. >> >>>>>> >> >>>>>> >> >>>>>> Dan >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> In addition: Warning messages: >> >>>>>> >> >>>>>> 1: replacing previous import ?plot? when loading ?graphics? >> >>>>>> >> >>>>>> 2: replacing previous import ?as? when loading ?methods? >> >>>>>> >> >>>>>> Error: package/namespace load failed for ?flowQ?. >> >> >>>>>> >> >>>>>> >> >>>>>> I have installed ImageMagick using Macports as has been suggested >> >>>>>> and I have >> >>>>>> also run >> >>>>>> >> >>>>>> convert -list configure, which gave the following: >> >>>>>> >> >>>>>> Path: /opt/local/lib/ImageMagick-6.8.0/config/configure.xml >> >>>>>> >> >>>>>> >> >>>>>> Name Value >> >>>>>> >> >>>>>> >> >>>>>> ------------------------------------------------------------ ------------------- >> >>>>>> >> >>>>>> CC /usr/bin/gcc-4.2 -std=gnu99 -std=gnu99 >> >>>>>> >> >>>>>> CFLAGS -D_THREAD_SAFE -D_THREAD_SAFE -pthread -fopenmp -pipe >> >>>>>> -O2 >> >>>>>> -arch x86_64 -Wall -D_THREAD_SAFE -pthread >> >>>>>> >> >>>>>> CODER_PATH /opt/local/lib/ImageMagick-6.8.0/modules-Q16/coders >> >>>>>> >> >>>>>> CONFIGURE ./configure '--prefix=/opt/local' '--enable- shared' >> >>>>>> '--enable-static' '--disable-ltdl-install' '--disable- silent-rules' >> >>>>>> '--with-frozenpaths' '--without-openexr' '--disable-hdri' >> >>>>>> '--with-dps' >> >>>>>> '--with-bzlib' '--with-fontconfig' '--with-gslib' '--with- jpeg' >> >>>>>> '--with-lcms' '--with-png' '--with-tiff' '--with-webp' >> >>>>>> '--with-zlib' >> >>>>>> '--with-modules' '--with-xml' '--with-x' '--without-perl' >> >>>>>> '--without-fpx' >> >>>>>> '--without-jbig' '--without-jp2' '--without-wmf' '--without- gvc' >> >>>>>> '--without-rsvg' '--without-lqr' '--without-pango' >> >>>>>> '--with-gs-font-dir=/opt/local/share/fonts/urw-fonts' >> >>>>>> '--with-quantum-depth=16' 'CC=/usr/bin/gcc-4.2' 'CFLAGS=-pipe -O2 >> >>>>>> -arch >> >>>>>> x86_64' 'LDFLAGS=-L/opt/local/lib -arch x86_64' >> >>>>>> 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/g++-4.2' >> >>>>>> 'CXXFLAGS=-pipe -O2 >> >>>>>> -arch x86_64' >> >>>>>> >> >>>>>> CONFIGURE_PATH /opt/local/etc/ImageMagick/ >> >>>>>> >> >>>>>> COPYRIGHT Copyright (C) 1999-2012 ImageMagick Studio LLC >> >>>>>> >> >>>>>> CPPFLAGS -I/opt/local/include/ImageMagick >> >>>>>> >> >>>>>> CXX /usr/bin/g++-4.2 >> >>>>>> >> >>>>>> CXXFLAGS -pipe -O2 -arch x86_64 -D_THREAD_SAFE -pthread >> >>>>>> >> >>>>>> DEFS -DHAVE_CONFIG_H >> >>>>>> >> >>>>>> DELEGATES bzlib fftw fontconfig freetype gs jpeg jng lcms2 lzma >> >>>>>> png tiff >> >>>>>> x11 xml zlib >> >>>>>> >> >>>>>> DISTCHECK_CONFIG_FLAGS 'CC=/usr/bin/gcc-4.2' 'CFLAGS=-pipe -O2 >> >>>>>> -arch x86_64' >> >>>>>> 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/g++-4.2' >> >>>>>> 'LDFLAGS=-L/opt/local/lib -arch x86_64' --disable-deprecated >> >>>>>> --with-quantum-depth=16 --with-umem=no --with-autotrace=no >> >>>>>> --with-fpx=no >> >>>>>> --with-fontpath= >> >>>>>> --with-gs-font-dir=/opt/local/share/fonts/urw-fonts >> >>>>>> --with-gvc=no --with-jp2=no --with-lqr=no --with-openexr=no >> >>>>>> --with-pango=no >> >>>>>> --with-rsvg=no --with-wmf=no --with-perl=no >> >>>>>> >> >>>>>> DOCUMENTATION_PATH /opt/local/share/doc/ImageMagick-6.8.0 >> >>>>>> >> >>>>>> EXEC-PREFIX /opt/local >> >>>>>> >> >>>>>> EXECUTABLE_PATH /opt/local/bin >> >>>>>> >> >>>>>> FEATURES OpenCL OpenMP >> >>>>>> >> >>>>>> FILTER_PATH /opt/local/lib/ImageMagick-6.8.0/modules-Q16/filters >> >>>>>> >> >>>>>> HOST x86_64-apple-darwin10.8.0 >> >>>>>> >> >>>>>> INCLUDE_PATH /opt/local/include/ImageMagick >> >>>>>> >> >>>>>> LDFLAGS -L/opt/local/lib -L/opt/local/lib -arch x86_64 >> >>>>>> -L/opt/local/lib -L/opt/local/lib >> >>>>>> >> >>>>>> LIB_VERSION 0x680 >> >>>>>> >> >>>>>> LIB_VERSION_NUMBER 6,8,0,7 >> >>>>>> >> >>>>>> LIBRARY_PATH /opt/local/lib/ImageMagick-6.8.0 >> >>>>>> >> >>>>>> LIBS -lMagickCore -llcms2 -lfreetype -lfftw3 >> >>>>>> -L/opt/local/lib >> >>>>>> -lfontconfig -lXext -lSM -lICE -lX11 -lXt -L/opt/local/lib -llzma >> >>>>>> -lbz2 -lz >> >>>>>> -lltdl -lm -lgomp -lclparser -Wl,-framework,OpenCL >> >>>>>> -L/System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries >> >>>>>> -lm >> >>>>>> -lpthread >> >>>>>> >> >>>>>> NAME ImageMagick >> >>>>>> >> >>>>>> PCFLAGS -fopenmp >> >>>>>> >> >>>>>> PREFIX /opt/local >> >>>>>> >> >>>>>> QuantumDepth 16 >> >>>>>> >> >>>>>> RELEASE_DATE 2013-03-04 >> >>>>>> >> >>>>>> SHARE_PATH /opt/local/share/ImageMagick-6.8.0 >> >>>>>> >> >>>>>> SVN_REVISION 10029 >> >>>>>> >> >>>>>> TARGET_CPU x86_64 >> >>>>>> >> >>>>>> TARGET_OS darwin10.8.0 >> >>>>>> >> >>>>>> TARGET_VENDOR apple >> >>>>>> >> >>>>>> VERSION 6.8.0 >> >>>>>> >> >>>>>> WEBSITE http://www.imagemagick.org >> >>>>>> >> >>>>>> >> >>>>>> Path: [built-in] >> >>>>>> >> >>>>>> >> >>>>>> Name Value >> >>>>>> >> >>>>>> >> >>>>>> ------------------------------------------------------------ ------------------- >> >>>>>> >> >>>>>> NAME ImageMagick >> >>>>>> >> >>>>>> >> >>>>>> Any help would be appreciated. Thanks >> >>>>>> >> >>>>>> >> >>>>>> -- output of sessionInfo(): >> >>>>>> >> >>>>>> >> >>>>>> R version 2.15.2 (2012-10-26) >> >>>>>> >> >>>>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >> >>>>>> >> >>>>>> >> >>>>>> locale: >> >>>>>> >> >>>>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >>>>>> >> >>>>>> >> >>>>>> attached base packages: >> >>>>>> >> >>>>>> [1] tools stats graphics grDevices utils datasets >> >>>>>> methods >> >>>>>> base >> >>>>>> >> >>>>>> >> >>>>>> other attached packages: >> >>>>>> >> >>>>>> [1] latticeExtra_0.6-24 RColorBrewer_1.0-5 parody_1.16.0 >> >>>>>> bioDist_1.30.0 >> >>>>>> >> >>>>>> [5] KernSmooth_2.23-8 mvoutlier_1.9.9 sgeostat_1.0-25 >> >>>>>> robCompositions_1.6.3 >> >>>>>> >> >>>>>> [9] car_2.0-16 nnet_7.3-5 compositions_1.20-1 >> >>>>>> energy_1.4-0 >> >>>>>> >> >>>>>> [13] MASS_7.3-23 boot_1.3-7 tensorA_0.36 >> >>>>>> rgl_0.93.928 >> >>>>>> >> >>>>>> [17] flowViz_1.22.0 flowCore_1.24.2 rrcov_1.3-02 >> >>>>>> pcaPP_1.9-48 >> >>>>>> >> >>>>>> [21] mvtnorm_0.9-9994 robustbase_0.9-5 Biobase_2.18.0 >> >>>>>> lattice_0.20-13 >> >>>>>> >> >>>>>> [25] outliers_0.14 BiocGenerics_0.4.0 >> >>>>>> BiocInstaller_1.8.3 >> >>>>>> >> >>>>>> >> >>>>>> loaded via a namespace (and not attached): >> >>>>>> >> >>>>>> [1] annotate_1.36.0 AnnotationDbi_1.20.5 DBI_0.2-5 >> >>>>>> feature_1.2.8 >> >>>>>> >> >>>>>> [5] flowQ_1.18.0 geneplotter_1.36.0 graph_1.36.2 >> >>>>>> grid_2.15.2 >> >>>>>> >> >>>>>> [9] hexbin_1.26.1 IDPmisc_1.1.17 IRanges_1.16.6 >> >>>>>> ks_1.8.11 >> >>>>>> >> >>>>>> [13] parallel_2.15.2 RSQLite_0.11.2 stats4_2.15.2 >> >>>>>> XML_3.95-0.1 >> >>>>>> >> >>>>>> [17] xtable_1.7-1 >> >>>>>> >> >>>>>> >> >>>>>> -- >> >>>>>> >> >>>>>> Sent via the guest posting facility at bioconductor.org. >> >>>>>> >> >>>>>> >> >>>>>> _______________________________________________ >> >>>>>> >> >>>>>> Bioconductor mailing list >> >>>>>> >> >>>>>> Bioconductor at r-project.org >> >>>>>> >> >>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >>>>>> >> >>>>>> Search the archives: >> >>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> Chandra Jack >> >>>>>> >> >>>>>> Postdoctoral Research Assoc. >> >>>>>> >> >>>>>> Dept. of Bioengineering >> >>>>>> >> >>>>>> Rice University >> >>>>>> >> >>>>>> chanj at rice.edu >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> Chandra Jack >> >>>>>> Postdoctoral Research Assoc. >> >>>>>> Dept. of Bioengineering >> >>>>>> Rice University >> >>>>>> chanj at rice.edu >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>> >> >>>> >> >>>> Chandra Jack >> >>>> Postdoctoral Research Assoc. >> >>>> Dept. of Bioengineering >> >>>> Rice University >> >>>> chanj at rice.edu >> >>>> >> >>>> >> >>>> >> >>> >> >> >> >> Chandra Jack >> >> Postdoctoral Research Assoc. >> >> Dept. of Bioengineering >> >> Rice University >> >> chanj at rice.edu >> >> >> >> >> >> >> > >> >> Chandra Jack >> Postdoctoral Research Assoc. >> Dept. of Bioengineering >> Rice University >> chanj at rice.edu >> >> >> >> >> [[alternative HTML version deleted]] >> >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >
ADD REPLYlink written 6.7 years ago by Dan Tenenbaum8.2k
I didn't have a ~/.profile so I created one. All I put in it was export PATH = $PATH:opt/local/bin. But I got the same message that /bin/sh: convert: command not found. I read that .bash_profile may need to call .profile and also tried putting source ~/.profile at the end of the file but that gave me the same message. On Mar 5, 2013, at 9:41 AM, Dan Tenenbaum wrote: > On Tue, Mar 5, 2013 at 12:21 AM, Nikolas Pontikos <n.pontikos@gmail.com> wrote: >> From your R error message, system is calling /bin/sh not /bin/bash (which >> should be the same program but i don't think sh reads the .bashrc config >> file). >> Maybe the convert command is not available from /bin/sh? > > > In that case the file to be edited is ~/.profile > > Dan > >> >> >> On 5 March 2013 06:42, Chandra Jack <chanj@rice.edu> wrote: >>> >>> Yes. I've been restarting R after everytime I changed bash_profile. I also >>> just tried reinstalling R but that didn't help either. >>> >>> On Mar 5, 2013, at 12:20 AM, Dan Tenenbaum wrote: >>> >>>> On Mon, Mar 4, 2013 at 10:06 PM, Chandra Jack <chanj@rice.edu> wrote: >>>>> >>>>> On Mar 4, 2013, at 11:57 PM, Dan Tenenbaum wrote: >>>>> >>>>>> On Mon, Mar 4, 2013 at 9:53 PM, Chandra Jack <chanj@rice.edu> wrote: >>>>>>> Thank you so much for your help. >>>>>>> >>>>>>> Chandra-Jacks-MacBook:~ chanj$ source ~/.bash_profile >>>>>>> Chandra-Jacks-MacBook:~ chanj$ echo $PATH >>>>>>> >>>>>>> /Library/Frameworks/Python.framework/Versions/2.7/bin:/Library /Frameworks/EPD64.framework/Versions/Current/bin:/Library/Frameworks/P ython.framework/Versions/2.7/bin:/Library/Frameworks/EPD64.framework/V ersions/Current/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/ X11/bin:/opt/local/bin:/opt/local/bin >>>>>>> Chandra-Jacks-MacBook:~ chanj$ which convert >>>>>>> /opt/local/bin/convert >>>>>>> >>>>>> >>>>>> It looks like convert is in your PATH. >>>>>> >>>>>> What happens if you type >>>>>> convert >>>>>> at the terminal prompt? >>>>> >>>>> I think it opens ImageMagick >>>>> Chandra-Jacks-MacBook:~ chanj$ convert >>>>> Version: ImageMagick 6.8.0-7 2013-03-04 Q16 http://www.imagemagick.org >>>>> Copyright: Copyright (C) 1999-2012 ImageMagick Studio LLC >>>>> Features: OpenMP OpenCL >>>>> >>>>> Usage: convert [options ...] file [ [options ...] file ...] [options >>>>> ...] file >>>>> >>>>> Image Settings: >>>>> -adjoin join images into a single multi-image file >>>>> >>>>> etc.... >>>>> >>>>> >>>>> >>>>>> >>>>>> What if you go into R and type >>>>>> system("convert") >>>>>> ? >>>>>> >>>>> system("convert") >>>>> /bin/sh: convert: command not found >>>>> >>>> >>>> This means convert is in your path but R can't see it. Did you restart >>>> R after editing .bash_profile? >>>> >>>> Dan >>>> >>>> >>>>>> Dan >>>>>> >>>>>>> On Mar 4, 2013, at 11:45 PM, Dan Tenenbaum wrote: >>>>>>> >>>>>>>> On Mon, Mar 4, 2013 at 9:30 PM, Chandra Jack <chanj@rice.edu> wrote: >>>>>>>>> I replaced the original export line with the one you wrote but it >>>>>>>>> still >>>>>>>>> didn't work. >>>>>>>>> >>>>>>>> >>>>>>>> OK, at a terminal prompt, please enter the following commands and >>>>>>>> send >>>>>>>> me the output they produce: >>>>>>>> >>>>>>>> source ~/.bash_profile >>>>>>>> echo $PATH >>>>>>>> which convert >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> thanks, >>>>>>>> Dan >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>> On Mar 4, 2013, at 10:18 PM, Dan Tenenbaum wrote: >>>>>>>>> >>>>>>>>> On Mon, Mar 4, 2013 at 8:07 PM, Chandra Jack <chanj@rice.edu> >>>>>>>>> wrote: >>>>>>>>> >>>>>>>>> The convert command isn't in my PATH but adding the newIt doesn't >>>>>>>>> seem to be >>>>>>>>> working. I don't have a .bashrc file but I have a .bash_profile. >>>>>>>>> The >>>>>>>>> original file was: >>>>>>>>> >>>>>>>>> # Setting PATH for EPD-7.1-2 >>>>>>>>> >>>>>>>>> # The orginal version is saved in .bash_profile.pysave >>>>>>>>> >>>>>>>>> >>>>>>>>> PATH="/Library/Frameworks/EPD64.framework/Versions/Current/b in:${PATH}" >>>>>>>>> >>>>>>>>> export PATH >>>>>>>>> >>>>>>>>> >>>>>>>>> MKL_NUM_THREADS=1 >>>>>>>>> >>>>>>>>> export MKL_NUM_THREADS >>>>>>>>> >>>>>>>>> >>>>>>>>> # Setting PATH for Python 2.7 >>>>>>>>> >>>>>>>>> # The orginal version is saved in .bash_profile.pysave >>>>>>>>> >>>>>>>>> >>>>>>>>> PATH="/Library/Frameworks/Python.framework/Versions/2.7/bin:${PATH}" >>>>>>>>> >>>>>>>>> export PATH >>>>>>>>> >>>>>>>>> >>>>>>>>> ## >>>>>>>>> >>>>>>>>> # Your previous /Users/chanj/.bash_profile file was backed up as >>>>>>>>> /Users/chanj/.bash_profile.macports- saved_2013-03-04_at_14:30:35 >>>>>>>>> >>>>>>>>> ## >>>>>>>>> >>>>>>>>> >>>>>>>>> # MacPorts Installer addition on 2013-03-04_at_14:30:35: adding an >>>>>>>>> appropriate PATH variable for use with MacPorts. >>>>>>>>> >>>>>>>>> export PATH=/opt/local/bin:/opt/local/sbin:$PATH >>>>>>>>> >>>>>>>>> # Finished adapting your PATH environment variable for use with >>>>>>>>> MacPorts. >>>>>>>>> >>>>>>>>> >>>>>>>>> I added PATH=$PATH:/opt/local/bin after the export line, resaved >>>>>>>>> the text >>>>>>>>> edit file and quit the terminal. When I checked Terminal again the >>>>>>>>> file was >>>>>>>>> updated but R couldn't find the command still. >>>>>>>>> >>>>>>>>> >>>>>>>>> Sorry, it needs to say: >>>>>>>>> >>>>>>>>> export PATH=$PATH:/opt/local/bin >>>>>>>>> >>>>>>>>> I forgot the 'export' before. >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> I also tried adding it before the export line, replacing the part >>>>>>>>> after the >>>>>>>>> export line with it, adding quotation marks but nothing seemed to >>>>>>>>> work. I >>>>>>>>> went in and found the convert command file and it is in >>>>>>>>> opt/local/bin. I >>>>>>>>> tried Sys.which with another file that was in the same location and >>>>>>>>> R output >>>>>>>>> "/usr/bin/clear" . Could it be related to the backup file that was >>>>>>>>> created >>>>>>>>> before I changed it? >>>>>>>>> >>>>>>>>> >>>>>>>>> No, that just means there is a 'clear' executable in two locations. >>>>>>>>> Dan >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> >>>>>>>>> >>>>>>>>> On Mar 4, 2013, at 4:15 PM, Dan Tenenbaum wrote: >>>>>>>>> >>>>>>>>> >>>>>>>>> On Mon, Mar 4, 2013 at 2:09 PM, Chandra Jack [guest] >>>>>>>>> >>>>>>>>> <guest@bioconductor.org> wrote: >>>>>>>>> >>>>>>>>> >>>>>>>>> Hi All, >>>>>>>>> >>>>>>>>> >>>>>>>>> I'm having a problem that has been mentioned here before but I'm >>>>>>>>> not sure >>>>>>>>> how to fix it. I tried to load flowQ and got: >>>>>>>>> >>>>>>>>> >>>>>>>>> Error : .onAttach failed in attachNamespace() for 'flowQ', details: >>>>>>>>> >>>>>>>>> call: mysys("convert -list configure", intern = TRUE, ignore.stderr >>>>>>>>> = TRUE) >>>>>>>>> >>>>>>>>> error: error in running command >>>>>>>>> >>>>>>>>> >>>>>>>>> Is the 'convert' command in your PATH? >>>>>>>>> >>>>>>>>> >>>>>>>>> What is the output of the R command: >>>>>>>>> >>>>>>>>> Sys.which("convert") >>>>>>>>> >>>>>>>>> ? >>>>>>>>> >>>>>>>>> >>>>>>>>> If it does not output anything, then the convert command is not in >>>>>>>>> your >>>>>>>>> PATH. >>>>>>>>> >>>>>>>>> >>>>>>>>> I'm not sure where the convert command ended up, but I'm guessing >>>>>>>>> it's >>>>>>>>> >>>>>>>>> in /opt/local/bin, >>>>>>>>> >>>>>>>>> so I think you need to edit your ~/.bashrc >>>>>>>>> >>>>>>>>> file and add the following line: >>>>>>>>> >>>>>>>>> >>>>>>>>> PATH=$PATH:/opt/local/bin >>>>>>>>> >>>>>>>>> >>>>>>>>> Then, start a new terminal window to make sure this setting is >>>>>>>>> >>>>>>>>> enabled, and try again. >>>>>>>>> >>>>>>>>> >>>>>>>>> Dan >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> In addition: Warning messages: >>>>>>>>> >>>>>>>>> 1: replacing previous import ‘plot’ when loading ‘graphics’ >>>>>>>>> >>>>>>>>> 2: replacing previous import ‘as’ when loading ‘methods’ >>>>>>>>> >>>>>>>>> Error: package/namespace load failed for ‘flowQ’. >>> >>>>>>>>> >>>>>>>>> >>>>>>>>> I have installed ImageMagick using Macports as has been suggested >>>>>>>>> and I have >>>>>>>>> also run >>>>>>>>> >>>>>>>>> convert -list configure, which gave the following: >>>>>>>>> >>>>>>>>> Path: /opt/local/lib/ImageMagick-6.8.0/config/configure.xml >>>>>>>>> >>>>>>>>> >>>>>>>>> Name Value >>>>>>>>> >>>>>>>>> >>>>>>>>> ------------------------------------------------------------ ------------------- >>>>>>>>> >>>>>>>>> CC /usr/bin/gcc-4.2 -std=gnu99 -std=gnu99 >>>>>>>>> >>>>>>>>> CFLAGS -D_THREAD_SAFE -D_THREAD_SAFE -pthread -fopenmp -pipe >>>>>>>>> -O2 >>>>>>>>> -arch x86_64 -Wall -D_THREAD_SAFE -pthread >>>>>>>>> >>>>>>>>> CODER_PATH /opt/local/lib/ImageMagick-6.8.0/modules-Q16/coders >>>>>>>>> >>>>>>>>> CONFIGURE ./configure '--prefix=/opt/local' '--enable- shared' >>>>>>>>> '--enable-static' '--disable-ltdl-install' '--disable- silent-rules' >>>>>>>>> '--with-frozenpaths' '--without-openexr' '--disable-hdri' >>>>>>>>> '--with-dps' >>>>>>>>> '--with-bzlib' '--with-fontconfig' '--with-gslib' '--with- jpeg' >>>>>>>>> '--with-lcms' '--with-png' '--with-tiff' '--with-webp' >>>>>>>>> '--with-zlib' >>>>>>>>> '--with-modules' '--with-xml' '--with-x' '--without-perl' >>>>>>>>> '--without-fpx' >>>>>>>>> '--without-jbig' '--without-jp2' '--without-wmf' '--without- gvc' >>>>>>>>> '--without-rsvg' '--without-lqr' '--without-pango' >>>>>>>>> '--with-gs-font-dir=/opt/local/share/fonts/urw-fonts' >>>>>>>>> '--with-quantum-depth=16' 'CC=/usr/bin/gcc-4.2' 'CFLAGS=-pipe -O2 >>>>>>>>> -arch >>>>>>>>> x86_64' 'LDFLAGS=-L/opt/local/lib -arch x86_64' >>>>>>>>> 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/g++-4.2' >>>>>>>>> 'CXXFLAGS=-pipe -O2 >>>>>>>>> -arch x86_64' >>>>>>>>> >>>>>>>>> CONFIGURE_PATH /opt/local/etc/ImageMagick/ >>>>>>>>> >>>>>>>>> COPYRIGHT Copyright (C) 1999-2012 ImageMagick Studio LLC >>>>>>>>> >>>>>>>>> CPPFLAGS -I/opt/local/include/ImageMagick >>>>>>>>> >>>>>>>>> CXX /usr/bin/g++-4.2 >>>>>>>>> >>>>>>>>> CXXFLAGS -pipe -O2 -arch x86_64 -D_THREAD_SAFE -pthread >>>>>>>>> >>>>>>>>> DEFS -DHAVE_CONFIG_H >>>>>>>>> >>>>>>>>> DELEGATES bzlib fftw fontconfig freetype gs jpeg jng lcms2 lzma >>>>>>>>> png tiff >>>>>>>>> x11 xml zlib >>>>>>>>> >>>>>>>>> DISTCHECK_CONFIG_FLAGS 'CC=/usr/bin/gcc-4.2' 'CFLAGS=-pipe -O2 >>>>>>>>> -arch x86_64' >>>>>>>>> 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/g++-4.2' >>>>>>>>> 'LDFLAGS=-L/opt/local/lib -arch x86_64' --disable-deprecated >>>>>>>>> --with-quantum-depth=16 --with-umem=no --with-autotrace=no >>>>>>>>> --with-fpx=no >>>>>>>>> --with-fontpath= >>>>>>>>> --with-gs-font-dir=/opt/local/share/fonts/urw-fonts >>>>>>>>> --with-gvc=no --with-jp2=no --with-lqr=no --with-openexr=no >>>>>>>>> --with-pango=no >>>>>>>>> --with-rsvg=no --with-wmf=no --with-perl=no >>>>>>>>> >>>>>>>>> DOCUMENTATION_PATH /opt/local/share/doc/ImageMagick-6.8.0 >>>>>>>>> >>>>>>>>> EXEC-PREFIX /opt/local >>>>>>>>> >>>>>>>>> EXECUTABLE_PATH /opt/local/bin >>>>>>>>> >>>>>>>>> FEATURES OpenCL OpenMP >>>>>>>>> >>>>>>>>> FILTER_PATH /opt/local/lib/ImageMagick-6.8.0/modules-Q16/filters >>>>>>>>> >>>>>>>>> HOST x86_64-apple-darwin10.8.0 >>>>>>>>> >>>>>>>>> INCLUDE_PATH /opt/local/include/ImageMagick >>>>>>>>> >>>>>>>>> LDFLAGS -L/opt/local/lib -L/opt/local/lib -arch x86_64 >>>>>>>>> -L/opt/local/lib -L/opt/local/lib >>>>>>>>> >>>>>>>>> LIB_VERSION 0x680 >>>>>>>>> >>>>>>>>> LIB_VERSION_NUMBER 6,8,0,7 >>>>>>>>> >>>>>>>>> LIBRARY_PATH /opt/local/lib/ImageMagick-6.8.0 >>>>>>>>> >>>>>>>>> LIBS -lMagickCore -llcms2 -lfreetype -lfftw3 >>>>>>>>> -L/opt/local/lib >>>>>>>>> -lfontconfig -lXext -lSM -lICE -lX11 -lXt -L/opt/local/lib -llzma >>>>>>>>> -lbz2 -lz >>>>>>>>> -lltdl -lm -lgomp -lclparser -Wl,-framework,OpenCL >>>>>>>>> -L/System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries >>>>>>>>> -lm >>>>>>>>> -lpthread >>>>>>>>> >>>>>>>>> NAME ImageMagick >>>>>>>>> >>>>>>>>> PCFLAGS -fopenmp >>>>>>>>> >>>>>>>>> PREFIX /opt/local >>>>>>>>> >>>>>>>>> QuantumDepth 16 >>>>>>>>> >>>>>>>>> RELEASE_DATE 2013-03-04 >>>>>>>>> >>>>>>>>> SHARE_PATH /opt/local/share/ImageMagick-6.8.0 >>>>>>>>> >>>>>>>>> SVN_REVISION 10029 >>>>>>>>> >>>>>>>>> TARGET_CPU x86_64 >>>>>>>>> >>>>>>>>> TARGET_OS darwin10.8.0 >>>>>>>>> >>>>>>>>> TARGET_VENDOR apple >>>>>>>>> >>>>>>>>> VERSION 6.8.0 >>>>>>>>> >>>>>>>>> WEBSITE http://www.imagemagick.org >>>>>>>>> >>>>>>>>> >>>>>>>>> Path: [built-in] >>>>>>>>> >>>>>>>>> >>>>>>>>> Name Value >>>>>>>>> >>>>>>>>> >>>>>>>>> ------------------------------------------------------------ ------------------- >>>>>>>>> >>>>>>>>> NAME ImageMagick >>>>>>>>> >>>>>>>>> >>>>>>>>> Any help would be appreciated. Thanks >>>>>>>>> >>>>>>>>> >>>>>>>>> -- output of sessionInfo(): >>>>>>>>> >>>>>>>>> >>>>>>>>> R version 2.15.2 (2012-10-26) >>>>>>>>> >>>>>>>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >>>>>>>>> >>>>>>>>> >>>>>>>>> locale: >>>>>>>>> >>>>>>>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>>>>>>>> >>>>>>>>> >>>>>>>>> attached base packages: >>>>>>>>> >>>>>>>>> [1] tools stats graphics grDevices utils datasets >>>>>>>>> methods >>>>>>>>> base >>>>>>>>> >>>>>>>>> >>>>>>>>> other attached packages: >>>>>>>>> >>>>>>>>> [1] latticeExtra_0.6-24 RColorBrewer_1.0-5 parody_1.16.0 >>>>>>>>> bioDist_1.30.0 >>>>>>>>> >>>>>>>>> [5] KernSmooth_2.23-8 mvoutlier_1.9.9 sgeostat_1.0-25 >>>>>>>>> robCompositions_1.6.3 >>>>>>>>> >>>>>>>>> [9] car_2.0-16 nnet_7.3-5 compositions_1.20-1 >>>>>>>>> energy_1.4-0 >>>>>>>>> >>>>>>>>> [13] MASS_7.3-23 boot_1.3-7 tensorA_0.36 >>>>>>>>> rgl_0.93.928 >>>>>>>>> >>>>>>>>> [17] flowViz_1.22.0 flowCore_1.24.2 rrcov_1.3-02 >>>>>>>>> pcaPP_1.9-48 >>>>>>>>> >>>>>>>>> [21] mvtnorm_0.9-9994 robustbase_0.9-5 Biobase_2.18.0 >>>>>>>>> lattice_0.20-13 >>>>>>>>> >>>>>>>>> [25] outliers_0.14 BiocGenerics_0.4.0 >>>>>>>>> BiocInstaller_1.8.3 >>>>>>>>> >>>>>>>>> >>>>>>>>> loaded via a namespace (and not attached): >>>>>>>>> >>>>>>>>> [1] annotate_1.36.0 AnnotationDbi_1.20.5 DBI_0.2-5 >>>>>>>>> feature_1.2.8 >>>>>>>>> >>>>>>>>> [5] flowQ_1.18.0 geneplotter_1.36.0 graph_1.36.2 >>>>>>>>> grid_2.15.2 >>>>>>>>> >>>>>>>>> [9] hexbin_1.26.1 IDPmisc_1.1.17 IRanges_1.16.6 >>>>>>>>> ks_1.8.11 >>>>>>>>> >>>>>>>>> [13] parallel_2.15.2 RSQLite_0.11.2 stats4_2.15.2 >>>>>>>>> XML_3.95-0.1 >>>>>>>>> >>>>>>>>> [17] xtable_1.7-1 >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> >>>>>>>>> Sent via the guest posting facility at bioconductor.org. >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> >>>>>>>>> Bioconductor mailing list >>>>>>>>> >>>>>>>>> Bioconductor@r-project.org >>>>>>>>> >>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>>>> >>>>>>>>> Search the archives: >>>>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> Chandra Jack >>>>>>>>> >>>>>>>>> Postdoctoral Research Assoc. >>>>>>>>> >>>>>>>>> Dept. of Bioengineering >>>>>>>>> >>>>>>>>> Rice University >>>>>>>>> >>>>>>>>> chanj@rice.edu >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> Chandra Jack >>>>>>>>> Postdoctoral Research Assoc. >>>>>>>>> Dept. of Bioengineering >>>>>>>>> Rice University >>>>>>>>> chanj@rice.edu >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>> >>>>>>> Chandra Jack >>>>>>> Postdoctoral Research Assoc. >>>>>>> Dept. of Bioengineering >>>>>>> Rice University >>>>>>> chanj@rice.edu >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>> >>>>> Chandra Jack >>>>> Postdoctoral Research Assoc. >>>>> Dept. of Bioengineering >>>>> Rice University >>>>> chanj@rice.edu >>>>> >>>>> >>>>> >>>> >>> >>> Chandra Jack >>> Postdoctoral Research Assoc. >>> Dept. of Bioengineering >>> Rice University >>> chanj@rice.edu >>> >>> >>> >>> >>> [[alternative HTML version deleted]] >>> >>> >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > Chandra Jack Postdoctoral Research Assoc. Dept. of Bioengineering Rice University chanj@rice.edu [[alternative HTML version deleted]]
ADD REPLYlink written 6.7 years ago by Chandra Jack90
On Tue, Mar 5, 2013 at 8:11 AM, Chandra Jack <chanj at="" rice.edu=""> wrote: > I didn't have a ~/.profile so I created one. All I put in it was export PATH > = $PATH:opt/local/bin. But I got the same message that /bin/sh: convert: > command not found. I read that .bash_profile may need to call .profile and > also tried putting source ~/.profile at the end of the file but that gave me > the same message. > > For .profile you don't want the word 'export' in the text that you add. Dan > On Mar 5, 2013, at 9:41 AM, Dan Tenenbaum wrote: > > On Tue, Mar 5, 2013 at 12:21 AM, Nikolas Pontikos <n.pontikos at="" gmail.com=""> > wrote: > > From your R error message, system is calling /bin/sh not /bin/bash (which > > should be the same program but i don't think sh reads the .bashrc config > > file). > > Maybe the convert command is not available from /bin/sh? > > > > In that case the file to be edited is ~/.profile > > Dan > > > > On 5 March 2013 06:42, Chandra Jack <chanj at="" rice.edu=""> wrote: > > > Yes. I've been restarting R after everytime I changed bash_profile. I also > > just tried reinstalling R but that didn't help either. > > > On Mar 5, 2013, at 12:20 AM, Dan Tenenbaum wrote: > > > On Mon, Mar 4, 2013 at 10:06 PM, Chandra Jack <chanj at="" rice.edu=""> wrote: > > > On Mar 4, 2013, at 11:57 PM, Dan Tenenbaum wrote: > > > On Mon, Mar 4, 2013 at 9:53 PM, Chandra Jack <chanj at="" rice.edu=""> wrote: > > Thank you so much for your help. > > > Chandra-Jacks-MacBook:~ chanj$ source ~/.bash_profile > > Chandra-Jacks-MacBook:~ chanj$ echo $PATH > > > /Library/Frameworks/Python.framework/Versions/2.7/bin:/Library/Frame works/EPD64.framework/Versions/Current/bin:/Library/Frameworks/Python. framework/Versions/2.7/bin:/Library/Frameworks/EPD64.framework/Version s/Current/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bi n:/opt/local/bin:/opt/local/bin > > Chandra-Jacks-MacBook:~ chanj$ which convert > > /opt/local/bin/convert > > > > It looks like convert is in your PATH. > > > What happens if you type > > convert > > at the terminal prompt? > > > I think it opens ImageMagick > > Chandra-Jacks-MacBook:~ chanj$ convert > > Version: ImageMagick 6.8.0-7 2013-03-04 Q16 http://www.imagemagick.org > > Copyright: Copyright (C) 1999-2012 ImageMagick Studio LLC > > Features: OpenMP OpenCL > > > Usage: convert [options ...] file [ [options ...] file ...] [options > > ...] file > > > Image Settings: > > -adjoin join images into a single multi-image file > > > etc.... > > > > > > What if you go into R and type > > system("convert") > > ? > > > system("convert") > > /bin/sh: convert: command not found > > > > This means convert is in your path but R can't see it. Did you restart > > R after editing .bash_profile? > > > Dan > > > > Dan > > > On Mar 4, 2013, at 11:45 PM, Dan Tenenbaum wrote: > > > On Mon, Mar 4, 2013 at 9:30 PM, Chandra Jack <chanj at="" rice.edu=""> wrote: > > I replaced the original export line with the one you wrote but it > > still > > didn't work. > > > > OK, at a terminal prompt, please enter the following commands and > > send > > me the output they produce: > > > source ~/.bash_profile > > echo $PATH > > which convert > > > > > thanks, > > Dan > > > > > On Mar 4, 2013, at 10:18 PM, Dan Tenenbaum wrote: > > > On Mon, Mar 4, 2013 at 8:07 PM, Chandra Jack <chanj at="" rice.edu=""> > > wrote: > > > The convert command isn't in my PATH but adding the newIt doesn't > > seem to be > > working. I don't have a .bashrc file but I have a .bash_profile. > > The > > original file was: > > > # Setting PATH for EPD-7.1-2 > > > # The orginal version is saved in .bash_profile.pysave > > > > PATH="/Library/Frameworks/EPD64.framework/Versions/Current/bin:${PAT H}" > > > export PATH > > > > MKL_NUM_THREADS=1 > > > export MKL_NUM_THREADS > > > > # Setting PATH for Python 2.7 > > > # The orginal version is saved in .bash_profile.pysave > > > > PATH="/Library/Frameworks/Python.framework/Versions/2.7/bin:${PATH}" > > > export PATH > > > > ## > > > # Your previous /Users/chanj/.bash_profile file was backed up as > > /Users/chanj/.bash_profile.macports-saved_2013-03-04_at_14:30:35 > > > ## > > > > # MacPorts Installer addition on 2013-03-04_at_14:30:35: adding an > > appropriate PATH variable for use with MacPorts. > > > export PATH=/opt/local/bin:/opt/local/sbin:$PATH > > > # Finished adapting your PATH environment variable for use with > > MacPorts. > > > > I added PATH=$PATH:/opt/local/bin after the export line, resaved > > the text > > edit file and quit the terminal. When I checked Terminal again the > > file was > > updated but R couldn't find the command still. > > > > Sorry, it needs to say: > > > export PATH=$PATH:/opt/local/bin > > > I forgot the 'export' before. > > > > > > > > I also tried adding it before the export line, replacing the part > > after the > > export line with it, adding quotation marks but nothing seemed to > > work. I > > went in and found the convert command file and it is in > > opt/local/bin. I > > tried Sys.which with another file that was in the same location and > > R output > > "/usr/bin/clear" . Could it be related to the backup file that was > > created > > before I changed it? > > > > No, that just means there is a 'clear' executable in two locations. > > Dan > > > > > Thanks > > > > On Mar 4, 2013, at 4:15 PM, Dan Tenenbaum wrote: > > > > On Mon, Mar 4, 2013 at 2:09 PM, Chandra Jack [guest] > > > <guest at="" bioconductor.org=""> wrote: > > > > Hi All, > > > > I'm having a problem that has been mentioned here before but I'm > > not sure > > how to fix it. I tried to load flowQ and got: > > > > Error : .onAttach failed in attachNamespace() for 'flowQ', details: > > > call: mysys("convert -list configure", intern = TRUE, ignore.stderr > > = TRUE) > > > error: error in running command > > > > Is the 'convert' command in your PATH? > > > > What is the output of the R command: > > > Sys.which("convert") > > > ? > > > > If it does not output anything, then the convert command is not in > > your > > PATH. > > > > I'm not sure where the convert command ended up, but I'm guessing > > it's > > > in /opt/local/bin, > > > so I think you need to edit your ~/.bashrc > > > file and add the following line: > > > > PATH=$PATH:/opt/local/bin > > > > Then, start a new terminal window to make sure this setting is > > > enabled, and try again. > > > > Dan > > > > > In addition: Warning messages: > > > 1: replacing previous import ?plot? when loading ?graphics? > > > 2: replacing previous import ?as? when loading ?methods? > > > Error: package/namespace load failed for ?flowQ?. > > > > > I have installed ImageMagick using Macports as has been suggested > > and I have > > also run > > > convert -list configure, which gave the following: > > > Path: /opt/local/lib/ImageMagick-6.8.0/config/configure.xml > > > > Name Value > > > > -------------------------------------------------------------------- ----------- > > > CC /usr/bin/gcc-4.2 -std=gnu99 -std=gnu99 > > > CFLAGS -D_THREAD_SAFE -D_THREAD_SAFE -pthread -fopenmp -pipe > > -O2 > > -arch x86_64 -Wall -D_THREAD_SAFE -pthread > > > CODER_PATH /opt/local/lib/ImageMagick-6.8.0/modules-Q16/coders > > > CONFIGURE ./configure '--prefix=/opt/local' '--enable-shared' > > '--enable-static' '--disable-ltdl-install' '--disable-silent-rules' > > '--with-frozenpaths' '--without-openexr' '--disable-hdri' > > '--with-dps' > > '--with-bzlib' '--with-fontconfig' '--with-gslib' '--with-jpeg' > > '--with-lcms' '--with-png' '--with-tiff' '--with-webp' > > '--with-zlib' > > '--with-modules' '--with-xml' '--with-x' '--without-perl' > > '--without-fpx' > > '--without-jbig' '--without-jp2' '--without-wmf' '--without-gvc' > > '--without-rsvg' '--without-lqr' '--without-pango' > > '--with-gs-font-dir=/opt/local/share/fonts/urw-fonts' > > '--with-quantum-depth=16' 'CC=/usr/bin/gcc-4.2' 'CFLAGS=-pipe -O2 > > -arch > > x86_64' 'LDFLAGS=-L/opt/local/lib -arch x86_64' > > 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/g++-4.2' > > 'CXXFLAGS=-pipe -O2 > > -arch x86_64' > > > CONFIGURE_PATH /opt/local/etc/ImageMagick/ > > > COPYRIGHT Copyright (C) 1999-2012 ImageMagick Studio LLC > > > CPPFLAGS -I/opt/local/include/ImageMagick > > > CXX /usr/bin/g++-4.2 > > > CXXFLAGS -pipe -O2 -arch x86_64 -D_THREAD_SAFE -pthread > > > DEFS -DHAVE_CONFIG_H > > > DELEGATES bzlib fftw fontconfig freetype gs jpeg jng lcms2 lzma > > png tiff > > x11 xml zlib > > > DISTCHECK_CONFIG_FLAGS 'CC=/usr/bin/gcc-4.2' 'CFLAGS=-pipe -O2 > > -arch x86_64' > > 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/g++-4.2' > > 'LDFLAGS=-L/opt/local/lib -arch x86_64' --disable-deprecated > > --with-quantum-depth=16 --with-umem=no --with-autotrace=no > > --with-fpx=no > > --with-fontpath= > > --with-gs-font-dir=/opt/local/share/fonts/urw-fonts > > --with-gvc=no --with-jp2=no --with-lqr=no --with-openexr=no > > --with-pango=no > > --with-rsvg=no --with-wmf=no --with-perl=no > > > DOCUMENTATION_PATH /opt/local/share/doc/ImageMagick-6.8.0 > > > EXEC-PREFIX /opt/local > > > EXECUTABLE_PATH /opt/local/bin > > > FEATURES OpenCL OpenMP > > > FILTER_PATH /opt/local/lib/ImageMagick-6.8.0/modules-Q16/filters > > > HOST x86_64-apple-darwin10.8.0 > > > INCLUDE_PATH /opt/local/include/ImageMagick > > > LDFLAGS -L/opt/local/lib -L/opt/local/lib -arch x86_64 > > -L/opt/local/lib -L/opt/local/lib > > > LIB_VERSION 0x680 > > > LIB_VERSION_NUMBER 6,8,0,7 > > > LIBRARY_PATH /opt/local/lib/ImageMagick-6.8.0 > > > LIBS -lMagickCore -llcms2 -lfreetype -lfftw3 > > -L/opt/local/lib > > -lfontconfig -lXext -lSM -lICE -lX11 -lXt -L/opt/local/lib -llzma > > -lbz2 -lz > > -lltdl -lm -lgomp -lclparser -Wl,-framework,OpenCL > > -L/System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries > > -lm > > -lpthread > > > NAME ImageMagick > > > PCFLAGS -fopenmp > > > PREFIX /opt/local > > > QuantumDepth 16 > > > RELEASE_DATE 2013-03-04 > > > SHARE_PATH /opt/local/share/ImageMagick-6.8.0 > > > SVN_REVISION 10029 > > > TARGET_CPU x86_64 > > > TARGET_OS darwin10.8.0 > > > TARGET_VENDOR apple > > > VERSION 6.8.0 > > > WEBSITE http://www.imagemagick.org > > > > Path: [built-in] > > > > Name Value > > > > -------------------------------------------------------------------- ----------- > > > NAME ImageMagick > > > > Any help would be appreciated. Thanks > > > > -- output of sessionInfo(): > > > > R version 2.15.2 (2012-10-26) > > > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > > > locale: > > > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > > > attached base packages: > > > [1] tools stats graphics grDevices utils datasets > > methods > > base > > > > other attached packages: > > > [1] latticeExtra_0.6-24 RColorBrewer_1.0-5 parody_1.16.0 > > bioDist_1.30.0 > > > [5] KernSmooth_2.23-8 mvoutlier_1.9.9 sgeostat_1.0-25 > > robCompositions_1.6.3 > > > [9] car_2.0-16 nnet_7.3-5 compositions_1.20-1 > > energy_1.4-0 > > > [13] MASS_7.3-23 boot_1.3-7 tensorA_0.36 > > rgl_0.93.928 > > > [17] flowViz_1.22.0 flowCore_1.24.2 rrcov_1.3-02 > > pcaPP_1.9-48 > > > [21] mvtnorm_0.9-9994 robustbase_0.9-5 Biobase_2.18.0 > > lattice_0.20-13 > > > [25] outliers_0.14 BiocGenerics_0.4.0 > > BiocInstaller_1.8.3 > > > > loaded via a namespace (and not attached): > > > [1] annotate_1.36.0 AnnotationDbi_1.20.5 DBI_0.2-5 > > feature_1.2.8 > > > [5] flowQ_1.18.0 geneplotter_1.36.0 graph_1.36.2 > > grid_2.15.2 > > > [9] hexbin_1.26.1 IDPmisc_1.1.17 IRanges_1.16.6 > > ks_1.8.11 > > > [13] parallel_2.15.2 RSQLite_0.11.2 stats4_2.15.2 > > XML_3.95-0.1 > > > [17] xtable_1.7-1 > > > > -- > > > Sent via the guest posting facility at bioconductor.org. > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor at r-project.org > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > Chandra Jack > > > Postdoctoral Research Assoc. > > > Dept. of Bioengineering > > > Rice University > > > chanj at rice.edu > > > > > > > > Chandra Jack > > Postdoctoral Research Assoc. > > Dept. of Bioengineering > > Rice University > > chanj at rice.edu > > > > > > > Chandra Jack > > Postdoctoral Research Assoc. > > Dept. of Bioengineering > > Rice University > > chanj at rice.edu > > > > > > > Chandra Jack > > Postdoctoral Research Assoc. > > Dept. of Bioengineering > > Rice University > > chanj at rice.edu > > > > > > > Chandra Jack > > Postdoctoral Research Assoc. > > Dept. of Bioengineering > > Rice University > > chanj at rice.edu > > > > > > [[alternative HTML version deleted]] > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > Chandra Jack > Postdoctoral Research Assoc. > Dept. of Bioengineering > Rice University > chanj at rice.edu > > >
ADD REPLYlink written 6.7 years ago by Dan Tenenbaum8.2k
I haven't been listening too closely, but... Exactly what you wrote would have been a bash/sh syntax error. There cannot be spaces around the '='. If you are on the right track, then you need something like PATH=$PATH:opt/local/bin While we are at it, I believe that resetting a variable that is already exported, as with PATH, does not necessitate the 'export' command, in order to reset the exported value. For example, sh-3.2$ export foo=bar sh-3.2$ env | grep foo foo=bar sh-3.2$ foo=bar2 sh-3.2$ env | grep foo foo=bar2 On Mar 5, 2013, at 11:11 AM, Chandra Jack wrote: > I didn't have a ~/.profile so I created one. All I put in it was export PATH = $PATH:opt/local/bin. But I got the same message that /bin/sh: convert: command not found. I read that .bash_profile may need to call .profile and also tried putting source ~/.profile at the end of the file but that gave me the same message. > > > On Mar 5, 2013, at 9:41 AM, Dan Tenenbaum wrote: > >> On Tue, Mar 5, 2013 at 12:21 AM, Nikolas Pontikos <n.pontikos at="" gmail.com=""> wrote: >>> From your R error message, system is calling /bin/sh not /bin/bash (which >>> should be the same program but i don't think sh reads the .bashrc config >>> file). >>> Maybe the convert command is not available from /bin/sh? >> >> >> In that case the file to be edited is ~/.profile >> >> Dan >> >>> >>> >>> On 5 March 2013 06:42, Chandra Jack <chanj at="" rice.edu=""> wrote: >>>> >>>> Yes. I've been restarting R after everytime I changed bash_profile. I also >>>> just tried reinstalling R but that didn't help either. >>>> >>>> On Mar 5, 2013, at 12:20 AM, Dan Tenenbaum wrote: >>>> >>>>> On Mon, Mar 4, 2013 at 10:06 PM, Chandra Jack <chanj at="" rice.edu=""> wrote: >>>>>> >>>>>> On Mar 4, 2013, at 11:57 PM, Dan Tenenbaum wrote: >>>>>> >>>>>>> On Mon, Mar 4, 2013 at 9:53 PM, Chandra Jack <chanj at="" rice.edu=""> wrote: >>>>>>>> Thank you so much for your help. >>>>>>>> >>>>>>>> Chandra-Jacks-MacBook:~ chanj$ source ~/.bash_profile >>>>>>>> Chandra-Jacks-MacBook:~ chanj$ echo $PATH >>>>>>>> >>>>>>>> /Library/Frameworks/Python.framework/Versions/2.7/bin:/Librar y/Frameworks/EPD64.framework/Versions/Current/bin:/Library/Frameworks/ Python.framework/Versions/2.7/bin:/Library/Frameworks/EPD64.framework/ Versions/Current/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr /X11/bin:/opt/local/bin:/opt/local/bin >>>>>>>> Chandra-Jacks-MacBook:~ chanj$ which convert >>>>>>>> /opt/local/bin/convert >>>>>>>> >>>>>>> >>>>>>> It looks like convert is in your PATH. >>>>>>> >>>>>>> What happens if you type >>>>>>> convert >>>>>>> at the terminal prompt? >>>>>> >>>>>> I think it opens ImageMagick >>>>>> Chandra-Jacks-MacBook:~ chanj$ convert >>>>>> Version: ImageMagick 6.8.0-7 2013-03-04 Q16 http://www.imagemagick.org >>>>>> Copyright: Copyright (C) 1999-2012 ImageMagick Studio LLC >>>>>> Features: OpenMP OpenCL >>>>>> >>>>>> Usage: convert [options ...] file [ [options ...] file ...] [options >>>>>> ...] file >>>>>> >>>>>> Image Settings: >>>>>> -adjoin join images into a single multi-image file >>>>>> >>>>>> etc.... >>>>>> >>>>>> >>>>>> >>>>>>> >>>>>>> What if you go into R and type >>>>>>> system("convert") >>>>>>> ? >>>>>>> >>>>>> system("convert") >>>>>> /bin/sh: convert: command not found >>>>>> >>>>> >>>>> This means convert is in your path but R can't see it. Did you restart >>>>> R after editing .bash_profile? >>>>> >>>>> Dan >>>>> >>>>> >>>>>>> Dan >>>>>>> >>>>>>>> On Mar 4, 2013, at 11:45 PM, Dan Tenenbaum wrote: >>>>>>>> >>>>>>>>> On Mon, Mar 4, 2013 at 9:30 PM, Chandra Jack <chanj at="" rice.edu=""> wrote: >>>>>>>>>> I replaced the original export line with the one you wrote but it >>>>>>>>>> still >>>>>>>>>> didn't work. >>>>>>>>>> >>>>>>>>> >>>>>>>>> OK, at a terminal prompt, please enter the following commands and >>>>>>>>> send >>>>>>>>> me the output they produce: >>>>>>>>> >>>>>>>>> source ~/.bash_profile >>>>>>>>> echo $PATH >>>>>>>>> which convert >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> thanks, >>>>>>>>> Dan >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>>> On Mar 4, 2013, at 10:18 PM, Dan Tenenbaum wrote: >>>>>>>>>> >>>>>>>>>> On Mon, Mar 4, 2013 at 8:07 PM, Chandra Jack <chanj at="" rice.edu=""> >>>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>> The convert command isn't in my PATH but adding the newIt doesn't >>>>>>>>>> seem to be >>>>>>>>>> working. I don't have a .bashrc file but I have a .bash_profile. >>>>>>>>>> The >>>>>>>>>> original file was: >>>>>>>>>> >>>>>>>>>> # Setting PATH for EPD-7.1-2 >>>>>>>>>> >>>>>>>>>> # The orginal version is saved in .bash_profile.pysave >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> PATH="/Library/Frameworks/EPD64.framework/Versions/Current/ bin:${PATH}" >>>>>>>>>> >>>>>>>>>> export PATH >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> MKL_NUM_THREADS=1 >>>>>>>>>> >>>>>>>>>> export MKL_NUM_THREADS >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> # Setting PATH for Python 2.7 >>>>>>>>>> >>>>>>>>>> # The orginal version is saved in .bash_profile.pysave >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> PATH="/Library/Frameworks/Python.framework/Versions/2.7/bin:${PATH}" >>>>>>>>>> >>>>>>>>>> export PATH >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> ## >>>>>>>>>> >>>>>>>>>> # Your previous /Users/chanj/.bash_profile file was backed up as >>>>>>>>>> /Users/chanj/.bash_profile.macports- saved_2013-03-04_at_14:30:35 >>>>>>>>>> >>>>>>>>>> ## >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> # MacPorts Installer addition on 2013-03-04_at_14:30:35: adding an >>>>>>>>>> appropriate PATH variable for use with MacPorts. >>>>>>>>>> >>>>>>>>>> export PATH=/opt/local/bin:/opt/local/sbin:$PATH >>>>>>>>>> >>>>>>>>>> # Finished adapting your PATH environment variable for use with >>>>>>>>>> MacPorts. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> I added PATH=$PATH:/opt/local/bin after the export line, resaved >>>>>>>>>> the text >>>>>>>>>> edit file and quit the terminal. When I checked Terminal again the >>>>>>>>>> file was >>>>>>>>>> updated but R couldn't find the command still. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Sorry, it needs to say: >>>>>>>>>> >>>>>>>>>> export PATH=$PATH:/opt/local/bin >>>>>>>>>> >>>>>>>>>> I forgot the 'export' before. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> I also tried adding it before the export line, replacing the part >>>>>>>>>> after the >>>>>>>>>> export line with it, adding quotation marks but nothing seemed to >>>>>>>>>> work. I >>>>>>>>>> went in and found the convert command file and it is in >>>>>>>>>> opt/local/bin. I >>>>>>>>>> tried Sys.which with another file that was in the same location and >>>>>>>>>> R output >>>>>>>>>> "/usr/bin/clear" . Could it be related to the backup file that was >>>>>>>>>> created >>>>>>>>>> before I changed it? >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> No, that just means there is a 'clear' executable in two locations. >>>>>>>>>> Dan >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Thanks >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Mar 4, 2013, at 4:15 PM, Dan Tenenbaum wrote: >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Mon, Mar 4, 2013 at 2:09 PM, Chandra Jack [guest] >>>>>>>>>> >>>>>>>>>> <guest at="" bioconductor.org=""> wrote: >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Hi All, >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> I'm having a problem that has been mentioned here before but I'm >>>>>>>>>> not sure >>>>>>>>>> how to fix it. I tried to load flowQ and got: >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Error : .onAttach failed in attachNamespace() for 'flowQ', details: >>>>>>>>>> >>>>>>>>>> call: mysys("convert -list configure", intern = TRUE, ignore.stderr >>>>>>>>>> = TRUE) >>>>>>>>>> >>>>>>>>>> error: error in running command >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Is the 'convert' command in your PATH? >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> What is the output of the R command: >>>>>>>>>> >>>>>>>>>> Sys.which("convert") >>>>>>>>>> >>>>>>>>>> ? >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> If it does not output anything, then the convert command is not in >>>>>>>>>> your >>>>>>>>>> PATH. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> I'm not sure where the convert command ended up, but I'm guessing >>>>>>>>>> it's >>>>>>>>>> >>>>>>>>>> in /opt/local/bin, >>>>>>>>>> >>>>>>>>>> so I think you need to edit your ~/.bashrc >>>>>>>>>> >>>>>>>>>> file and add the following line: >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> PATH=$PATH:/opt/local/bin >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Then, start a new terminal window to make sure this setting is >>>>>>>>>> >>>>>>>>>> enabled, and try again. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Dan >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> In addition: Warning messages: >>>>>>>>>> >>>>>>>>>> 1: replacing previous import ?plot? when loading ?graphics? >>>>>>>>>> >>>>>>>>>> 2: replacing previous import ?as? when loading ?methods? >>>>>>>>>> >>>>>>>>>> Error: package/namespace load failed for ?flowQ?. >>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> I have installed ImageMagick using Macports as has been suggested >>>>>>>>>> and I have >>>>>>>>>> also run >>>>>>>>>> >>>>>>>>>> convert -list configure, which gave the following: >>>>>>>>>> >>>>>>>>>> Path: /opt/local/lib/ImageMagick-6.8.0/config/configure.xml >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Name Value >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> ----------------------------------------------------------- -------------------- >>>>>>>>>> >>>>>>>>>> CC /usr/bin/gcc-4.2 -std=gnu99 -std=gnu99 >>>>>>>>>> >>>>>>>>>> CFLAGS -D_THREAD_SAFE -D_THREAD_SAFE -pthread -fopenmp -pipe >>>>>>>>>> -O2 >>>>>>>>>> -arch x86_64 -Wall -D_THREAD_SAFE -pthread >>>>>>>>>> >>>>>>>>>> CODER_PATH /opt/local/lib/ImageMagick-6.8.0/modules-Q16/coders >>>>>>>>>> >>>>>>>>>> CONFIGURE ./configure '--prefix=/opt/local' '--enable- shared' >>>>>>>>>> '--enable-static' '--disable-ltdl-install' '--disable- silent-rules' >>>>>>>>>> '--with-frozenpaths' '--without-openexr' '--disable-hdri' >>>>>>>>>> '--with-dps' >>>>>>>>>> '--with-bzlib' '--with-fontconfig' '--with-gslib' '--with- jpeg' >>>>>>>>>> '--with-lcms' '--with-png' '--with-tiff' '--with-webp' >>>>>>>>>> '--with-zlib' >>>>>>>>>> '--with-modules' '--with-xml' '--with-x' '--without-perl' >>>>>>>>>> '--without-fpx' >>>>>>>>>> '--without-jbig' '--without-jp2' '--without-wmf' '--without-gvc' >>>>>>>>>> '--without-rsvg' '--without-lqr' '--without-pango' >>>>>>>>>> '--with-gs-font-dir=/opt/local/share/fonts/urw-fonts' >>>>>>>>>> '--with-quantum-depth=16' 'CC=/usr/bin/gcc-4.2' 'CFLAGS=-pipe -O2 >>>>>>>>>> -arch >>>>>>>>>> x86_64' 'LDFLAGS=-L/opt/local/lib -arch x86_64' >>>>>>>>>> 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/g++-4.2' >>>>>>>>>> 'CXXFLAGS=-pipe -O2 >>>>>>>>>> -arch x86_64' >>>>>>>>>> >>>>>>>>>> CONFIGURE_PATH /opt/local/etc/ImageMagick/ >>>>>>>>>> >>>>>>>>>> COPYRIGHT Copyright (C) 1999-2012 ImageMagick Studio LLC >>>>>>>>>> >>>>>>>>>> CPPFLAGS -I/opt/local/include/ImageMagick >>>>>>>>>> >>>>>>>>>> CXX /usr/bin/g++-4.2 >>>>>>>>>> >>>>>>>>>> CXXFLAGS -pipe -O2 -arch x86_64 -D_THREAD_SAFE -pthread >>>>>>>>>> >>>>>>>>>> DEFS -DHAVE_CONFIG_H >>>>>>>>>> >>>>>>>>>> DELEGATES bzlib fftw fontconfig freetype gs jpeg jng lcms2 lzma >>>>>>>>>> png tiff >>>>>>>>>> x11 xml zlib >>>>>>>>>> >>>>>>>>>> DISTCHECK_CONFIG_FLAGS 'CC=/usr/bin/gcc-4.2' 'CFLAGS=-pipe -O2 >>>>>>>>>> -arch x86_64' >>>>>>>>>> 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/g++-4.2' >>>>>>>>>> 'LDFLAGS=-L/opt/local/lib -arch x86_64' --disable- deprecated >>>>>>>>>> --with-quantum-depth=16 --with-umem=no --with-autotrace=no >>>>>>>>>> --with-fpx=no >>>>>>>>>> --with-fontpath= >>>>>>>>>> --with-gs-font-dir=/opt/local/share/fonts/urw-fonts >>>>>>>>>> --with-gvc=no --with-jp2=no --with-lqr=no --with-openexr=no >>>>>>>>>> --with-pango=no >>>>>>>>>> --with-rsvg=no --with-wmf=no --with-perl=no >>>>>>>>>> >>>>>>>>>> DOCUMENTATION_PATH /opt/local/share/doc/ImageMagick-6.8.0 >>>>>>>>>> >>>>>>>>>> EXEC-PREFIX /opt/local >>>>>>>>>> >>>>>>>>>> EXECUTABLE_PATH /opt/local/bin >>>>>>>>>> >>>>>>>>>> FEATURES OpenCL OpenMP >>>>>>>>>> >>>>>>>>>> FILTER_PATH /opt/local/lib/ImageMagick-6.8.0/modules-Q16/filters >>>>>>>>>> >>>>>>>>>> HOST x86_64-apple-darwin10.8.0 >>>>>>>>>> >>>>>>>>>> INCLUDE_PATH /opt/local/include/ImageMagick >>>>>>>>>> >>>>>>>>>> LDFLAGS -L/opt/local/lib -L/opt/local/lib -arch x86_64 >>>>>>>>>> -L/opt/local/lib -L/opt/local/lib >>>>>>>>>> >>>>>>>>>> LIB_VERSION 0x680 >>>>>>>>>> >>>>>>>>>> LIB_VERSION_NUMBER 6,8,0,7 >>>>>>>>>> >>>>>>>>>> LIBRARY_PATH /opt/local/lib/ImageMagick-6.8.0 >>>>>>>>>> >>>>>>>>>> LIBS -lMagickCore -llcms2 -lfreetype -lfftw3 >>>>>>>>>> -L/opt/local/lib >>>>>>>>>> -lfontconfig -lXext -lSM -lICE -lX11 -lXt -L/opt/local/lib -llzma >>>>>>>>>> -lbz2 -lz >>>>>>>>>> -lltdl -lm -lgomp -lclparser -Wl,-framework,OpenCL >>>>>>>>>> -L/System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries >>>>>>>>>> -lm >>>>>>>>>> -lpthread >>>>>>>>>> >>>>>>>>>> NAME ImageMagick >>>>>>>>>> >>>>>>>>>> PCFLAGS -fopenmp >>>>>>>>>> >>>>>>>>>> PREFIX /opt/local >>>>>>>>>> >>>>>>>>>> QuantumDepth 16 >>>>>>>>>> >>>>>>>>>> RELEASE_DATE 2013-03-04 >>>>>>>>>> >>>>>>>>>> SHARE_PATH /opt/local/share/ImageMagick-6.8.0 >>>>>>>>>> >>>>>>>>>> SVN_REVISION 10029 >>>>>>>>>> >>>>>>>>>> TARGET_CPU x86_64 >>>>>>>>>> >>>>>>>>>> TARGET_OS darwin10.8.0 >>>>>>>>>> >>>>>>>>>> TARGET_VENDOR apple >>>>>>>>>> >>>>>>>>>> VERSION 6.8.0 >>>>>>>>>> >>>>>>>>>> WEBSITE http://www.imagemagick.org >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Path: [built-in] >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Name Value >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> ----------------------------------------------------------- -------------------- >>>>>>>>>> >>>>>>>>>> NAME ImageMagick >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Any help would be appreciated. Thanks >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> -- output of sessionInfo(): >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> R version 2.15.2 (2012-10-26) >>>>>>>>>> >>>>>>>>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> locale: >>>>>>>>>> >>>>>>>>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> attached base packages: >>>>>>>>>> >>>>>>>>>> [1] tools stats graphics grDevices utils datasets >>>>>>>>>> methods >>>>>>>>>> base >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> other attached packages: >>>>>>>>>> >>>>>>>>>> [1] latticeExtra_0.6-24 RColorBrewer_1.0-5 parody_1.16.0 >>>>>>>>>> bioDist_1.30.0 >>>>>>>>>> >>>>>>>>>> [5] KernSmooth_2.23-8 mvoutlier_1.9.9 sgeostat_1.0-25 >>>>>>>>>> robCompositions_1.6.3 >>>>>>>>>> >>>>>>>>>> [9] car_2.0-16 nnet_7.3-5 compositions_1.20-1 >>>>>>>>>> energy_1.4-0 >>>>>>>>>> >>>>>>>>>> [13] MASS_7.3-23 boot_1.3-7 tensorA_0.36 >>>>>>>>>> rgl_0.93.928 >>>>>>>>>> >>>>>>>>>> [17] flowViz_1.22.0 flowCore_1.24.2 rrcov_1.3-02 >>>>>>>>>> pcaPP_1.9-48 >>>>>>>>>> >>>>>>>>>> [21] mvtnorm_0.9-9994 robustbase_0.9-5 Biobase_2.18.0 >>>>>>>>>> lattice_0.20-13 >>>>>>>>>> >>>>>>>>>> [25] outliers_0.14 BiocGenerics_0.4.0 >>>>>>>>>> BiocInstaller_1.8.3 >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> loaded via a namespace (and not attached): >>>>>>>>>> >>>>>>>>>> [1] annotate_1.36.0 AnnotationDbi_1.20.5 DBI_0.2-5 >>>>>>>>>> feature_1.2.8 >>>>>>>>>> >>>>>>>>>> [5] flowQ_1.18.0 geneplotter_1.36.0 graph_1.36.2 >>>>>>>>>> grid_2.15.2 >>>>>>>>>> >>>>>>>>>> [9] hexbin_1.26.1 IDPmisc_1.1.17 IRanges_1.16.6 >>>>>>>>>> ks_1.8.11 >>>>>>>>>> >>>>>>>>>> [13] parallel_2.15.2 RSQLite_0.11.2 stats4_2.15.2 >>>>>>>>>> XML_3.95-0.1 >>>>>>>>>> >>>>>>>>>> [17] xtable_1.7-1 >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> >>>>>>>>>> Sent via the guest posting facility at bioconductor.org. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> >>>>>>>>>> Bioconductor mailing list >>>>>>>>>> >>>>>>>>>> Bioconductor at r-project.org >>>>>>>>>> >>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>>>>> >>>>>>>>>> Search the archives: >>>>>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Chandra Jack >>>>>>>>>> >>>>>>>>>> Postdoctoral Research Assoc. >>>>>>>>>> >>>>>>>>>> Dept. of Bioengineering >>>>>>>>>> >>>>>>>>>> Rice University >>>>>>>>>> >>>>>>>>>> chanj at rice.edu >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Chandra Jack >>>>>>>>>> Postdoctoral Research Assoc. >>>>>>>>>> Dept. of Bioengineering >>>>>>>>>> Rice University >>>>>>>>>> chanj at rice.edu >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> Chandra Jack >>>>>>>> Postdoctoral Research Assoc. >>>>>>>> Dept. of Bioengineering >>>>>>>> Rice University >>>>>>>> chanj at rice.edu >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>>> Chandra Jack >>>>>> Postdoctoral Research Assoc. >>>>>> Dept. of Bioengineering >>>>>> Rice University >>>>>> chanj at rice.edu >>>>>> >>>>>> >>>>>> >>>>> >>>> >>>> Chandra Jack >>>> Postdoctoral Research Assoc. >>>> Dept. of Bioengineering >>>> Rice University >>>> chanj at rice.edu >>>> >>>> >>>> >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >> > > Chandra Jack > Postdoctoral Research Assoc. > Dept. of Bioengineering > Rice University > chanj at rice.edu > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 6.7 years ago by Harris A. Jaffee590
I have removed the export and made sure that there are no spaces and still get the same message. On Mar 5, 2013, at 10:31 AM, Harris A. Jaffee wrote: > I haven't been listening too closely, but... > > Exactly what you wrote would have been a bash/sh syntax error. There cannot be spaces around the '='. If > you are on the right track, then you need something like > > PATH=$PATH:opt/local/bin > > While we are at it, I believe that resetting a variable that is already exported, as with PATH, does not > necessitate the 'export' command, in order to reset the exported value. For example, > > sh-3.2$ export foo=bar > sh-3.2$ env | grep foo > foo=bar > sh-3.2$ foo=bar2 > sh-3.2$ env | grep foo > foo=bar2 > > > On Mar 5, 2013, at 11:11 AM, Chandra Jack wrote: > >> I didn't have a ~/.profile so I created one. All I put in it was export PATH = $PATH:opt/local/bin. But I got the same message that /bin/sh: convert: command not found. I read that .bash_profile may need to call .profile and also tried putting source ~/.profile at the end of the file but that gave me the same message. >> >> >> On Mar 5, 2013, at 9:41 AM, Dan Tenenbaum wrote: >> >>> On Tue, Mar 5, 2013 at 12:21 AM, Nikolas Pontikos <n.pontikos@gmail.com> wrote: >>>> From your R error message, system is calling /bin/sh not /bin/bash (which >>>> should be the same program but i don't think sh reads the .bashrc config >>>> file). >>>> Maybe the convert command is not available from /bin/sh? >>> >>> >>> In that case the file to be edited is ~/.profile >>> >>> Dan >>> >>>> >>>> >>>> On 5 March 2013 06:42, Chandra Jack <chanj@rice.edu> wrote: >>>>> >>>>> Yes. I've been restarting R after everytime I changed bash_profile. I also >>>>> just tried reinstalling R but that didn't help either. >>>>> >>>>> On Mar 5, 2013, at 12:20 AM, Dan Tenenbaum wrote: >>>>> >>>>>> On Mon, Mar 4, 2013 at 10:06 PM, Chandra Jack <chanj@rice.edu> wrote: >>>>>>> >>>>>>> On Mar 4, 2013, at 11:57 PM, Dan Tenenbaum wrote: >>>>>>> >>>>>>>> On Mon, Mar 4, 2013 at 9:53 PM, Chandra Jack <chanj@rice.edu> wrote: >>>>>>>>> Thank you so much for your help. >>>>>>>>> >>>>>>>>> Chandra-Jacks-MacBook:~ chanj$ source ~/.bash_profile >>>>>>>>> Chandra-Jacks-MacBook:~ chanj$ echo $PATH >>>>>>>>> >>>>>>>>> /Library/Frameworks/Python.framework/Versions/2.7/bin:/Libra ry/Frameworks/EPD64.framework/Versions/Current/bin:/Library/Frameworks /Python.framework/Versions/2.7/bin:/Library/Frameworks/EPD64.framework /Versions/Current/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/us r/X11/bin:/opt/local/bin:/opt/local/bin >>>>>>>>> Chandra-Jacks-MacBook:~ chanj$ which convert >>>>>>>>> /opt/local/bin/convert >>>>>>>>> >>>>>>>> >>>>>>>> It looks like convert is in your PATH. >>>>>>>> >>>>>>>> What happens if you type >>>>>>>> convert >>>>>>>> at the terminal prompt? >>>>>>> >>>>>>> I think it opens ImageMagick >>>>>>> Chandra-Jacks-MacBook:~ chanj$ convert >>>>>>> Version: ImageMagick 6.8.0-7 2013-03-04 Q16 http://www.imagemagick.org >>>>>>> Copyright: Copyright (C) 1999-2012 ImageMagick Studio LLC >>>>>>> Features: OpenMP OpenCL >>>>>>> >>>>>>> Usage: convert [options ...] file [ [options ...] file ...] [options >>>>>>> ...] file >>>>>>> >>>>>>> Image Settings: >>>>>>> -adjoin join images into a single multi-image file >>>>>>> >>>>>>> etc.... >>>>>>> >>>>>>> >>>>>>> >>>>>>>> >>>>>>>> What if you go into R and type >>>>>>>> system("convert") >>>>>>>> ? >>>>>>>> >>>>>>> system("convert") >>>>>>> /bin/sh: convert: command not found >>>>>>> >>>>>> >>>>>> This means convert is in your path but R can't see it. Did you restart >>>>>> R after editing .bash_profile? >>>>>> >>>>>> Dan >>>>>> >>>>>> >>>>>>>> Dan >>>>>>>> >>>>>>>>> On Mar 4, 2013, at 11:45 PM, Dan Tenenbaum wrote: >>>>>>>>> >>>>>>>>>> On Mon, Mar 4, 2013 at 9:30 PM, Chandra Jack <chanj@rice.edu> wrote: >>>>>>>>>>> I replaced the original export line with the one you wrote but it >>>>>>>>>>> still >>>>>>>>>>> didn't work. >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> OK, at a terminal prompt, please enter the following commands and >>>>>>>>>> send >>>>>>>>>> me the output they produce: >>>>>>>>>> >>>>>>>>>> source ~/.bash_profile >>>>>>>>>> echo $PATH >>>>>>>>>> which convert >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> thanks, >>>>>>>>>> Dan >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>>> On Mar 4, 2013, at 10:18 PM, Dan Tenenbaum wrote: >>>>>>>>>>> >>>>>>>>>>> On Mon, Mar 4, 2013 at 8:07 PM, Chandra Jack <chanj@rice.edu> >>>>>>>>>>> wrote: >>>>>>>>>>> >>>>>>>>>>> The convert command isn't in my PATH but adding the newIt doesn't >>>>>>>>>>> seem to be >>>>>>>>>>> working. I don't have a .bashrc file but I have a .bash_profile. >>>>>>>>>>> The >>>>>>>>>>> original file was: >>>>>>>>>>> >>>>>>>>>>> # Setting PATH for EPD-7.1-2 >>>>>>>>>>> >>>>>>>>>>> # The orginal version is saved in .bash_profile.pysave >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> PATH="/Library/Frameworks/EPD64.framework/Versions/Current /bin:${PATH}" >>>>>>>>>>> >>>>>>>>>>> export PATH >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> MKL_NUM_THREADS=1 >>>>>>>>>>> >>>>>>>>>>> export MKL_NUM_THREADS >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> # Setting PATH for Python 2.7 >>>>>>>>>>> >>>>>>>>>>> # The orginal version is saved in .bash_profile.pysave >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> PATH="/Library/Frameworks/Python.framework/Versions/2.7/bin:${PATH}" >>>>>>>>>>> >>>>>>>>>>> export PATH >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> ## >>>>>>>>>>> >>>>>>>>>>> # Your previous /Users/chanj/.bash_profile file was backed up as >>>>>>>>>>> /Users/chanj/.bash_profile.macports- saved_2013-03-04_at_14:30:35 >>>>>>>>>>> >>>>>>>>>>> ## >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> # MacPorts Installer addition on 2013-03-04_at_14:30:35: adding an >>>>>>>>>>> appropriate PATH variable for use with MacPorts. >>>>>>>>>>> >>>>>>>>>>> export PATH=/opt/local/bin:/opt/local/sbin:$PATH >>>>>>>>>>> >>>>>>>>>>> # Finished adapting your PATH environment variable for use with >>>>>>>>>>> MacPorts. >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> I added PATH=$PATH:/opt/local/bin after the export line, resaved >>>>>>>>>>> the text >>>>>>>>>>> edit file and quit the terminal. When I checked Terminal again the >>>>>>>>>>> file was >>>>>>>>>>> updated but R couldn't find the command still. >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Sorry, it needs to say: >>>>>>>>>>> >>>>>>>>>>> export PATH=$PATH:/opt/local/bin >>>>>>>>>>> >>>>>>>>>>> I forgot the 'export' before. >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> I also tried adding it before the export line, replacing the part >>>>>>>>>>> after the >>>>>>>>>>> export line with it, adding quotation marks but nothing seemed to >>>>>>>>>>> work. I >>>>>>>>>>> went in and found the convert command file and it is in >>>>>>>>>>> opt/local/bin. I >>>>>>>>>>> tried Sys.which with another file that was in the same location and >>>>>>>>>>> R output >>>>>>>>>>> "/usr/bin/clear" . Could it be related to the backup file that was >>>>>>>>>>> created >>>>>>>>>>> before I changed it? >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> No, that just means there is a 'clear' executable in two locations. >>>>>>>>>>> Dan >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Thanks >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Mar 4, 2013, at 4:15 PM, Dan Tenenbaum wrote: >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Mon, Mar 4, 2013 at 2:09 PM, Chandra Jack [guest] >>>>>>>>>>> >>>>>>>>>>> <guest@bioconductor.org> wrote: >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Hi All, >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> I'm having a problem that has been mentioned here before but I'm >>>>>>>>>>> not sure >>>>>>>>>>> how to fix it. I tried to load flowQ and got: >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Error : .onAttach failed in attachNamespace() for 'flowQ', details: >>>>>>>>>>> >>>>>>>>>>> call: mysys("convert -list configure", intern = TRUE, ignore.stderr >>>>>>>>>>> = TRUE) >>>>>>>>>>> >>>>>>>>>>> error: error in running command >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Is the 'convert' command in your PATH? >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> What is the output of the R command: >>>>>>>>>>> >>>>>>>>>>> Sys.which("convert") >>>>>>>>>>> >>>>>>>>>>> ? >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> If it does not output anything, then the convert command is not in >>>>>>>>>>> your >>>>>>>>>>> PATH. >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> I'm not sure where the convert command ended up, but I'm guessing >>>>>>>>>>> it's >>>>>>>>>>> >>>>>>>>>>> in /opt/local/bin, >>>>>>>>>>> >>>>>>>>>>> so I think you need to edit your ~/.bashrc >>>>>>>>>>> >>>>>>>>>>> file and add the following line: >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> PATH=$PATH:/opt/local/bin >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Then, start a new terminal window to make sure this setting is >>>>>>>>>>> >>>>>>>>>>> enabled, and try again. >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Dan >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> In addition: Warning messages: >>>>>>>>>>> >>>>>>>>>>> 1: replacing previous import Œplot‚ when loading Œgraphics‚ >>>>>>>>>>> >>>>>>>>>>> 2: replacing previous import Œas‚ when loading Œmethods‚ >>>>>>>>>>> >>>>>>>>>>> Error: package/namespace load failed for ŒflowQ‚. >>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> I have installed ImageMagick using Macports as has been suggested >>>>>>>>>>> and I have >>>>>>>>>>> also run >>>>>>>>>>> >>>>>>>>>>> convert -list configure, which gave the following: >>>>>>>>>>> >>>>>>>>>>> Path: /opt/local/lib/ImageMagick-6.8.0/config/configure.xml >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Name Value >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> ---------------------------------------------------------- --------------------- >>>>>>>>>>> >>>>>>>>>>> CC /usr/bin/gcc-4.2 -std=gnu99 -std=gnu99 >>>>>>>>>>> >>>>>>>>>>> CFLAGS -D_THREAD_SAFE -D_THREAD_SAFE -pthread -fopenmp -pipe >>>>>>>>>>> -O2 >>>>>>>>>>> -arch x86_64 -Wall -D_THREAD_SAFE -pthread >>>>>>>>>>> >>>>>>>>>>> CODER_PATH /opt/local/lib/ImageMagick-6.8.0/modules-Q16/coders >>>>>>>>>>> >>>>>>>>>>> CONFIGURE ./configure '--prefix=/opt/local' '--enable-shared' >>>>>>>>>>> '--enable-static' '--disable-ltdl-install' '--disable- silent-rules' >>>>>>>>>>> '--with-frozenpaths' '--without-openexr' '--disable-hdri' >>>>>>>>>>> '--with-dps' >>>>>>>>>>> '--with-bzlib' '--with-fontconfig' '--with-gslib' '--with- jpeg' >>>>>>>>>>> '--with-lcms' '--with-png' '--with-tiff' '--with-webp' >>>>>>>>>>> '--with-zlib' >>>>>>>>>>> '--with-modules' '--with-xml' '--with-x' '--without-perl' >>>>>>>>>>> '--without-fpx' >>>>>>>>>>> '--without-jbig' '--without-jp2' '--without-wmf' '--without-gvc' >>>>>>>>>>> '--without-rsvg' '--without-lqr' '--without-pango' >>>>>>>>>>> '--with-gs-font-dir=/opt/local/share/fonts/urw-fonts' >>>>>>>>>>> '--with-quantum-depth=16' 'CC=/usr/bin/gcc-4.2' 'CFLAGS=-pipe -O2 >>>>>>>>>>> -arch >>>>>>>>>>> x86_64' 'LDFLAGS=-L/opt/local/lib -arch x86_64' >>>>>>>>>>> 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/g++-4.2' >>>>>>>>>>> 'CXXFLAGS=-pipe -O2 >>>>>>>>>>> -arch x86_64' >>>>>>>>>>> >>>>>>>>>>> CONFIGURE_PATH /opt/local/etc/ImageMagick/ >>>>>>>>>>> >>>>>>>>>>> COPYRIGHT Copyright (C) 1999-2012 ImageMagick Studio LLC >>>>>>>>>>> >>>>>>>>>>> CPPFLAGS -I/opt/local/include/ImageMagick >>>>>>>>>>> >>>>>>>>>>> CXX /usr/bin/g++-4.2 >>>>>>>>>>> >>>>>>>>>>> CXXFLAGS -pipe -O2 -arch x86_64 -D_THREAD_SAFE -pthread >>>>>>>>>>> >>>>>>>>>>> DEFS -DHAVE_CONFIG_H >>>>>>>>>>> >>>>>>>>>>> DELEGATES bzlib fftw fontconfig freetype gs jpeg jng lcms2 lzma >>>>>>>>>>> png tiff >>>>>>>>>>> x11 xml zlib >>>>>>>>>>> >>>>>>>>>>> DISTCHECK_CONFIG_FLAGS 'CC=/usr/bin/gcc-4.2' 'CFLAGS=-pipe -O2 >>>>>>>>>>> -arch x86_64' >>>>>>>>>>> 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/g++-4.2' >>>>>>>>>>> 'LDFLAGS=-L/opt/local/lib -arch x86_64' --disable- deprecated >>>>>>>>>>> --with-quantum-depth=16 --with-umem=no --with-autotrace=no >>>>>>>>>>> --with-fpx=no >>>>>>>>>>> --with-fontpath= >>>>>>>>>>> --with-gs-font-dir=/opt/local/share/fonts/urw-fonts >>>>>>>>>>> --with-gvc=no --with-jp2=no --with-lqr=no --with- openexr=no >>>>>>>>>>> --with-pango=no >>>>>>>>>>> --with-rsvg=no --with-wmf=no --with-perl=no >>>>>>>>>>> >>>>>>>>>>> DOCUMENTATION_PATH /opt/local/share/doc/ImageMagick-6.8.0 >>>>>>>>>>> >>>>>>>>>>> EXEC-PREFIX /opt/local >>>>>>>>>>> >>>>>>>>>>> EXECUTABLE_PATH /opt/local/bin >>>>>>>>>>> >>>>>>>>>>> FEATURES OpenCL OpenMP >>>>>>>>>>> >>>>>>>>>>> FILTER_PATH /opt/local/lib/ImageMagick-6.8.0/modules-Q16/filters >>>>>>>>>>> >>>>>>>>>>> HOST x86_64-apple-darwin10.8.0 >>>>>>>>>>> >>>>>>>>>>> INCLUDE_PATH /opt/local/include/ImageMagick >>>>>>>>>>> >>>>>>>>>>> LDFLAGS -L/opt/local/lib -L/opt/local/lib -arch x86_64 >>>>>>>>>>> -L/opt/local/lib -L/opt/local/lib >>>>>>>>>>> >>>>>>>>>>> LIB_VERSION 0x680 >>>>>>>>>>> >>>>>>>>>>> LIB_VERSION_NUMBER 6,8,0,7 >>>>>>>>>>> >>>>>>>>>>> LIBRARY_PATH /opt/local/lib/ImageMagick-6.8.0 >>>>>>>>>>> >>>>>>>>>>> LIBS -lMagickCore -llcms2 -lfreetype -lfftw3 >>>>>>>>>>> -L/opt/local/lib >>>>>>>>>>> -lfontconfig -lXext -lSM -lICE -lX11 -lXt -L/opt/local/lib -llzma >>>>>>>>>>> -lbz2 -lz >>>>>>>>>>> -lltdl -lm -lgomp -lclparser -Wl,-framework,OpenCL >>>>>>>>>>> -L/System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries >>>>>>>>>>> -lm >>>>>>>>>>> -lpthread >>>>>>>>>>> >>>>>>>>>>> NAME ImageMagick >>>>>>>>>>> >>>>>>>>>>> PCFLAGS -fopenmp >>>>>>>>>>> >>>>>>>>>>> PREFIX /opt/local >>>>>>>>>>> >>>>>>>>>>> QuantumDepth 16 >>>>>>>>>>> >>>>>>>>>>> RELEASE_DATE 2013-03-04 >>>>>>>>>>> >>>>>>>>>>> SHARE_PATH /opt/local/share/ImageMagick-6.8.0 >>>>>>>>>>> >>>>>>>>>>> SVN_REVISION 10029 >>>>>>>>>>> >>>>>>>>>>> TARGET_CPU x86_64 >>>>>>>>>>> >>>>>>>>>>> TARGET_OS darwin10.8.0 >>>>>>>>>>> >>>>>>>>>>> TARGET_VENDOR apple >>>>>>>>>>> >>>>>>>>>>> VERSION 6.8.0 >>>>>>>>>>> >>>>>>>>>>> WEBSITE http://www.imagemagick.org >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Path: [built-in] >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Name Value >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> ---------------------------------------------------------- --------------------- >>>>>>>>>>> >>>>>>>>>>> NAME ImageMagick >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Any help would be appreciated. Thanks >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> -- output of sessionInfo(): >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> R version 2.15.2 (2012-10-26) >>>>>>>>>>> >>>>>>>>>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> locale: >>>>>>>>>>> >>>>>>>>>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> attached base packages: >>>>>>>>>>> >>>>>>>>>>> [1] tools stats graphics grDevices utils datasets >>>>>>>>>>> methods >>>>>>>>>>> base >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> other attached packages: >>>>>>>>>>> >>>>>>>>>>> [1] latticeExtra_0.6-24 RColorBrewer_1.0-5 parody_1.16.0 >>>>>>>>>>> bioDist_1.30.0 >>>>>>>>>>> >>>>>>>>>>> [5] KernSmooth_2.23-8 mvoutlier_1.9.9 sgeostat_1.0-25 >>>>>>>>>>> robCompositions_1.6.3 >>>>>>>>>>> >>>>>>>>>>> [9] car_2.0-16 nnet_7.3-5 compositions_1.20-1 >>>>>>>>>>> energy_1.4-0 >>>>>>>>>>> >>>>>>>>>>> [13] MASS_7.3-23 boot_1.3-7 tensorA_0.36 >>>>>>>>>>> rgl_0.93.928 >>>>>>>>>>> >>>>>>>>>>> [17] flowViz_1.22.0 flowCore_1.24.2 rrcov_1.3-02 >>>>>>>>>>> pcaPP_1.9-48 >>>>>>>>>>> >>>>>>>>>>> [21] mvtnorm_0.9-9994 robustbase_0.9-5 Biobase_2.18.0 >>>>>>>>>>> lattice_0.20-13 >>>>>>>>>>> >>>>>>>>>>> [25] outliers_0.14 BiocGenerics_0.4.0 >>>>>>>>>>> BiocInstaller_1.8.3 >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> loaded via a namespace (and not attached): >>>>>>>>>>> >>>>>>>>>>> [1] annotate_1.36.0 AnnotationDbi_1.20.5 DBI_0.2-5 >>>>>>>>>>> feature_1.2.8 >>>>>>>>>>> >>>>>>>>>>> [5] flowQ_1.18.0 geneplotter_1.36.0 graph_1.36.2 >>>>>>>>>>> grid_2.15.2 >>>>>>>>>>> >>>>>>>>>>> [9] hexbin_1.26.1 IDPmisc_1.1.17 IRanges_1.16.6 >>>>>>>>>>> ks_1.8.11 >>>>>>>>>>> >>>>>>>>>>> [13] parallel_2.15.2 RSQLite_0.11.2 stats4_2.15.2 >>>>>>>>>>> XML_3.95-0.1 >>>>>>>>>>> >>>>>>>>>>> [17] xtable_1.7-1 >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> >>>>>>>>>>> Sent via the guest posting facility at bioconductor.org. >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> >>>>>>>>>>> Bioconductor mailing list >>>>>>>>>>> >>>>>>>>>>> Bioconductor@r-project.org >>>>>>>>>>> >>>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>>>>>> >>>>>>>>>>> Search the archives: >>>>>>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Chandra Jack >>>>>>>>>>> >>>>>>>>>>> Postdoctoral Research Assoc. >>>>>>>>>>> >>>>>>>>>>> Dept. of Bioengineering >>>>>>>>>>> >>>>>>>>>>> Rice University >>>>>>>>>>> >>>>>>>>>>> chanj@rice.edu >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Chandra Jack >>>>>>>>>>> Postdoctoral Research Assoc. >>>>>>>>>>> Dept. of Bioengineering >>>>>>>>>>> Rice University >>>>>>>>>>> chanj@rice.edu >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>>> Chandra Jack >>>>>>>>> Postdoctoral Research Assoc. >>>>>>>>> Dept. of Bioengineering >>>>>>>>> Rice University >>>>>>>>> chanj@rice.edu >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>> >>>>>>> Chandra Jack >>>>>>> Postdoctoral Research Assoc. >>>>>>> Dept. of Bioengineering >>>>>>> Rice University >>>>>>> chanj@rice.edu >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>> >>>>> Chandra Jack >>>>> Postdoctoral Research Assoc. >>>>> Dept. of Bioengineering >>>>> Rice University >>>>> chanj@rice.edu >>>>> >>>>> >>>>> >>>>> >>>>> [[alternative HTML version deleted]] >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor@r-project.org >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: >>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>>> >>> >> >> Chandra Jack >> Postdoctoral Research Assoc. >> Dept. of Bioengineering >> Rice University >> chanj@rice.edu >> >> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > Chandra Jack Postdoctoral Research Assoc. Dept. of Bioengineering Rice University chanj@rice.edu [[alternative HTML version deleted]]
ADD REPLYlink written 6.7 years ago by Chandra Jack90
I got the following steps to work on a machine similar to yours. This is not a recommended long term solution but I'd be interested to see if it works for you. in R: path <- Sys.getenv("PATH") path # let me know what this says Sys.setenv(PATH=paste0(path, ":", "/opt/local/bin")) library(flowQ) Dan On Tue, Mar 5, 2013 at 8:49 AM, Chandra Jack <chanj at="" rice.edu=""> wrote: > I have removed the export and made sure that there are no spaces and still > get the same message. > > On Mar 5, 2013, at 10:31 AM, Harris A. Jaffee wrote: > > I haven't been listening too closely, but... > > Exactly what you wrote would have been a bash/sh syntax error. There cannot > be spaces around the '='. If > you are on the right track, then you need something like > > PATH=$PATH:opt/local/bin > > While we are at it, I believe that resetting a variable that is already > exported, as with PATH, does not > necessitate the 'export' command, in order to reset the exported value. For > example, > > sh-3.2$ export foo=bar > sh-3.2$ env | grep foo > foo=bar > sh-3.2$ foo=bar2 > sh-3.2$ env | grep foo > foo=bar2 > > > On Mar 5, 2013, at 11:11 AM, Chandra Jack wrote: > > I didn't have a ~/.profile so I created one. All I put in it was export PATH > = $PATH:opt/local/bin. But I got the same message that /bin/sh: convert: > command not found. I read that .bash_profile may need to call .profile and > also tried putting source ~/.profile at the end of the file but that gave me > the same message. > > > > On Mar 5, 2013, at 9:41 AM, Dan Tenenbaum wrote: > > > On Tue, Mar 5, 2013 at 12:21 AM, Nikolas Pontikos <n.pontikos at="" gmail.com=""> > wrote: > > From your R error message, system is calling /bin/sh not /bin/bash (which > > should be the same program but i don't think sh reads the .bashrc config > > file). > > Maybe the convert command is not available from /bin/sh? > > > > In that case the file to be edited is ~/.profile > > > Dan > > > > > On 5 March 2013 06:42, Chandra Jack <chanj at="" rice.edu=""> wrote: > > > Yes. I've been restarting R after everytime I changed bash_profile. I also > > just tried reinstalling R but that didn't help either. > > > On Mar 5, 2013, at 12:20 AM, Dan Tenenbaum wrote: > > > On Mon, Mar 4, 2013 at 10:06 PM, Chandra Jack <chanj at="" rice.edu=""> wrote: > > > On Mar 4, 2013, at 11:57 PM, Dan Tenenbaum wrote: > > > On Mon, Mar 4, 2013 at 9:53 PM, Chandra Jack <chanj at="" rice.edu=""> wrote: > > Thank you so much for your help. > > > Chandra-Jacks-MacBook:~ chanj$ source ~/.bash_profile > > Chandra-Jacks-MacBook:~ chanj$ echo $PATH > > > /Library/Frameworks/Python.framework/Versions/2.7/bin:/Library/Frame works/EPD64.framework/Versions/Current/bin:/Library/Frameworks/Python. framework/Versions/2.7/bin:/Library/Frameworks/EPD64.framework/Version s/Current/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bi n:/opt/local/bin:/opt/local/bin > > Chandra-Jacks-MacBook:~ chanj$ which convert > > /opt/local/bin/convert > > > > It looks like convert is in your PATH. > > > What happens if you type > > convert > > at the terminal prompt? > > > I think it opens ImageMagick > > Chandra-Jacks-MacBook:~ chanj$ convert > > Version: ImageMagick 6.8.0-7 2013-03-04 Q16 http://www.imagemagick.org > > Copyright: Copyright (C) 1999-2012 ImageMagick Studio LLC > > Features: OpenMP OpenCL > > > Usage: convert [options ...] file [ [options ...] file ...] [options > > ...] file > > > Image Settings: > > -adjoin join images into a single multi-image file > > > etc.... > > > > > > What if you go into R and type > > system("convert") > > ? > > > system("convert") > > /bin/sh: convert: command not found > > > > This means convert is in your path but R can't see it. Did you restart > > R after editing .bash_profile? > > > Dan > > > > Dan > > > On Mar 4, 2013, at 11:45 PM, Dan Tenenbaum wrote: > > > On Mon, Mar 4, 2013 at 9:30 PM, Chandra Jack <chanj at="" rice.edu=""> wrote: > > I replaced the original export line with the one you wrote but it > > still > > didn't work. > > > > OK, at a terminal prompt, please enter the following commands and > > send > > me the output they produce: > > > source ~/.bash_profile > > echo $PATH > > which convert > > > > > thanks, > > Dan > > > > > On Mar 4, 2013, at 10:18 PM, Dan Tenenbaum wrote: > > > On Mon, Mar 4, 2013 at 8:07 PM, Chandra Jack <chanj at="" rice.edu=""> > > wrote: > > > The convert command isn't in my PATH but adding the newIt doesn't > > seem to be > > working. I don't have a .bashrc file but I have a .bash_profile. > > The > > original file was: > > > # Setting PATH for EPD-7.1-2 > > > # The orginal version is saved in .bash_profile.pysave > > > > PATH="/Library/Frameworks/EPD64.framework/Versions/Current/bin:${PAT H}" > > > export PATH > > > > MKL_NUM_THREADS=1 > > > export MKL_NUM_THREADS > > > > # Setting PATH for Python 2.7 > > > # The orginal version is saved in .bash_profile.pysave > > > > PATH="/Library/Frameworks/Python.framework/Versions/2.7/bin:${PATH}" > > > export PATH > > > > ## > > > # Your previous /Users/chanj/.bash_profile file was backed up as > > /Users/chanj/.bash_profile.macports-saved_2013-03-04_at_14:30:35 > > > ## > > > > # MacPorts Installer addition on 2013-03-04_at_14:30:35: adding an > > appropriate PATH variable for use with MacPorts. > > > export PATH=/opt/local/bin:/opt/local/sbin:$PATH > > > # Finished adapting your PATH environment variable for use with > > MacPorts. > > > > I added PATH=$PATH:/opt/local/bin after the export line, resaved > > the text > > edit file and quit the terminal. When I checked Terminal again the > > file was > > updated but R couldn't find the command still. > > > > Sorry, it needs to say: > > > export PATH=$PATH:/opt/local/bin > > > I forgot the 'export' before. > > > > > > > > I also tried adding it before the export line, replacing the part > > after the > > export line with it, adding quotation marks but nothing seemed to > > work. I > > went in and found the convert command file and it is in > > opt/local/bin. I > > tried Sys.which with another file that was in the same location and > > R output > > "/usr/bin/clear" . Could it be related to the backup file that was > > created > > before I changed it? > > > > No, that just means there is a 'clear' executable in two locations. > > Dan > > > > > Thanks > > > > On Mar 4, 2013, at 4:15 PM, Dan Tenenbaum wrote: > > > > On Mon, Mar 4, 2013 at 2:09 PM, Chandra Jack [guest] > > > <guest at="" bioconductor.org=""> wrote: > > > > Hi All, > > > > I'm having a problem that has been mentioned here before but I'm > > not sure > > how to fix it. I tried to load flowQ and got: > > > > Error : .onAttach failed in attachNamespace() for 'flowQ', details: > > > call: mysys("convert -list configure", intern = TRUE, ignore.stderr > > = TRUE) > > > error: error in running command > > > > Is the 'convert' command in your PATH? > > > > What is the output of the R command: > > > Sys.which("convert") > > > ? > > > > If it does not output anything, then the convert command is not in > > your > > PATH. > > > > I'm not sure where the convert command ended up, but I'm guessing > > it's > > > in /opt/local/bin, > > > so I think you need to edit your ~/.bashrc > > > file and add the following line: > > > > PATH=$PATH:/opt/local/bin > > > > Then, start a new terminal window to make sure this setting is > > > enabled, and try again. > > > > Dan > > > > > In addition: Warning messages: > > > 1: replacing previous import ?plot? when loading ?graphics? > > > 2: replacing previous import ?as? when loading ?methods? > > > Error: package/namespace load failed for ?flowQ?. > > > > > I have installed ImageMagick using Macports as has been suggested > > and I have > > also run > > > convert -list configure, which gave the following: > > > Path: /opt/local/lib/ImageMagick-6.8.0/config/configure.xml > > > > Name Value > > > > -------------------------------------------------------------------- ----------- > > > CC /usr/bin/gcc-4.2 -std=gnu99 -std=gnu99 > > > CFLAGS -D_THREAD_SAFE -D_THREAD_SAFE -pthread -fopenmp -pipe > > -O2 > > -arch x86_64 -Wall -D_THREAD_SAFE -pthread > > > CODER_PATH /opt/local/lib/ImageMagick-6.8.0/modules-Q16/coders > > > CONFIGURE ./configure '--prefix=/opt/local' '--enable-shared' > > '--enable-static' '--disable-ltdl-install' '--disable-silent-rules' > > '--with-frozenpaths' '--without-openexr' '--disable-hdri' > > '--with-dps' > > '--with-bzlib' '--with-fontconfig' '--with-gslib' '--with-jpeg' > > '--with-lcms' '--with-png' '--with-tiff' '--with-webp' > > '--with-zlib' > > '--with-modules' '--with-xml' '--with-x' '--without-perl' > > '--without-fpx' > > '--without-jbig' '--without-jp2' '--without-wmf' '--without-gvc' > > '--without-rsvg' '--without-lqr' '--without-pango' > > '--with-gs-font-dir=/opt/local/share/fonts/urw-fonts' > > '--with-quantum-depth=16' 'CC=/usr/bin/gcc-4.2' 'CFLAGS=-pipe -O2 > > -arch > > x86_64' 'LDFLAGS=-L/opt/local/lib -arch x86_64' > > 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/g++-4.2' > > 'CXXFLAGS=-pipe -O2 > > -arch x86_64' > > > CONFIGURE_PATH /opt/local/etc/ImageMagick/ > > > COPYRIGHT Copyright (C) 1999-2012 ImageMagick Studio LLC > > > CPPFLAGS -I/opt/local/include/ImageMagick > > > CXX /usr/bin/g++-4.2 > > > CXXFLAGS -pipe -O2 -arch x86_64 -D_THREAD_SAFE -pthread > > > DEFS -DHAVE_CONFIG_H > > > DELEGATES bzlib fftw fontconfig freetype gs jpeg jng lcms2 lzma > > png tiff > > x11 xml zlib > > > DISTCHECK_CONFIG_FLAGS 'CC=/usr/bin/gcc-4.2' 'CFLAGS=-pipe -O2 > > -arch x86_64' > > 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/g++-4.2' > > 'LDFLAGS=-L/opt/local/lib -arch x86_64' --disable-deprecated > > --with-quantum-depth=16 --with-umem=no --with-autotrace=no > > --with-fpx=no > > --with-fontpath= > > --with-gs-font-dir=/opt/local/share/fonts/urw-fonts > > --with-gvc=no --with-jp2=no --with-lqr=no --with-openexr=no > > --with-pango=no > > --with-rsvg=no --with-wmf=no --with-perl=no > > > DOCUMENTATION_PATH /opt/local/share/doc/ImageMagick-6.8.0 > > > EXEC-PREFIX /opt/local > > > EXECUTABLE_PATH /opt/local/bin > > > FEATURES OpenCL OpenMP > > > FILTER_PATH /opt/local/lib/ImageMagick-6.8.0/modules-Q16/filters > > > HOST x86_64-apple-darwin10.8.0 > > > INCLUDE_PATH /opt/local/include/ImageMagick > > > LDFLAGS -L/opt/local/lib -L/opt/local/lib -arch x86_64 > > -L/opt/local/lib -L/opt/local/lib > > > LIB_VERSION 0x680 > > > LIB_VERSION_NUMBER 6,8,0,7 > > > LIBRARY_PATH /opt/local/lib/ImageMagick-6.8.0 > > > LIBS -lMagickCore -llcms2 -lfreetype -lfftw3 > > -L/opt/local/lib > > -lfontconfig -lXext -lSM -lICE -lX11 -lXt -L/opt/local/lib -llzma > > -lbz2 -lz > > -lltdl -lm -lgomp -lclparser -Wl,-framework,OpenCL > > -L/System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries > > -lm > > -lpthread > > > NAME ImageMagick > > > PCFLAGS -fopenmp > > > PREFIX /opt/local > > > QuantumDepth 16 > > > RELEASE_DATE 2013-03-04 > > > SHARE_PATH /opt/local/share/ImageMagick-6.8.0 > > > SVN_REVISION 10029 > > > TARGET_CPU x86_64 > > > TARGET_OS darwin10.8.0 > > > TARGET_VENDOR apple > > > VERSION 6.8.0 > > > WEBSITE http://www.imagemagick.org > > > > Path: [built-in] > > > > Name Value > > > > -------------------------------------------------------------------- ----------- > > > NAME ImageMagick > > > > Any help would be appreciated. Thanks > > > > -- output of sessionInfo(): > > > > R version 2.15.2 (2012-10-26) > > > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > > > locale: > > > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > > > attached base packages: > > > [1] tools stats graphics grDevices utils datasets > > methods > > base > > > > other attached packages: > > > [1] latticeExtra_0.6-24 RColorBrewer_1.0-5 parody_1.16.0 > > bioDist_1.30.0 > > > [5] KernSmooth_2.23-8 mvoutlier_1.9.9 sgeostat_1.0-25 > > robCompositions_1.6.3 > > > [9] car_2.0-16 nnet_7.3-5 compositions_1.20-1 > > energy_1.4-0 > > > [13] MASS_7.3-23 boot_1.3-7 tensorA_0.36 > > rgl_0.93.928 > > > [17] flowViz_1.22.0 flowCore_1.24.2 rrcov_1.3-02 > > pcaPP_1.9-48 > > > [21] mvtnorm_0.9-9994 robustbase_0.9-5 Biobase_2.18.0 > > lattice_0.20-13 > > > [25] outliers_0.14 BiocGenerics_0.4.0 > > BiocInstaller_1.8.3 > > > > loaded via a namespace (and not attached): > > > [1] annotate_1.36.0 AnnotationDbi_1.20.5 DBI_0.2-5 > > feature_1.2.8 > > > [5] flowQ_1.18.0 geneplotter_1.36.0 graph_1.36.2 > > grid_2.15.2 > > > [9] hexbin_1.26.1 IDPmisc_1.1.17 IRanges_1.16.6 > > ks_1.8.11 > > > [13] parallel_2.15.2 RSQLite_0.11.2 stats4_2.15.2 > > XML_3.95-0.1 > > > [17] xtable_1.7-1 > > > > -- > > > Sent via the guest posting facility at bioconductor.org. > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor at r-project.org > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > Chandra Jack > > > Postdoctoral Research Assoc. > > > Dept. of Bioengineering > > > Rice University > > > chanj at rice.edu > > > > > > > > Chandra Jack > > Postdoctoral Research Assoc. > > Dept. of Bioengineering > > Rice University > > chanj at rice.edu > > > > > > > Chandra Jack > > Postdoctoral Research Assoc. > > Dept. of Bioengineering > > Rice University > > chanj at rice.edu > > > > > > > Chandra Jack > > Postdoctoral Research Assoc. > > Dept. of Bioengineering > > Rice University > > chanj at rice.edu > > > > > > > Chandra Jack > > Postdoctoral Research Assoc. > > Dept. of Bioengineering > > Rice University > > chanj at rice.edu > > > > > > [[alternative HTML version deleted]] > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > Chandra Jack > > Postdoctoral Research Assoc. > > Dept. of Bioengineering > > Rice University > > chanj at rice.edu > > > > > > [[alternative HTML version deleted]] > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > Chandra Jack > Postdoctoral Research Assoc. > Dept. of Bioengineering > Rice University > chanj at rice.edu > > >
ADD REPLYlink written 6.7 years ago by Dan Tenenbaum8.2k
It works! Thanks so much for your help! path <- Sys.getenv("PATH") > path [1] "/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin" Why is is not a recommended long term solution? Will I need to call path each time I tried to load flowQ? On Mar 5, 2013, at 11:26 AM, Dan Tenenbaum wrote: > I got the following steps to work on a machine similar to yours. This > is not a recommended long term solution but I'd be interested to see > if it works for you. > > in R: > path <- Sys.getenv("PATH") > path # let me know what this says > Sys.setenv(PATH=paste0(path, ":", "/opt/local/bin")) > library(flowQ) > > Dan > > > On Tue, Mar 5, 2013 at 8:49 AM, Chandra Jack <chanj at="" rice.edu=""> wrote: >> I have removed the export and made sure that there are no spaces and still >> get the same message. >> >> On Mar 5, 2013, at 10:31 AM, Harris A. Jaffee wrote: >> >> I haven't been listening too closely, but... >> >> Exactly what you wrote would have been a bash/sh syntax error. There cannot >> be spaces around the '='. If >> you are on the right track, then you need something like >> >> PATH=$PATH:opt/local/bin >> >> While we are at it, I believe that resetting a variable that is already >> exported, as with PATH, does not >> necessitate the 'export' command, in order to reset the exported value. For >> example, >> >> sh-3.2$ export foo=bar >> sh-3.2$ env | grep foo >> foo=bar >> sh-3.2$ foo=bar2 >> sh-3.2$ env | grep foo >> foo=bar2 >> >> >> On Mar 5, 2013, at 11:11 AM, Chandra Jack wrote: >> >> I didn't have a ~/.profile so I created one. All I put in it was export PATH >> = $PATH:opt/local/bin. But I got the same message that /bin/sh: convert: >> command not found. I read that .bash_profile may need to call .profile and >> also tried putting source ~/.profile at the end of the file but that gave me >> the same message. >> >> >> >> On Mar 5, 2013, at 9:41 AM, Dan Tenenbaum wrote: >> >> >> On Tue, Mar 5, 2013 at 12:21 AM, Nikolas Pontikos <n.pontikos at="" gmail.com=""> >> wrote: >> >> From your R error message, system is calling /bin/sh not /bin/bash (which >> >> should be the same program but i don't think sh reads the .bashrc config >> >> file). >> >> Maybe the convert command is not available from /bin/sh? >> >> >> >> In that case the file to be edited is ~/.profile >> >> >> Dan >> >> >> >> >> On 5 March 2013 06:42, Chandra Jack <chanj at="" rice.edu=""> wrote: >> >> >> Yes. I've been restarting R after everytime I changed bash_profile. I also >> >> just tried reinstalling R but that didn't help either. >> >> >> On Mar 5, 2013, at 12:20 AM, Dan Tenenbaum wrote: >> >> >> On Mon, Mar 4, 2013 at 10:06 PM, Chandra Jack <chanj at="" rice.edu=""> wrote: >> >> >> On Mar 4, 2013, at 11:57 PM, Dan Tenenbaum wrote: >> >> >> On Mon, Mar 4, 2013 at 9:53 PM, Chandra Jack <chanj at="" rice.edu=""> wrote: >> >> Thank you so much for your help. >> >> >> Chandra-Jacks-MacBook:~ chanj$ source ~/.bash_profile >> >> Chandra-Jacks-MacBook:~ chanj$ echo $PATH >> >> >> /Library/Frameworks/Python.framework/Versions/2.7/bin:/Library/Fram eworks/EPD64.framework/Versions/Current/bin:/Library/Frameworks/Python .framework/Versions/2.7/bin:/Library/Frameworks/EPD64.framework/Versio ns/Current/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/b in:/opt/local/bin:/opt/local/bin >> >> Chandra-Jacks-MacBook:~ chanj$ which convert >> >> /opt/local/bin/convert >> >> >> >> It looks like convert is in your PATH. >> >> >> What happens if you type >> >> convert >> >> at the terminal prompt? >> >> >> I think it opens ImageMagick >> >> Chandra-Jacks-MacBook:~ chanj$ convert >> >> Version: ImageMagick 6.8.0-7 2013-03-04 Q16 http://www.imagemagick.org >> >> Copyright: Copyright (C) 1999-2012 ImageMagick Studio LLC >> >> Features: OpenMP OpenCL >> >> >> Usage: convert [options ...] file [ [options ...] file ...] [options >> >> ...] file >> >> >> Image Settings: >> >> -adjoin join images into a single multi-image file >> >> >> etc.... >> >> >> >> >> >> What if you go into R and type >> >> system("convert") >> >> ? >> >> >> system("convert") >> >> /bin/sh: convert: command not found >> >> >> >> This means convert is in your path but R can't see it. Did you restart >> >> R after editing .bash_profile? >> >> >> Dan >> >> >> >> Dan >> >> >> On Mar 4, 2013, at 11:45 PM, Dan Tenenbaum wrote: >> >> >> On Mon, Mar 4, 2013 at 9:30 PM, Chandra Jack <chanj at="" rice.edu=""> wrote: >> >> I replaced the original export line with the one you wrote but it >> >> still >> >> didn't work. >> >> >> >> OK, at a terminal prompt, please enter the following commands and >> >> send >> >> me the output they produce: >> >> >> source ~/.bash_profile >> >> echo $PATH >> >> which convert >> >> >> >> >> thanks, >> >> Dan >> >> >> >> >> On Mar 4, 2013, at 10:18 PM, Dan Tenenbaum wrote: >> >> >> On Mon, Mar 4, 2013 at 8:07 PM, Chandra Jack <chanj at="" rice.edu=""> >> >> wrote: >> >> >> The convert command isn't in my PATH but adding the newIt doesn't >> >> seem to be >> >> working. I don't have a .bashrc file but I have a .bash_profile. >> >> The >> >> original file was: >> >> >> # Setting PATH for EPD-7.1-2 >> >> >> # The orginal version is saved in .bash_profile.pysave >> >> >> >> PATH="/Library/Frameworks/EPD64.framework/Versions/Current/bin:${PA TH}" >> >> >> export PATH >> >> >> >> MKL_NUM_THREADS=1 >> >> >> export MKL_NUM_THREADS >> >> >> >> # Setting PATH for Python 2.7 >> >> >> # The orginal version is saved in .bash_profile.pysave >> >> >> >> PATH="/Library/Frameworks/Python.framework/Versions/2.7/bin:${PATH}" >> >> >> export PATH >> >> >> >> ## >> >> >> # Your previous /Users/chanj/.bash_profile file was backed up as >> >> /Users/chanj/.bash_profile.macports-saved_2013-03-04_at_14:30:35 >> >> >> ## >> >> >> >> # MacPorts Installer addition on 2013-03-04_at_14:30:35: adding an >> >> appropriate PATH variable for use with MacPorts. >> >> >> export PATH=/opt/local/bin:/opt/local/sbin:$PATH >> >> >> # Finished adapting your PATH environment variable for use with >> >> MacPorts. >> >> >> >> I added PATH=$PATH:/opt/local/bin after the export line, resaved >> >> the text >> >> edit file and quit the terminal. When I checked Terminal again the >> >> file was >> >> updated but R couldn't find the command still. >> >> >> >> Sorry, it needs to say: >> >> >> export PATH=$PATH:/opt/local/bin >> >> >> I forgot the 'export' before. >> >> >> >> >> >> >> >> I also tried adding it before the export line, replacing the part >> >> after the >> >> export line with it, adding quotation marks but nothing seemed to >> >> work. I >> >> went in and found the convert command file and it is in >> >> opt/local/bin. I >> >> tried Sys.which with another file that was in the same location and >> >> R output >> >> "/usr/bin/clear" . Could it be related to the backup file that was >> >> created >> >> before I changed it? >> >> >> >> No, that just means there is a 'clear' executable in two locations. >> >> Dan >> >> >> >> >> Thanks >> >> >> >> On Mar 4, 2013, at 4:15 PM, Dan Tenenbaum wrote: >> >> >> >> On Mon, Mar 4, 2013 at 2:09 PM, Chandra Jack [guest] >> >> >> <guest at="" bioconductor.org=""> wrote: >> >> >> >> Hi All, >> >> >> >> I'm having a problem that has been mentioned here before but I'm >> >> not sure >> >> how to fix it. I tried to load flowQ and got: >> >> >> >> Error : .onAttach failed in attachNamespace() for 'flowQ', details: >> >> >> call: mysys("convert -list configure", intern = TRUE, ignore.stderr >> >> = TRUE) >> >> >> error: error in running command >> >> >> >> Is the 'convert' command in your PATH? >> >> >> >> What is the output of the R command: >> >> >> Sys.which("convert") >> >> >> ? >> >> >> >> If it does not output anything, then the convert command is not in >> >> your >> >> PATH. >> >> >> >> I'm not sure where the convert command ended up, but I'm guessing >> >> it's >> >> >> in /opt/local/bin, >> >> >> so I think you need to edit your ~/.bashrc >> >> >> file and add the following line: >> >> >> >> PATH=$PATH:/opt/local/bin >> >> >> >> Then, start a new terminal window to make sure this setting is >> >> >> enabled, and try again. >> >> >> >> Dan >> >> >> >> >> In addition: Warning messages: >> >> >> 1: replacing previous import ?plot? when loading ?graphics? >> >> >> 2: replacing previous import ?as? when loading ?methods? >> >> >> Error: package/namespace load failed for ?flowQ?. >> >> >> >> >> I have installed ImageMagick using Macports as has been suggested >> >> and I have >> >> also run >> >> >> convert -list configure, which gave the following: >> >> >> Path: /opt/local/lib/ImageMagick-6.8.0/config/configure.xml >> >> >> >> Name Value >> >> >> >> ------------------------------------------------------------------- ------------ >> >> >> CC /usr/bin/gcc-4.2 -std=gnu99 -std=gnu99 >> >> >> CFLAGS -D_THREAD_SAFE -D_THREAD_SAFE -pthread -fopenmp -pipe >> >> -O2 >> >> -arch x86_64 -Wall -D_THREAD_SAFE -pthread >> >> >> CODER_PATH /opt/local/lib/ImageMagick-6.8.0/modules-Q16/coders >> >> >> CONFIGURE ./configure '--prefix=/opt/local' '--enable-shared' >> >> '--enable-static' '--disable-ltdl-install' '--disable-silent-rules' >> >> '--with-frozenpaths' '--without-openexr' '--disable-hdri' >> >> '--with-dps' >> >> '--with-bzlib' '--with-fontconfig' '--with-gslib' '--with-jpeg' >> >> '--with-lcms' '--with-png' '--with-tiff' '--with-webp' >> >> '--with-zlib' >> >> '--with-modules' '--with-xml' '--with-x' '--without-perl' >> >> '--without-fpx' >> >> '--without-jbig' '--without-jp2' '--without-wmf' '--without-gvc' >> >> '--without-rsvg' '--without-lqr' '--without-pango' >> >> '--with-gs-font-dir=/opt/local/share/fonts/urw-fonts' >> >> '--with-quantum-depth=16' 'CC=/usr/bin/gcc-4.2' 'CFLAGS=-pipe -O2 >> >> -arch >> >> x86_64' 'LDFLAGS=-L/opt/local/lib -arch x86_64' >> >> 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/g++-4.2' >> >> 'CXXFLAGS=-pipe -O2 >> >> -arch x86_64' >> >> >> CONFIGURE_PATH /opt/local/etc/ImageMagick/ >> >> >> COPYRIGHT Copyright (C) 1999-2012 ImageMagick Studio LLC >> >> >> CPPFLAGS -I/opt/local/include/ImageMagick >> >> >> CXX /usr/bin/g++-4.2 >> >> >> CXXFLAGS -pipe -O2 -arch x86_64 -D_THREAD_SAFE -pthread >> >> >> DEFS -DHAVE_CONFIG_H >> >> >> DELEGATES bzlib fftw fontconfig freetype gs jpeg jng lcms2 lzma >> >> png tiff >> >> x11 xml zlib >> >> >> DISTCHECK_CONFIG_FLAGS 'CC=/usr/bin/gcc-4.2' 'CFLAGS=-pipe -O2 >> >> -arch x86_64' >> >> 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/g++-4.2' >> >> 'LDFLAGS=-L/opt/local/lib -arch x86_64' --disable-deprecated >> >> --with-quantum-depth=16 --with-umem=no --with-autotrace=no >> >> --with-fpx=no >> >> --with-fontpath= >> >> --with-gs-font-dir=/opt/local/share/fonts/urw-fonts >> >> --with-gvc=no --with-jp2=no --with-lqr=no --with-openexr=no >> >> --with-pango=no >> >> --with-rsvg=no --with-wmf=no --with-perl=no >> >> >> DOCUMENTATION_PATH /opt/local/share/doc/ImageMagick-6.8.0 >> >> >> EXEC-PREFIX /opt/local >> >> >> EXECUTABLE_PATH /opt/local/bin >> >> >> FEATURES OpenCL OpenMP >> >> >> FILTER_PATH /opt/local/lib/ImageMagick-6.8.0/modules-Q16/filters >> >> >> HOST x86_64-apple-darwin10.8.0 >> >> >> INCLUDE_PATH /opt/local/include/ImageMagick >> >> >> LDFLAGS -L/opt/local/lib -L/opt/local/lib -arch x86_64 >> >> -L/opt/local/lib -L/opt/local/lib >> >> >> LIB_VERSION 0x680 >> >> >> LIB_VERSION_NUMBER 6,8,0,7 >> >> >> LIBRARY_PATH /opt/local/lib/ImageMagick-6.8.0 >> >> >> LIBS -lMagickCore -llcms2 -lfreetype -lfftw3 >> >> -L/opt/local/lib >> >> -lfontconfig -lXext -lSM -lICE -lX11 -lXt -L/opt/local/lib -llzma >> >> -lbz2 -lz >> >> -lltdl -lm -lgomp -lclparser -Wl,-framework,OpenCL >> >> -L/System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries >> >> -lm >> >> -lpthread >> >> >> NAME ImageMagick >> >> >> PCFLAGS -fopenmp >> >> >> PREFIX /opt/local >> >> >> QuantumDepth 16 >> >> >> RELEASE_DATE 2013-03-04 >> >> >> SHARE_PATH /opt/local/share/ImageMagick-6.8.0 >> >> >> SVN_REVISION 10029 >> >> >> TARGET_CPU x86_64 >> >> >> TARGET_OS darwin10.8.0 >> >> >> TARGET_VENDOR apple >> >> >> VERSION 6.8.0 >> >> >> WEBSITE http://www.imagemagick.org >> >> >> >> Path: [built-in] >> >> >> >> Name Value >> >> >> >> ------------------------------------------------------------------- ------------ >> >> >> NAME ImageMagick >> >> >> >> Any help would be appreciated. Thanks >> >> >> >> -- output of sessionInfo(): >> >> >> >> R version 2.15.2 (2012-10-26) >> >> >> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >> >> >> >> locale: >> >> >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> >> >> attached base packages: >> >> >> [1] tools stats graphics grDevices utils datasets >> >> methods >> >> base >> >> >> >> other attached packages: >> >> >> [1] latticeExtra_0.6-24 RColorBrewer_1.0-5 parody_1.16.0 >> >> bioDist_1.30.0 >> >> >> [5] KernSmooth_2.23-8 mvoutlier_1.9.9 sgeostat_1.0-25 >> >> robCompositions_1.6.3 >> >> >> [9] car_2.0-16 nnet_7.3-5 compositions_1.20-1 >> >> energy_1.4-0 >> >> >> [13] MASS_7.3-23 boot_1.3-7 tensorA_0.36 >> >> rgl_0.93.928 >> >> >> [17] flowViz_1.22.0 flowCore_1.24.2 rrcov_1.3-02 >> >> pcaPP_1.9-48 >> >> >> [21] mvtnorm_0.9-9994 robustbase_0.9-5 Biobase_2.18.0 >> >> lattice_0.20-13 >> >> >> [25] outliers_0.14 BiocGenerics_0.4.0 >> >> BiocInstaller_1.8.3 >> >> >> >> loaded via a namespace (and not attached): >> >> >> [1] annotate_1.36.0 AnnotationDbi_1.20.5 DBI_0.2-5 >> >> feature_1.2.8 >> >> >> [5] flowQ_1.18.0 geneplotter_1.36.0 graph_1.36.2 >> >> grid_2.15.2 >> >> >> [9] hexbin_1.26.1 IDPmisc_1.1.17 IRanges_1.16.6 >> >> ks_1.8.11 >> >> >> [13] parallel_2.15.2 RSQLite_0.11.2 stats4_2.15.2 >> >> XML_3.95-0.1 >> >> >> [17] xtable_1.7-1 >> >> >> >> -- >> >> >> Sent via the guest posting facility at bioconductor.org. >> >> >> >> _______________________________________________ >> >> >> Bioconductor mailing list >> >> >> Bioconductor at r-project.org >> >> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> >> Search the archives: >> >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> >> >> Chandra Jack >> >> >> Postdoctoral Research Assoc. >> >> >> Dept. of Bioengineering >> >> >> Rice University >> >> >> chanj at rice.edu >> >> >> >> >> >> >> >> Chandra Jack >> >> Postdoctoral Research Assoc. >> >> Dept. of Bioengineering >> >> Rice University >> >> chanj at rice.edu >> >> >> >> >> >> >> Chandra Jack >> >> Postdoctoral Research Assoc. >> >> Dept. of Bioengineering >> >> Rice University >> >> chanj at rice.edu >> >> >> >> >> >> >> Chandra Jack >> >> Postdoctoral Research Assoc. >> >> Dept. of Bioengineering >> >> Rice University >> >> chanj at rice.edu >> >> >> >> >> >> >> Chandra Jack >> >> Postdoctoral Research Assoc. >> >> Dept. of Bioengineering >> >> Rice University >> >> chanj at rice.edu >> >> >> >> >> >> [[alternative HTML version deleted]] >> >> >> >> >> _______________________________________________ >> >> Bioconductor mailing list >> >> Bioconductor at r-project.org >> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> Search the archives: >> >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> >> >> >> Chandra Jack >> >> Postdoctoral Research Assoc. >> >> Dept. of Bioengineering >> >> Rice University >> >> chanj at rice.edu >> >> >> >> >> >> [[alternative HTML version deleted]] >> >> >> _______________________________________________ >> >> Bioconductor mailing list >> >> Bioconductor at r-project.org >> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> >> >> Chandra Jack >> Postdoctoral Research Assoc. >> Dept. of Bioengineering >> Rice University >> chanj at rice.edu >> >> >> > Chandra Jack Postdoctoral Research Assoc. Dept. of Bioengineering Rice University chanj at rice.edu
ADD REPLYlink written 6.7 years ago by Chandra Jack90
On Tue, Mar 5, 2013 at 10:01 AM, Chandra Jack <chanj at="" rice.edu=""> wrote: > It works! Thanks so much for your help! > > path <- Sys.getenv("PATH") >> path > [1] "/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin" > > Why is is not a recommended long term solution? Will I need to call path each time I tried to load flowQ? > You could put the Sys.setenv() command in your ~/.Rprofile and it would get run each time you start R. That would work and solve the problem. But it seems to me that for some reason your path within R differs from your system path and you may want to find out why. There are a number of configuration files (see ?Startup) where this could happen. If your R installation is unchanged, as far as you know, then there is some other problem. Dan > > On Mar 5, 2013, at 11:26 AM, Dan Tenenbaum wrote: > >> I got the following steps to work on a machine similar to yours. This >> is not a recommended long term solution but I'd be interested to see >> if it works for you. >> >> in R: >> path <- Sys.getenv("PATH") >> path # let me know what this says >> Sys.setenv(PATH=paste0(path, ":", "/opt/local/bin")) >> library(flowQ) >> >> Dan >> >> >> On Tue, Mar 5, 2013 at 8:49 AM, Chandra Jack <chanj at="" rice.edu=""> wrote: >>> I have removed the export and made sure that there are no spaces and still >>> get the same message. >>> >>> On Mar 5, 2013, at 10:31 AM, Harris A. Jaffee wrote: >>> >>> I haven't been listening too closely, but... >>> >>> Exactly what you wrote would have been a bash/sh syntax error. There cannot >>> be spaces around the '='. If >>> you are on the right track, then you need something like >>> >>> PATH=$PATH:opt/local/bin >>> >>> While we are at it, I believe that resetting a variable that is already >>> exported, as with PATH, does not >>> necessitate the 'export' command, in order to reset the exported value. For >>> example, >>> >>> sh-3.2$ export foo=bar >>> sh-3.2$ env | grep foo >>> foo=bar >>> sh-3.2$ foo=bar2 >>> sh-3.2$ env | grep foo >>> foo=bar2 >>> >>> >>> On Mar 5, 2013, at 11:11 AM, Chandra Jack wrote: >>> >>> I didn't have a ~/.profile so I created one. All I put in it was export PATH >>> = $PATH:opt/local/bin. But I got the same message that /bin/sh: convert: >>> command not found. I read that .bash_profile may need to call .profile and >>> also tried putting source ~/.profile at the end of the file but that gave me >>> the same message. >>> >>> >>> >>> On Mar 5, 2013, at 9:41 AM, Dan Tenenbaum wrote: >>> >>> >>> On Tue, Mar 5, 2013 at 12:21 AM, Nikolas Pontikos <n.pontikos at="" gmail.com=""> >>> wrote: >>> >>> From your R error message, system is calling /bin/sh not /bin/bash (which >>> >>> should be the same program but i don't think sh reads the .bashrc config >>> >>> file). >>> >>> Maybe the convert command is not available from /bin/sh? >>> >>> >>> >>> In that case the file to be edited is ~/.profile >>> >>> >>> Dan >>> >>> >>> >>> >>> On 5 March 2013 06:42, Chandra Jack <chanj at="" rice.edu=""> wrote: >>> >>> >>> Yes. I've been restarting R after everytime I changed bash_profile. I also >>> >>> just tried reinstalling R but that didn't help either. >>> >>> >>> On Mar 5, 2013, at 12:20 AM, Dan Tenenbaum wrote: >>> >>> >>> On Mon, Mar 4, 2013 at 10:06 PM, Chandra Jack <chanj at="" rice.edu=""> wrote: >>> >>> >>> On Mar 4, 2013, at 11:57 PM, Dan Tenenbaum wrote: >>> >>> >>> On Mon, Mar 4, 2013 at 9:53 PM, Chandra Jack <chanj at="" rice.edu=""> wrote: >>> >>> Thank you so much for your help. >>> >>> >>> Chandra-Jacks-MacBook:~ chanj$ source ~/.bash_profile >>> >>> Chandra-Jacks-MacBook:~ chanj$ echo $PATH >>> >>> >>> /Library/Frameworks/Python.framework/Versions/2.7/bin:/Library/Fra meworks/EPD64.framework/Versions/Current/bin:/Library/Frameworks/Pytho n.framework/Versions/2.7/bin:/Library/Frameworks/EPD64.framework/Versi ons/Current/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/ bin:/opt/local/bin:/opt/local/bin >>> >>> Chandra-Jacks-MacBook:~ chanj$ which convert >>> >>> /opt/local/bin/convert >>> >>> >>> >>> It looks like convert is in your PATH. >>> >>> >>> What happens if you type >>> >>> convert >>> >>> at the terminal prompt? >>> >>> >>> I think it opens ImageMagick >>> >>> Chandra-Jacks-MacBook:~ chanj$ convert >>> >>> Version: ImageMagick 6.8.0-7 2013-03-04 Q16 http://www.imagemagick.org >>> >>> Copyright: Copyright (C) 1999-2012 ImageMagick Studio LLC >>> >>> Features: OpenMP OpenCL >>> >>> >>> Usage: convert [options ...] file [ [options ...] file ...] [options >>> >>> ...] file >>> >>> >>> Image Settings: >>> >>> -adjoin join images into a single multi-image file >>> >>> >>> etc.... >>> >>> >>> >>> >>> >>> What if you go into R and type >>> >>> system("convert") >>> >>> ? >>> >>> >>> system("convert") >>> >>> /bin/sh: convert: command not found >>> >>> >>> >>> This means convert is in your path but R can't see it. Did you restart >>> >>> R after editing .bash_profile? >>> >>> >>> Dan >>> >>> >>> >>> Dan >>> >>> >>> On Mar 4, 2013, at 11:45 PM, Dan Tenenbaum wrote: >>> >>> >>> On Mon, Mar 4, 2013 at 9:30 PM, Chandra Jack <chanj at="" rice.edu=""> wrote: >>> >>> I replaced the original export line with the one you wrote but it >>> >>> still >>> >>> didn't work. >>> >>> >>> >>> OK, at a terminal prompt, please enter the following commands and >>> >>> send >>> >>> me the output they produce: >>> >>> >>> source ~/.bash_profile >>> >>> echo $PATH >>> >>> which convert >>> >>> >>> >>> >>> thanks, >>> >>> Dan >>> >>> >>> >>> >>> On Mar 4, 2013, at 10:18 PM, Dan Tenenbaum wrote: >>> >>> >>> On Mon, Mar 4, 2013 at 8:07 PM, Chandra Jack <chanj at="" rice.edu=""> >>> >>> wrote: >>> >>> >>> The convert command isn't in my PATH but adding the newIt doesn't >>> >>> seem to be >>> >>> working. I don't have a .bashrc file but I have a .bash_profile. >>> >>> The >>> >>> original file was: >>> >>> >>> # Setting PATH for EPD-7.1-2 >>> >>> >>> # The orginal version is saved in .bash_profile.pysave >>> >>> >>> >>> PATH="/Library/Frameworks/EPD64.framework/Versions/Current/bin:${P ATH}" >>> >>> >>> export PATH >>> >>> >>> >>> MKL_NUM_THREADS=1 >>> >>> >>> export MKL_NUM_THREADS >>> >>> >>> >>> # Setting PATH for Python 2.7 >>> >>> >>> # The orginal version is saved in .bash_profile.pysave >>> >>> >>> >>> PATH="/Library/Frameworks/Python.framework/Versions/2.7/bin:${PATH}" >>> >>> >>> export PATH >>> >>> >>> >>> ## >>> >>> >>> # Your previous /Users/chanj/.bash_profile file was backed up as >>> >>> /Users/chanj/.bash_profile.macports-saved_2013-03-04_at_14:30:35 >>> >>> >>> ## >>> >>> >>> >>> # MacPorts Installer addition on 2013-03-04_at_14:30:35: adding an >>> >>> appropriate PATH variable for use with MacPorts. >>> >>> >>> export PATH=/opt/local/bin:/opt/local/sbin:$PATH >>> >>> >>> # Finished adapting your PATH environment variable for use with >>> >>> MacPorts. >>> >>> >>> >>> I added PATH=$PATH:/opt/local/bin after the export line, resaved >>> >>> the text >>> >>> edit file and quit the terminal. When I checked Terminal again the >>> >>> file was >>> >>> updated but R couldn't find the command still. >>> >>> >>> >>> Sorry, it needs to say: >>> >>> >>> export PATH=$PATH:/opt/local/bin >>> >>> >>> I forgot the 'export' before. >>> >>> >>> >>> >>> >>> >>> >>> I also tried adding it before the export line, replacing the part >>> >>> after the >>> >>> export line with it, adding quotation marks but nothing seemed to >>> >>> work. I >>> >>> went in and found the convert command file and it is in >>> >>> opt/local/bin. I >>> >>> tried Sys.which with another file that was in the same location and >>> >>> R output >>> >>> "/usr/bin/clear" . Could it be related to the backup file that was >>> >>> created >>> >>> before I changed it? >>> >>> >>> >>> No, that just means there is a 'clear' executable in two locations. >>> >>> Dan >>> >>> >>> >>> >>> Thanks >>> >>> >>> >>> On Mar 4, 2013, at 4:15 PM, Dan Tenenbaum wrote: >>> >>> >>> >>> On Mon, Mar 4, 2013 at 2:09 PM, Chandra Jack [guest] >>> >>> >>> <guest at="" bioconductor.org=""> wrote: >>> >>> >>> >>> Hi All, >>> >>> >>> >>> I'm having a problem that has been mentioned here before but I'm >>> >>> not sure >>> >>> how to fix it. I tried to load flowQ and got: >>> >>> >>> >>> Error : .onAttach failed in attachNamespace() for 'flowQ', details: >>> >>> >>> call: mysys("convert -list configure", intern = TRUE, ignore.stderr >>> >>> = TRUE) >>> >>> >>> error: error in running command >>> >>> >>> >>> Is the 'convert' command in your PATH? >>> >>> >>> >>> What is the output of the R command: >>> >>> >>> Sys.which("convert") >>> >>> >>> ? >>> >>> >>> >>> If it does not output anything, then the convert command is not in >>> >>> your >>> >>> PATH. >>> >>> >>> >>> I'm not sure where the convert command ended up, but I'm guessing >>> >>> it's >>> >>> >>> in /opt/local/bin, >>> >>> >>> so I think you need to edit your ~/.bashrc >>> >>> >>> file and add the following line: >>> >>> >>> >>> PATH=$PATH:/opt/local/bin >>> >>> >>> >>> Then, start a new terminal window to make sure this setting is >>> >>> >>> enabled, and try again. >>> >>> >>> >>> Dan >>> >>> >>> >>> >>> In addition: Warning messages: >>> >>> >>> 1: replacing previous import ?plot? when loading ?graphics? >>> >>> >>> 2: replacing previous import ?as? when loading ?methods? >>> >>> >>> Error: package/namespace load failed for ?flowQ?. >>> >>> >>> >>> >>> I have installed ImageMagick using Macports as has been suggested >>> >>> and I have >>> >>> also run >>> >>> >>> convert -list configure, which gave the following: >>> >>> >>> Path: /opt/local/lib/ImageMagick-6.8.0/config/configure.xml >>> >>> >>> >>> Name Value >>> >>> >>> >>> ------------------------------------------------------------------ ------------- >>> >>> >>> CC /usr/bin/gcc-4.2 -std=gnu99 -std=gnu99 >>> >>> >>> CFLAGS -D_THREAD_SAFE -D_THREAD_SAFE -pthread -fopenmp -pipe >>> >>> -O2 >>> >>> -arch x86_64 -Wall -D_THREAD_SAFE -pthread >>> >>> >>> CODER_PATH /opt/local/lib/ImageMagick-6.8.0/modules-Q16/coders >>> >>> >>> CONFIGURE ./configure '--prefix=/opt/local' '--enable-shared' >>> >>> '--enable-static' '--disable-ltdl-install' '--disable-silent- rules' >>> >>> '--with-frozenpaths' '--without-openexr' '--disable-hdri' >>> >>> '--with-dps' >>> >>> '--with-bzlib' '--with-fontconfig' '--with-gslib' '--with-jpeg' >>> >>> '--with-lcms' '--with-png' '--with-tiff' '--with-webp' >>> >>> '--with-zlib' >>> >>> '--with-modules' '--with-xml' '--with-x' '--without-perl' >>> >>> '--without-fpx' >>> >>> '--without-jbig' '--without-jp2' '--without-wmf' '--without-gvc' >>> >>> '--without-rsvg' '--without-lqr' '--without-pango' >>> >>> '--with-gs-font-dir=/opt/local/share/fonts/urw-fonts' >>> >>> '--with-quantum-depth=16' 'CC=/usr/bin/gcc-4.2' 'CFLAGS=-pipe -O2 >>> >>> -arch >>> >>> x86_64' 'LDFLAGS=-L/opt/local/lib -arch x86_64' >>> >>> 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/g++-4.2' >>> >>> 'CXXFLAGS=-pipe -O2 >>> >>> -arch x86_64' >>> >>> >>> CONFIGURE_PATH /opt/local/etc/ImageMagick/ >>> >>> >>> COPYRIGHT Copyright (C) 1999-2012 ImageMagick Studio LLC >>> >>> >>> CPPFLAGS -I/opt/local/include/ImageMagick >>> >>> >>> CXX /usr/bin/g++-4.2 >>> >>> >>> CXXFLAGS -pipe -O2 -arch x86_64 -D_THREAD_SAFE -pthread >>> >>> >>> DEFS -DHAVE_CONFIG_H >>> >>> >>> DELEGATES bzlib fftw fontconfig freetype gs jpeg jng lcms2 lzma >>> >>> png tiff >>> >>> x11 xml zlib >>> >>> >>> DISTCHECK_CONFIG_FLAGS 'CC=/usr/bin/gcc-4.2' 'CFLAGS=-pipe -O2 >>> >>> -arch x86_64' >>> >>> 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/g++-4.2' >>> >>> 'LDFLAGS=-L/opt/local/lib -arch x86_64' --disable-deprecated >>> >>> --with-quantum-depth=16 --with-umem=no --with-autotrace=no >>> >>> --with-fpx=no >>> >>> --with-fontpath= >>> >>> --with-gs-font-dir=/opt/local/share/fonts/urw-fonts >>> >>> --with-gvc=no --with-jp2=no --with-lqr=no --with-openexr=no >>> >>> --with-pango=no >>> >>> --with-rsvg=no --with-wmf=no --with-perl=no >>> >>> >>> DOCUMENTATION_PATH /opt/local/share/doc/ImageMagick-6.8.0 >>> >>> >>> EXEC-PREFIX /opt/local >>> >>> >>> EXECUTABLE_PATH /opt/local/bin >>> >>> >>> FEATURES OpenCL OpenMP >>> >>> >>> FILTER_PATH /opt/local/lib/ImageMagick-6.8.0/modules-Q16/filters >>> >>> >>> HOST x86_64-apple-darwin10.8.0 >>> >>> >>> INCLUDE_PATH /opt/local/include/ImageMagick >>> >>> >>> LDFLAGS -L/opt/local/lib -L/opt/local/lib -arch x86_64 >>> >>> -L/opt/local/lib -L/opt/local/lib >>> >>> >>> LIB_VERSION 0x680 >>> >>> >>> LIB_VERSION_NUMBER 6,8,0,7 >>> >>> >>> LIBRARY_PATH /opt/local/lib/ImageMagick-6.8.0 >>> >>> >>> LIBS -lMagickCore -llcms2 -lfreetype -lfftw3 >>> >>> -L/opt/local/lib >>> >>> -lfontconfig -lXext -lSM -lICE -lX11 -lXt -L/opt/local/lib -llzma >>> >>> -lbz2 -lz >>> >>> -lltdl -lm -lgomp -lclparser -Wl,-framework,OpenCL >>> >>> -L/System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries >>> >>> -lm >>> >>> -lpthread >>> >>> >>> NAME ImageMagick >>> >>> >>> PCFLAGS -fopenmp >>> >>> >>> PREFIX /opt/local >>> >>> >>> QuantumDepth 16 >>> >>> >>> RELEASE_DATE 2013-03-04 >>> >>> >>> SHARE_PATH /opt/local/share/ImageMagick-6.8.0 >>> >>> >>> SVN_REVISION 10029 >>> >>> >>> TARGET_CPU x86_64 >>> >>> >>> TARGET_OS darwin10.8.0 >>> >>> >>> TARGET_VENDOR apple >>> >>> >>> VERSION 6.8.0 >>> >>> >>> WEBSITE http://www.imagemagick.org >>> >>> >>> >>> Path: [built-in] >>> >>> >>> >>> Name Value >>> >>> >>> >>> ------------------------------------------------------------------ ------------- >>> >>> >>> NAME ImageMagick >>> >>> >>> >>> Any help would be appreciated. Thanks >>> >>> >>> >>> -- output of sessionInfo(): >>> >>> >>> >>> R version 2.15.2 (2012-10-26) >>> >>> >>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >>> >>> >>> >>> locale: >>> >>> >>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>> >>> >>> >>> attached base packages: >>> >>> >>> [1] tools stats graphics grDevices utils datasets >>> >>> methods >>> >>> base >>> >>> >>> >>> other attached packages: >>> >>> >>> [1] latticeExtra_0.6-24 RColorBrewer_1.0-5 parody_1.16.0 >>> >>> bioDist_1.30.0 >>> >>> >>> [5] KernSmooth_2.23-8 mvoutlier_1.9.9 sgeostat_1.0-25 >>> >>> robCompositions_1.6.3 >>> >>> >>> [9] car_2.0-16 nnet_7.3-5 compositions_1.20-1 >>> >>> energy_1.4-0 >>> >>> >>> [13] MASS_7.3-23 boot_1.3-7 tensorA_0.36 >>> >>> rgl_0.93.928 >>> >>> >>> [17] flowViz_1.22.0 flowCore_1.24.2 rrcov_1.3-02 >>> >>> pcaPP_1.9-48 >>> >>> >>> [21] mvtnorm_0.9-9994 robustbase_0.9-5 Biobase_2.18.0 >>> >>> lattice_0.20-13 >>> >>> >>> [25] outliers_0.14 BiocGenerics_0.4.0 >>> >>> BiocInstaller_1.8.3 >>> >>> >>> >>> loaded via a namespace (and not attached): >>> >>> >>> [1] annotate_1.36.0 AnnotationDbi_1.20.5 DBI_0.2-5 >>> >>> feature_1.2.8 >>> >>> >>> [5] flowQ_1.18.0 geneplotter_1.36.0 graph_1.36.2 >>> >>> grid_2.15.2 >>> >>> >>> [9] hexbin_1.26.1 IDPmisc_1.1.17 IRanges_1.16.6 >>> >>> ks_1.8.11 >>> >>> >>> [13] parallel_2.15.2 RSQLite_0.11.2 stats4_2.15.2 >>> >>> XML_3.95-0.1 >>> >>> >>> [17] xtable_1.7-1 >>> >>> >>> >>> -- >>> >>> >>> Sent via the guest posting facility at bioconductor.org. >>> >>> >>> >>> _______________________________________________ >>> >>> >>> Bioconductor mailing list >>> >>> >>> Bioconductor at r-project.org >>> >>> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> >>> >>> Search the archives: >>> >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >>> >>> >>> Chandra Jack >>> >>> >>> Postdoctoral Research Assoc. >>> >>> >>> Dept. of Bioengineering >>> >>> >>> Rice University >>> >>> >>> chanj at rice.edu >>> >>> >>> >>> >>> >>> >>> >>> Chandra Jack >>> >>> Postdoctoral Research Assoc. >>> >>> Dept. of Bioengineering >>> >>> Rice University >>> >>> chanj at rice.edu >>> >>> >>> >>> >>> >>> >>> Chandra Jack >>> >>> Postdoctoral Research Assoc. >>> >>> Dept. of Bioengineering >>> >>> Rice University >>> >>> chanj at rice.edu >>> >>> >>> >>> >>> >>> >>> Chandra Jack >>> >>> Postdoctoral Research Assoc. >>> >>> Dept. of Bioengineering >>> >>> Rice University >>> >>> chanj at rice.edu >>> >>> >>> >>> >>> >>> >>> Chandra Jack >>> >>> Postdoctoral Research Assoc. >>> >>> Dept. of Bioengineering >>> >>> Rice University >>> >>> chanj at rice.edu >>> >>> >>> >>> >>> >>> [[alternative HTML version deleted]] >>> >>> >>> >>> >>> _______________________________________________ >>> >>> Bioconductor mailing list >>> >>> Bioconductor at r-project.org >>> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> >>> Search the archives: >>> >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >>> >>> >>> >>> Chandra Jack >>> >>> Postdoctoral Research Assoc. >>> >>> Dept. of Bioengineering >>> >>> Rice University >>> >>> chanj at rice.edu >>> >>> >>> >>> >>> >>> [[alternative HTML version deleted]] >>> >>> >>> _______________________________________________ >>> >>> Bioconductor mailing list >>> >>> Bioconductor at r-project.org >>> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >>> >>> >>> Chandra Jack >>> Postdoctoral Research Assoc. >>> Dept. of Bioengineering >>> Rice University >>> chanj at rice.edu >>> >>> >>> >> > > Chandra Jack > Postdoctoral Research Assoc. > Dept. of Bioengineering > Rice University > chanj at rice.edu > > >
ADD REPLYlink written 6.7 years ago by Dan Tenenbaum8.2k
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