Question: flowQ loading issue
0
gravatar for Fletez-Brant, Christopher NIH/VRC [C]
7.1 years ago by
Dear List, I am attempting to load flowQ and am getting the error message listed at the end of this message. It is similar to errors reported here: https://stat.ethz.ch/pipermail/bioconductor/2011-June/039962.html and here: https://stat.ethz.ch/pipermail/bioconductor/2011-August/040806.html However, I have ImageMagick installed already. On a whim I decided to run the ImageMagick command listed in the error message and got the following output: ~ $ convert -list configure Path: [built-in] Name Value ---------------------------------------------------------------------- --------- NAME ImageMagick convert: unable to access configure file `configure.xml' @ warning/configure.c/GetConfigureOptions/591. Is this related? R Errors, version info after signature. Thank you, Kipper Fletez-Brant R information: $platform [1] "x86_64-apple-darwin9.8.0" $version.string [1] "R version 2.15.0 (2012-03-30)" Error Message: Attaching package: ?latticeExtra? The following object(s) are masked from ?package:flowViz?: ecdfplot 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: package ?boot? was built under R version 2.15.1 2: package ?MASS? was built under R version 2.15.1 3: package ?nnet? was built under R version 2.15.1 4: package ?KernSmooth? was built under R version 2.15.1 Error: package/namespace load failed for ?flowQ?
convert flowq • 754 views
ADD COMMENTlink modified 7.1 years ago by Greg Finak240 • written 7.1 years ago by Fletez-Brant, Christopher NIH/VRC [C]60
Answer: flowQ loading issue
0
gravatar for Greg Finak
7.1 years ago by
Greg Finak240
United States
Greg Finak240 wrote:
Hi, Christopher Yes, it's related. It appears that your ImageMagick installation is not set up correctly. From the look of it, flowQ tries to run the 'convert' command and it fails for the same reasons you see runnung it from the command line. Greg Finak > ------------------------------ > > Message: 4 > Date: Thu, 12 Jul 2012 08:28:49 -0400 > From: "Fletez-Brant, Christopher (NIH/VRC) [C]" > <christopher.fletez-brant@nih.gov> > To: "bioconductor@r-project.org" <bioconductor@r-project.org> > Subject: [BioC] flowQ loading issue > Message-ID: <cc243b41.674%christopher.fletez-brant@nih.gov> > Content-Type: text/plain; charset="Windows-1252" > > Dear List, > > I am attempting to load flowQ and am getting the error message listed at the end of this message. It is similar to errors reported here: > > https://stat.ethz.ch/pipermail/bioconductor/2011-June/039962.html > > and here: > > https://stat.ethz.ch/pipermail/bioconductor/2011-August/040806.html > > However, I have ImageMagick installed already. On a whim I decided to run the ImageMagick command listed in the error message and got the following output: > > ~ $ convert -list configure > > Path: [built-in] > > Name Value > -------------------------------------------------------------------- ----------- > NAME ImageMagick > convert: unable to access configure file `configure.xml' @ warning/configure.c/GetConfigureOptions/591. > > Is this related? R Errors, version info after signature. > > Thank you, > Kipper Fletez-Brant > > R information: > > $platform > > [1] "x86_64-apple-darwin9.8.0" > > > $version.string > > [1] "R version 2.15.0 (2012-03-30)" > > Error Message: > > > Attaching package: ?latticeExtra? > > > The following object(s) are masked from ?package:flowViz?: > > > ecdfplot > > > 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: package ?boot? was built under R version 2.15.1 > > 2: package ?MASS? was built under R version 2.15.1 > > 3: package ?nnet? was built under R version 2.15.1 > > 4: package ?KernSmooth? was built under R version 2.15.1 > > Error: package/namespace load failed for ?flowQ? > > > > ------------------------------ [[alternative HTML version deleted]]
ADD COMMENTlink written 7.1 years ago by Greg Finak240
Thank you for the reply. I reinstalled ImageMagick per their instructions (that is, as I am using a Mac I installed via MacPorts), and when I run the convert command I get the attached output. However, R gives me the same error. Any help is appreciated. Thank you, Kipper convert -list configure Path: /opt/local/lib/ImageMagick-6.7.8/config/configure.xml Name Value ---------------------------------------------------------------------- ----- ---- CC /usr/bin/clang CFLAGS -D_THREAD_SAFE -D_THREAD_SAFE -pthread -pipe -O2 -arch x86_64 -Wall -D_THREAD_SAFE -pthread CODER_PATH /opt/local/lib/ImageMagick-6.7.8/modules-Q16/coders CONFIGURE ./configure '--prefix=/opt/local' '--enable-shared' '--enable-static' '--disable-ltdl-install' '--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/clang' 'CFLAGS=-pipe -O2 -arch x86_64' 'LDFLAGS=-L/opt/local/lib -arch x86_64' 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/clang++' '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/clang++ CXXFLAGS -pipe -O2 -arch x86_64 -D_THREAD_SAFE -pthread DEFS -DHAVE_CONFIG_H DELEGATES bzlib fontconfig freetype gs jpeg jng lcms2 lzma png tiff x11 xml zlib DISTCHECK_CONFIG_FLAGS 'CC=/usr/bin/clang' 'CFLAGS=-pipe -O2 -arch x86_64' 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/clang++' '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-6.7.8 EXEC-PREFIX /opt/local EXECUTABLE_PATH /opt/local/bin FEATURES OpenCL FILTER_PATH /opt/local/lib/ImageMagick-6.7.8/modules-Q16/filters HOST x86_64-apple-darwin11.4.0 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 0x678 LIB_VERSION_NUMBER 6,7,8,0 LIBRARY_PATH /opt/local/lib/ImageMagick-6.7.8 LIBS -lMagickCore -llcms2 -ltiff -lfreetype -ljpeg -L/opt/local/lib -lfontconfig -lXext -lSM -lICE -lX11 -lXt -L/opt/local/lib -llzma -lbz2 -lz -lm -Wl,-framework,OpenCL -lm -lpthread -lltdl NAME ImageMagick PCFLAGS PREFIX /opt/local QuantumDepth 16 RELEASE_DATE 2012-07-12 SHARE_PATH /opt/local/share/ImageMagick-6.7.8 SVN_REVISION 8563 TARGET_CPU x86_64 TARGET_OS darwin11.4.0 TARGET_VENDOR apple VERSION 6.7.8 WEBSITE http://www.imagemagick.org Path: [built-in] Name Value ---------------------------------------------------------------------- ----- ---- NAME ImageMagick > sessionInfo() R version 2.15.0 (2012-03-30) 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_0.6-19 parody_1.14.0 bioDist_1.28.0 KernSmooth_2.23-8 mvoutlier_1.9.7 sgeostat_1.0-24 robCompositions_1.6.0 [8] car_2.0-12 nnet_7.3-4 compositions_1.10-2 energy_1.4-0 MASS_7.3-19 boot_1.3-5 tensorA_0.36 [15] rgl_0.92.880 outliers_0.14 HTqPCR_1.10.0 limma_3.12.1 RColorBrewer_1.0-5 flowViz_1.20.0 lattice_0.20-6 [22] flowCore_1.22.1 rrcov_1.3-02 pcaPP_1.9-47 mvtnorm_0.9-9992 robustbase_0.9-2 Biobase_2.16.0 BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] affy_1.34.0 affyio_1.24.0 annotate_1.34.1 AnnotationDbi_1.18.1 BiocInstaller_1.4.7 DBI_0.2-5 feature_1.2.8 [8] flowQ_1.16.0 gdata_2.11.0 geneplotter_1.34.0 gplots_2.11.0 graph_1.34.0 grid_2.15.0 gtools_2.7.0 [15] IRanges_1.14.4 ks_1.8.8 preprocessCore_1.18.0 RSQLite_0.11.1 stats4_2.15.0 XML_3.9-4 xtable_1.7-0 [22] zlibbioc_1.2.0 On 7/13/12 11:39 AM, "Finak, Greg" <gfinak at="" fhcrc.org=""> wrote: >Hi, Christopher >Yes, it's related. >It appears that your ImageMagick installation is not set up correctly. >From the look of it, flowQ tries to run the 'convert' command and it >fails for the same reasons you see runnung it from the command line. > >Greg Finak > > >> ------------------------------ >> >> Message: 4 >> Date: Thu, 12 Jul 2012 08:28:49 -0400 >> From: "Fletez-Brant, Christopher (NIH/VRC) [C]" >> <christopher.fletez-brant at="" nih.gov=""> >> To: "bioconductor at r-project.org" <bioconductor at="" r-project.org=""> >> Subject: [BioC] flowQ loading issue >> Message-ID: <cc243b41.674%christopher.fletez-brant at="" nih.gov=""> >> Content-Type: text/plain; charset="Windows-1252" >> >> Dear List, >> >> I am attempting to load flowQ and am getting the error message listed >>at the end of this message. It is similar to errors reported here: >> >> https://stat.ethz.ch/pipermail/bioconductor/2011-June/039962.html >> >> and here: >> >> https://stat.ethz.ch/pipermail/bioconductor/2011-August/040806.html >> >> However, I have ImageMagick installed already. On a whim I decided to >>run the ImageMagick command listed in the error message and got the >>following output: >> >> ~ $ convert -list configure >> >> Path: [built-in] >> >> Name Value >> >>-------------------------------------------------------------------- ----- >>------ >> NAME ImageMagick >> convert: unable to access configure file `configure.xml' @ >>warning/configure.c/GetConfigureOptions/591. >> >> Is this related? R Errors, version info after signature. >> >> Thank you, >> Kipper Fletez-Brant >> >> R information: >> >> $platform >> >> [1] "x86_64-apple-darwin9.8.0" >> >> >> $version.string >> >> [1] "R version 2.15.0 (2012-03-30)" >> >> Error Message: >> >> >> Attaching package: ?latticeExtra? >> >> >> The following object(s) are masked from ?package:flowViz?: >> >> >> ecdfplot >> >> >> 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: package ?boot? was built under R version 2.15.1 >> >> 2: package ?MASS? was built under R version 2.15.1 >> >> 3: package ?nnet? was built under R version 2.15.1 >> >> 4: package ?KernSmooth? was built under R version 2.15.1 >> >> Error: package/namespace load failed for ?flowQ? >> >> >> >> ------------------------------ > > > [[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 7.1 years ago by Fletez-Brant, Christopher NIH/VRC [C]60
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