Install error affxparser for R 2.15
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David Ruau ▴ 60
@david-ruau-4280
Last seen 7.1 years ago
Hello, I am experiencing an error trying to install affxparser on my mac (Snow Leopard 10.6.8) I cannot install from source and the binary version that is not available from Mac OSX snow leopard. Below are the relevant lines of the install process. --- > biocLite("affxparser", type='source') BioC_mirror: http://bioconductor.org Using R version 2.15, BiocInstaller version 1.4.3. Installing package(s) 'affxparser' trying URL 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib /affxparser_1.28.0.tar.gz' [snip...] /opt/local/bin/g++-mp-4.5 -I/opt/local/lib/R/include -I/opt/local/lib/R/include/x86_64 -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include -fPIC -pipe -O2 -m64 -O0 -c fusion_sdk/calvin_files/fusion/src/FusionCELData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCELData.o In file included from fusion_sdk/calvin_files/fusion/src/GCOSAdapter/G COSCELDataAdapter.h:30:0, from fusion_sdk/calvin_files/fusion/src/FusionCELData.cpp:24: fusion_sdk/file/CELFileData.h:91:23: warning: malformed '#pragma options align={mac68k|power|reset}', ignoring fusion_sdk/file/CELFileData.h:127:23: error: too many #pragma options align=reset make: *** [fusion_sdk/calvin_files/fusion/src/FusionCELData.o] Error 1 ERROR: compilation failed for package ?affxparser? * removing ?/opt/local/lib/R/library/affxparser? * restoring previous ?/opt/local/lib/R/library/affxparser? The downloaded source packages are in ?/private/var/folders/e9/e9-5zLVqFgGBR2S8qU74+U+++TM/-Tmp-/Rtm pn4Zczi/downloaded_packages? Updating HTML index of packages in '.Library' Making packages.html ... done Old packages: 'affxparser', 'oligo', 'pd.mogene.1.0.st.v1' Update all/some/none? [a/s/n]: n Warning message: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ?affxparser? had non-zero exit status > sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.4.3 loaded via a namespace (and not attached): [1] inline_0.3.8 Rcpp_0.9.10 tools_2.15.0 Thanks, David
PROcess affxparser BiocInstaller PROcess affxparser BiocInstaller • 1.1k views
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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 8 months ago
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Hi David, On Mon, Apr 9, 2012 at 11:33 AM, David Ruau <druau at="" stanford.edu=""> wrote: > Hello, > > I am experiencing an error trying to install affxparser on my mac (Snow Leopard 10.6.8) > I cannot install from source and the binary version that is not available from Mac OSX snow leopard. Can you show the output of biocLite("affxparser") without type="source"? It works on my lion system with R 2.15.0 and BiocInstaller 1.4.3. Dan > Below are the relevant lines of the install process. > > --- >> biocLite("affxparser", type='source') > BioC_mirror: http://bioconductor.org > Using R version 2.15, BiocInstaller version 1.4.3. > Installing package(s) 'affxparser' > trying URL 'http://www.bioconductor.org/packages/2.10/bioc/src/contr ib/affxparser_1.28.0.tar.gz' > > [snip...] > > /opt/local/bin/g++-mp-4.5 -I/opt/local/lib/R/include -I/opt/local/lib/R/include/x86_64 -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include ? ?-fPIC ?-pipe -O2 -m64 ?-O0 -c fusion_sdk/calvin_files/fusion/src/FusionCELData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCELData.o > In file included from fusion_sdk/calvin_files/fusion/src/GCOSAdapter /GCOSCELDataAdapter.h:30:0, > ? ? ? ? ? ? ? ? from fusion_sdk/calvin_files/fusion/src/FusionCELData.cpp:24: > fusion_sdk/file/CELFileData.h:91:23: warning: malformed '#pragma options align={mac68k|power|reset}', ignoring > fusion_sdk/file/CELFileData.h:127:23: error: too many #pragma options align=reset > make: *** [fusion_sdk/calvin_files/fusion/src/FusionCELData.o] Error 1 > ERROR: compilation failed for package ?affxparser? > * removing ?/opt/local/lib/R/library/affxparser? > * restoring previous ?/opt/local/lib/R/library/affxparser? > > The downloaded source packages are in > ? ? ? ??/private/var/folders/e9/e9-5zLVqFgGBR2S8qU74+U+++TM/-Tmp-/Rt mpn4Zczi/downloaded_packages? > Updating HTML index of packages in '.Library' > Making packages.html ?... done > Old packages: 'affxparser', 'oligo', 'pd.mogene.1.0.st.v1' > Update all/some/none? [a/s/n]: n > Warning message: > In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > ?installation of package ?affxparser? had non-zero exit status > >> sessionInfo() > R version 2.15.0 (2012-03-30) > Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/C > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > [1] BiocInstaller_1.4.3 > > loaded via a namespace (and not attached): > [1] inline_0.3.8 Rcpp_0.9.10 ?tools_2.15.0 > > > Thanks, > David > > _______________________________________________ > 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
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Hi Dan, I pasted the output here http://pastebin.com/Lnt79kC5 biocLite() tries to install affxparser, fails and ask you if you want to update it (at the same time as other packages). And then fails again. Thanks, David On Apr 9, 2012, at 11:47 AM, Dan Tenenbaum wrote: > Hi David, > > On Mon, Apr 9, 2012 at 11:33 AM, David Ruau <druau at="" stanford.edu=""> wrote: >> Hello, >> >> I am experiencing an error trying to install affxparser on my mac (Snow Leopard 10.6.8) >> I cannot install from source and the binary version that is not available from Mac OSX snow leopard. > > > Can you show the output of > biocLite("affxparser") > > without type="source"? > > It works on my lion system with R 2.15.0 and BiocInstaller 1.4.3. > > Dan > > >> Below are the relevant lines of the install process. >> >> --- >>> biocLite("affxparser", type='source') >> BioC_mirror: http://bioconductor.org >> Using R version 2.15, BiocInstaller version 1.4.3. >> Installing package(s) 'affxparser' >> trying URL 'http://www.bioconductor.org/packages/2.10/bioc/src/cont rib/affxparser_1.28.0.tar.gz' >> >> [snip...] >> >> /opt/local/bin/g++-mp-4.5 -I/opt/local/lib/R/include -I/opt/local/lib/R/include/x86_64 -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include -fPIC -pipe -O2 -m64 -O0 -c fusion_sdk/calvin_files/fusion/src/FusionCELData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCELData.o >> In file included from fusion_sdk/calvin_files/fusion/src/GCOSAdapte r/GCOSCELDataAdapter.h:30:0, >> from fusion_sdk/calvin_files/fusion/src/FusionCELData.cpp:24: >> fusion_sdk/file/CELFileData.h:91:23: warning: malformed '#pragma options align={mac68k|power|reset}', ignoring >> fusion_sdk/file/CELFileData.h:127:23: error: too many #pragma options align=reset >> make: *** [fusion_sdk/calvin_files/fusion/src/FusionCELData.o] Error 1 >> ERROR: compilation failed for package ?affxparser? >> * removing ?/opt/local/lib/R/library/affxparser? >> * restoring previous ?/opt/local/lib/R/library/affxparser? >> >> The downloaded source packages are in >> ?/private/var/folders/e9/e9-5zLVqFgGBR2S8qU74+U+++TM/-Tmp-/R tmpn4Zczi/downloaded_packages? >> Updating HTML index of packages in '.Library' >> Making packages.html ... done >> Old packages: 'affxparser', 'oligo', 'pd.mogene.1.0.st.v1' >> Update all/some/none? [a/s/n]: n >> Warning message: >> In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : >> installation of package ?affxparser? had non-zero exit status >> >>> sessionInfo() >> R version 2.15.0 (2012-03-30) >> Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] BiocInstaller_1.4.3 >> >> loaded via a namespace (and not attached): >> [1] inline_0.3.8 Rcpp_0.9.10 tools_2.15.0 >> >> >> Thanks, >> David >> >> _______________________________________________ >> 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
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On Mon, Apr 9, 2012 at 12:23 PM, David Ruau <druau at="" stanford.edu=""> wrote: > Hi Dan, > > I pasted the output here http://pastebin.com/Lnt79kC5 > biocLite() tries to install affxparser, fails and ask you if you want to update it (at the same time as other packages). And then fails again. > OK, what if you do this: biocLite("affxparser", type="mac.binary.leopard") ? Dan > Thanks, > David > > On Apr 9, 2012, at 11:47 AM, Dan Tenenbaum wrote: > >> Hi David, >> >> On Mon, Apr 9, 2012 at 11:33 AM, David Ruau <druau at="" stanford.edu=""> wrote: >>> Hello, >>> >>> I am experiencing an error trying to install affxparser on my mac (Snow Leopard 10.6.8) >>> I cannot install from source and the binary version that is not available from Mac OSX snow leopard. >> >> >> Can you show the output of >> biocLite("affxparser") >> >> without type="source"? >> >> It works on my lion system with R 2.15.0 and BiocInstaller 1.4.3. >> >> Dan >> >> >>> Below are the relevant lines of the install process. >>> >>> --- >>>> biocLite("affxparser", type='source') >>> BioC_mirror: http://bioconductor.org >>> Using R version 2.15, BiocInstaller version 1.4.3. >>> Installing package(s) 'affxparser' >>> trying URL 'http://www.bioconductor.org/packages/2.10/bioc/src/con trib/affxparser_1.28.0.tar.gz' >>> >>> [snip...] >>> >>> /opt/local/bin/g++-mp-4.5 -I/opt/local/lib/R/include -I/opt/local/lib/R/include/x86_64 -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include ? ?-fPIC ?-pipe -O2 -m64 ?-O0 -c fusion_sdk/calvin_files/fusion/src/FusionCELData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCELData.o >>> In file included from fusion_sdk/calvin_files/fusion/src/GCOSAdapt er/GCOSCELDataAdapter.h:30:0, >>> ? ? ? ? ? ? ? ? from fusion_sdk/calvin_files/fusion/src/FusionCELData.cpp:24: >>> fusion_sdk/file/CELFileData.h:91:23: warning: malformed '#pragma options align={mac68k|power|reset}', ignoring >>> fusion_sdk/file/CELFileData.h:127:23: error: too many #pragma options align=reset >>> make: *** [fusion_sdk/calvin_files/fusion/src/FusionCELData.o] Error 1 >>> ERROR: compilation failed for package ?affxparser? >>> * removing ?/opt/local/lib/R/library/affxparser? >>> * restoring previous ?/opt/local/lib/R/library/affxparser? >>> >>> The downloaded source packages are in >>> ? ? ? ??/private/var/folders/e9/e9-5zLVqFgGBR2S8qU74+U+++TM/-Tmp-/ Rtmpn4Zczi/downloaded_packages? >>> Updating HTML index of packages in '.Library' >>> Making packages.html ?... done >>> Old packages: 'affxparser', 'oligo', 'pd.mogene.1.0.st.v1' >>> Update all/some/none? [a/s/n]: n >>> Warning message: >>> In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : >>> ?installation of package ?affxparser? had non-zero exit status >>> >>>> sessionInfo() >>> R version 2.15.0 (2012-03-30) >>> Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit) >>> >>> locale: >>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/C >>> >>> attached base packages: >>> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >>> >>> other attached packages: >>> [1] BiocInstaller_1.4.3 >>> >>> loaded via a namespace (and not attached): >>> [1] inline_0.3.8 Rcpp_0.9.10 ?tools_2.15.0 >>> >>> >>> Thanks, >>> David >>> >>> _______________________________________________ >>> 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 >
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Thanks, it worked. David On Apr 9, 2012, at 12:25 PM, Dan Tenenbaum wrote: > On Mon, Apr 9, 2012 at 12:23 PM, David Ruau <druau at="" stanford.edu=""> wrote: >> Hi Dan, >> >> I pasted the output here http://pastebin.com/Lnt79kC5 >> biocLite() tries to install affxparser, fails and ask you if you want to update it (at the same time as other packages). And then fails again. >> > OK, what if you do this: > biocLite("affxparser", type="mac.binary.leopard") > > ? > Dan > > >> Thanks, >> David >> >> On Apr 9, 2012, at 11:47 AM, Dan Tenenbaum wrote: >> >>> Hi David, >>> >>> On Mon, Apr 9, 2012 at 11:33 AM, David Ruau <druau at="" stanford.edu=""> wrote: >>>> Hello, >>>> >>>> I am experiencing an error trying to install affxparser on my mac (Snow Leopard 10.6.8) >>>> I cannot install from source and the binary version that is not available from Mac OSX snow leopard. >>> >>> >>> Can you show the output of >>> biocLite("affxparser") >>> >>> without type="source"? >>> >>> It works on my lion system with R 2.15.0 and BiocInstaller 1.4.3. >>> >>> Dan >>> >>> >>>> Below are the relevant lines of the install process. >>>> >>>> --- >>>>> biocLite("affxparser", type='source') >>>> BioC_mirror: http://bioconductor.org >>>> Using R version 2.15, BiocInstaller version 1.4.3. >>>> Installing package(s) 'affxparser' >>>> trying URL 'http://www.bioconductor.org/packages/2.10/bioc/src/co ntrib/affxparser_1.28.0.tar.gz' >>>> >>>> [snip...] >>>> >>>> /opt/local/bin/g++-mp-4.5 -I/opt/local/lib/R/include -I/opt/local/lib/R/include/x86_64 -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include -fPIC -pipe -O2 -m64 -O0 -c fusion_sdk/calvin_files/fusion/src/FusionCELData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCELData.o >>>> In file included from fusion_sdk/calvin_files/fusion/src/GCOSAdap ter/GCOSCELDataAdapter.h:30:0, >>>> from fusion_sdk/calvin_files/fusion/src/FusionCELData.cpp:24: >>>> fusion_sdk/file/CELFileData.h:91:23: warning: malformed '#pragma options align={mac68k|power|reset}', ignoring >>>> fusion_sdk/file/CELFileData.h:127:23: error: too many #pragma options align=reset >>>> make: *** [fusion_sdk/calvin_files/fusion/src/FusionCELData.o] Error 1 >>>> ERROR: compilation failed for package ?affxparser? >>>> * removing ?/opt/local/lib/R/library/affxparser? >>>> * restoring previous ?/opt/local/lib/R/library/affxparser? >>>> >>>> The downloaded source packages are in >>>> ?/private/var/folders/e9/e9-5zLVqFgGBR2S8qU74+U+++TM/-Tmp- /Rtmpn4Zczi/downloaded_packages? >>>> Updating HTML index of packages in '.Library' >>>> Making packages.html ... done >>>> Old packages: 'affxparser', 'oligo', 'pd.mogene.1.0.st.v1' >>>> Update all/some/none? [a/s/n]: n >>>> Warning message: >>>> In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : >>>> installation of package ?affxparser? had non-zero exit status >>>> >>>>> sessionInfo() >>>> R version 2.15.0 (2012-03-30) >>>> Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit) >>>> >>>> locale: >>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/C >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> >>>> other attached packages: >>>> [1] BiocInstaller_1.4.3 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] inline_0.3.8 Rcpp_0.9.10 tools_2.15.0 >>>> >>>> >>>> Thanks, >>>> David >>>> >>>> _______________________________________________ >>>> 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 >>
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On Mon, Apr 9, 2012 at 12:35 PM, David Ruau <druau at="" stanford.edu=""> wrote: > Thanks, it worked. > Great. I'm guessing you built R from source and that is why getOption("pkgType") returns "source". So biocLite() will always try to install from source unless you pass type="mac.binary.leopard" If you want, you can put options("pkgType" = "mac.binary.leopard") in your ~/.Rprofile and biocLite will always do a binary install. Or options("pkgType" = "both") will cause it to install binary unless a newer source package is available. Dan > David > > On Apr 9, 2012, at 12:25 PM, Dan Tenenbaum wrote: > >> On Mon, Apr 9, 2012 at 12:23 PM, David Ruau <druau at="" stanford.edu=""> wrote: >>> Hi Dan, >>> >>> I pasted the output here http://pastebin.com/Lnt79kC5 >>> biocLite() tries to install affxparser, fails and ask you if you want to update it (at the same time as other packages). And then fails again. >>> >> OK, what if you do this: >> biocLite("affxparser", type="mac.binary.leopard") >> >> ? >> Dan >> >> >>> Thanks, >>> David >>> >>> On Apr 9, 2012, at 11:47 AM, Dan Tenenbaum wrote: >>> >>>> Hi David, >>>> >>>> On Mon, Apr 9, 2012 at 11:33 AM, David Ruau <druau at="" stanford.edu=""> wrote: >>>>> Hello, >>>>> >>>>> I am experiencing an error trying to install affxparser on my mac (Snow Leopard 10.6.8) >>>>> I cannot install from source and the binary version that is not available from Mac OSX snow leopard. >>>> >>>> >>>> Can you show the output of >>>> biocLite("affxparser") >>>> >>>> without type="source"? >>>> >>>> It works on my lion system with R 2.15.0 and BiocInstaller 1.4.3. >>>> >>>> Dan >>>> >>>> >>>>> Below are the relevant lines of the install process. >>>>> >>>>> --- >>>>>> biocLite("affxparser", type='source') >>>>> BioC_mirror: http://bioconductor.org >>>>> Using R version 2.15, BiocInstaller version 1.4.3. >>>>> Installing package(s) 'affxparser' >>>>> trying URL 'http://www.bioconductor.org/packages/2.10/bioc/src/c ontrib/affxparser_1.28.0.tar.gz' >>>>> >>>>> [snip...] >>>>> >>>>> /opt/local/bin/g++-mp-4.5 -I/opt/local/lib/R/include -I/opt/local/lib/R/include/x86_64 -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include ? ?-fPIC ?-pipe -O2 -m64 ?-O0 -c fusion_sdk/calvin_files/fusion/src/FusionCELData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCELData.o >>>>> In file included from fusion_sdk/calvin_files/fusion/src/GCOSAda pter/GCOSCELDataAdapter.h:30:0, >>>>> ? ? ? ? ? ? ? ? from fusion_sdk/calvin_files/fusion/src/FusionCELData.cpp:24: >>>>> fusion_sdk/file/CELFileData.h:91:23: warning: malformed '#pragma options align={mac68k|power|reset}', ignoring >>>>> fusion_sdk/file/CELFileData.h:127:23: error: too many #pragma options align=reset >>>>> make: *** [fusion_sdk/calvin_files/fusion/src/FusionCELData.o] Error 1 >>>>> ERROR: compilation failed for package ?affxparser? >>>>> * removing ?/opt/local/lib/R/library/affxparser? >>>>> * restoring previous ?/opt/local/lib/R/library/affxparser? >>>>> >>>>> The downloaded source packages are in >>>>> ? ? ? ??/private/var/folders/e9/e9-5zLVqFgGBR2S8qU74+U+++TM/-Tmp -/Rtmpn4Zczi/downloaded_packages? >>>>> Updating HTML index of packages in '.Library' >>>>> Making packages.html ?... done >>>>> Old packages: 'affxparser', 'oligo', 'pd.mogene.1.0.st.v1' >>>>> Update all/some/none? [a/s/n]: n >>>>> Warning message: >>>>> In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : >>>>> ?installation of package ?affxparser? had non-zero exit status >>>>> >>>>>> sessionInfo() >>>>> R version 2.15.0 (2012-03-30) >>>>> Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit) >>>>> >>>>> locale: >>>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/C >>>>> >>>>> attached base packages: >>>>> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >>>>> >>>>> other attached packages: >>>>> [1] BiocInstaller_1.4.3 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] inline_0.3.8 Rcpp_0.9.10 ?tools_2.15.0 >>>>> >>>>> >>>>> Thanks, >>>>> David >>>>> >>>>> _______________________________________________ >>>>> 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 >>> >
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Yes, I do build R from source. I use the macport package manager. It's strange I always had a problems with affxparser and rgl. For rgl I could download the binary version and install it with R CMD INSTALL but today I could not download the binary version of affxparser from bioconductor.org. Thanks for your help! David On Apr 9, 2012, at 12:37 PM, Dan Tenenbaum wrote: > On Mon, Apr 9, 2012 at 12:35 PM, David Ruau <druau at="" stanford.edu=""> wrote: >> Thanks, it worked. >> > > Great. I'm guessing you built R from source and that is why > getOption("pkgType") > returns "source". > So biocLite() will always try to install from source unless you pass > type="mac.binary.leopard" > > If you want, you can put > options("pkgType" = "mac.binary.leopard") > in your ~/.Rprofile > and biocLite will always do a binary install. > Or > options("pkgType" = "both") > will cause it to install binary unless a newer source package is available. > > Dan > > > >> David >> >> On Apr 9, 2012, at 12:25 PM, Dan Tenenbaum wrote: >> >>> On Mon, Apr 9, 2012 at 12:23 PM, David Ruau <druau at="" stanford.edu=""> wrote: >>>> Hi Dan, >>>> >>>> I pasted the output here http://pastebin.com/Lnt79kC5 >>>> biocLite() tries to install affxparser, fails and ask you if you want to update it (at the same time as other packages). And then fails again. >>>> >>> OK, what if you do this: >>> biocLite("affxparser", type="mac.binary.leopard") >>> >>> ? >>> Dan >>> >>> >>>> Thanks, >>>> David >>>> >>>> On Apr 9, 2012, at 11:47 AM, Dan Tenenbaum wrote: >>>> >>>>> Hi David, >>>>> >>>>> On Mon, Apr 9, 2012 at 11:33 AM, David Ruau <druau at="" stanford.edu=""> wrote: >>>>>> Hello, >>>>>> >>>>>> I am experiencing an error trying to install affxparser on my mac (Snow Leopard 10.6.8) >>>>>> I cannot install from source and the binary version that is not available from Mac OSX snow leopard. >>>>> >>>>> >>>>> Can you show the output of >>>>> biocLite("affxparser") >>>>> >>>>> without type="source"? >>>>> >>>>> It works on my lion system with R 2.15.0 and BiocInstaller 1.4.3. >>>>> >>>>> Dan >>>>> >>>>> >>>>>> Below are the relevant lines of the install process. >>>>>> >>>>>> --- >>>>>>> biocLite("affxparser", type='source') >>>>>> BioC_mirror: http://bioconductor.org >>>>>> Using R version 2.15, BiocInstaller version 1.4.3. >>>>>> Installing package(s) 'affxparser' >>>>>> trying URL 'http://www.bioconductor.org/packages/2.10/bioc/src/ contrib/affxparser_1.28.0.tar.gz' >>>>>> >>>>>> [snip...] >>>>>> >>>>>> /opt/local/bin/g++-mp-4.5 -I/opt/local/lib/R/include -I/opt/local/lib/R/include/x86_64 -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include -fPIC -pipe -O2 -m64 -O0 -c fusion_sdk/calvin_files/fusion/src/FusionCELData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCELData.o >>>>>> In file included from fusion_sdk/calvin_files/fusion/src/GCOSAd apter/GCOSCELDataAdapter.h:30:0, >>>>>> from fusion_sdk/calvin_files/fusion/src/FusionCELData.cpp:24: >>>>>> fusion_sdk/file/CELFileData.h:91:23: warning: malformed '#pragma options align={mac68k|power|reset}', ignoring >>>>>> fusion_sdk/file/CELFileData.h:127:23: error: too many #pragma options align=reset >>>>>> make: *** [fusion_sdk/calvin_files/fusion/src/FusionCELData.o] Error 1 >>>>>> ERROR: compilation failed for package ?affxparser? >>>>>> * removing ?/opt/local/lib/R/library/affxparser? >>>>>> * restoring previous ?/opt/local/lib/R/library/affxparser? >>>>>> >>>>>> The downloaded source packages are in >>>>>> ?/private/var/folders/e9/e9-5zLVqFgGBR2S8qU74+U+++TM/-Tm p-/Rtmpn4Zczi/downloaded_packages? >>>>>> Updating HTML index of packages in '.Library' >>>>>> Making packages.html ... done >>>>>> Old packages: 'affxparser', 'oligo', 'pd.mogene.1.0.st.v1' >>>>>> Update all/some/none? [a/s/n]: n >>>>>> Warning message: >>>>>> In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : >>>>>> installation of package ?affxparser? had non-zero exit status >>>>>> >>>>>>> sessionInfo() >>>>>> R version 2.15.0 (2012-03-30) >>>>>> Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit) >>>>>> >>>>>> locale: >>>>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/C >>>>>> >>>>>> attached base packages: >>>>>> [1] stats graphics grDevices utils datasets methods base >>>>>> >>>>>> other attached packages: >>>>>> [1] BiocInstaller_1.4.3 >>>>>> >>>>>> loaded via a namespace (and not attached): >>>>>> [1] inline_0.3.8 Rcpp_0.9.10 tools_2.15.0 >>>>>> >>>>>> >>>>>> Thanks, >>>>>> David >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>> >>
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On Mon, Apr 9, 2012 at 3:56 PM, David Ruau <druau at="" stanford.edu=""> wrote: > Yes, I do build R from source. I use the macport package manager. > It's strange I always had a problems with affxparser and rgl. > For rgl I could download the binary version and install it with R CMD INSTALL but today I could not download the binary version of affxparser from bioconductor.org. We have seen many reports of people having problems with Macports and similar projects (of course, there may be tons of users out there where it just works) Kasper
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