[BioC] flowQ loading error after installing ImageMagick

Dan Tenenbaum dtenenba at fhcrc.org
Tue Mar 5 16:41:02 CET 2013 

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 $PATH
>> >>>>
>> >>>> /Library/Frameworks/Python.framework/Versions/2.7/bin:/Library/Frameworks/EPD64.framework/Versions/Current/bin:/Library/Frameworks/Python.framework/Versions/2.7/bin:/Library/Frameworks/EPD64.framework/Versions/Current/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/opt/local/bin:/opt/local/bin
>> >>>> Chandra-Jacks-MacBook:~ chanj$ 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]]
>>
>>
>>
>> _______________________________________________
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>
>

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