[BioC] flowQ loading error after installing ImageMagick

Tue Mar 5 07:06:14 CET 2013

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

> 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 â€˜plotâ€™ when loading â€˜graphicsâ€™
>>>> 
>>>> 2: replacing previous import â€˜asâ€™ when loading â€˜methodsâ€™
>>>> 
>>>> Error: package/namespace load failed for â€˜flowQâ€™.
>>>> 
>>>> 
>>>> 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.
>>>> 
>>>> 
>>>> _______________________________________________
>>>> 
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>>>> 
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>>>> 
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>>>> 
>>>> Search the archives:
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>>>> 
>>>> 
>>>> 
>>>> 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