[BioC] flowQ loading error after installing ImageMagick

Tue Mar 5 06:57:41 CET 2013

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?

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 $PATH
>> which convert
>>
>>
>>
>> thanks,
>> Dan
>>
>>
>>
>>> On Mar 4, 2013, at 10:18 PM, Dan Tenenbaum wrote:
>>>
>>> On Mon, Mar 4, 2013 at 8:07 PM, Chandra Jack <chanj at rice.edu> wrote:
>>>
>>> The convert command isn't in my PATH but adding the newIt doesn't seem to be
>>> working. I don't have a .bashrc file but I have a .bash_profile. The
>>> original file was:
>>>
>>> # Setting PATH for EPD-7.1-2
>>>
>>> # The orginal version is saved in .bash_profile.pysave
>>>
>>> PATH="/Library/Frameworks/EPD64.framework/Versions/Current/bin:${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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>>>
>>>
>>>
>>> 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
>
>
>