[BioC] flowQ loading error after installing ImageMagick
Dan Tenenbaum
dtenenba at fhcrc.org
Tue Mar 5 07:20:13 CET 2013
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
>
>
>
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