[BioC] flowQ loading error after installing ImageMagick

Dan Tenenbaum dtenenba at fhcrc.org
Tue Mar 5 20:26:49 CET 2013


On Tue, Mar 5, 2013 at 10:01 AM, Chandra Jack <chanj at rice.edu> wrote:
> It works! Thanks so much for your help!
>
> path <- Sys.getenv("PATH")
>> path
> [1] "/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin"
>
> Why is is not a recommended long term solution? Will I need to call path each time I tried to load flowQ?
>

You could put the Sys.setenv() command in your ~/.Rprofile and it
would get run each time you start R.

That would work and solve the problem.

But it seems to me that for some reason your path within R differs
from your system path and you may want to find out why. There are a
number of configuration files (see ?Startup) where this could happen.
If your R installation is unchanged, as far as you know, then there is
some other problem.

Dan


>
> On Mar 5, 2013, at 11:26 AM, Dan Tenenbaum wrote:
>
>> I got the following steps to work on a machine similar to yours. This
>> is not a recommended long term solution but I'd be interested to see
>> if it works for you.
>>
>> in R:
>> path <- Sys.getenv("PATH")
>> path # let me know what this says
>> Sys.setenv(PATH=paste0(path, ":", "/opt/local/bin"))
>> library(flowQ)
>>
>> Dan
>>
>>
>> On Tue, Mar 5, 2013 at 8:49 AM, Chandra Jack <chanj at rice.edu> wrote:
>>> I have removed the export and made sure that there are no spaces and still
>>> get the same message.
>>>
>>> On Mar 5, 2013, at 10:31 AM, Harris A. Jaffee wrote:
>>>
>>> I haven't been listening too closely, but...
>>>
>>> Exactly what you wrote would have been a bash/sh syntax error.  There cannot
>>> be spaces around the '='.  If
>>> you are on the right track, then you need something like
>>>
>>> PATH=$PATH:opt/local/bin
>>>
>>> While we are at it, I believe that resetting a variable that is already
>>> exported, as with PATH, does not
>>> necessitate the 'export' command, in order to reset the exported value.  For
>>> example,
>>>
>>> sh-3.2$ export foo=bar
>>> sh-3.2$ env | grep foo
>>> foo=bar
>>> sh-3.2$ foo=bar2
>>> sh-3.2$ env | grep foo
>>> foo=bar2
>>>
>>>
>>> On Mar 5, 2013, at 11:11 AM, Chandra Jack wrote:
>>>
>>> I didn't have a ~/.profile so I created one. All I put in it was export PATH
>>> = $PATH:opt/local/bin. But I got the same message that /bin/sh: convert:
>>> command not found.  I read that .bash_profile may need to call .profile and
>>> also tried putting source ~/.profile at the end of the file but that gave me
>>> the same message.
>>>
>>>
>>>
>>> On Mar 5, 2013, at 9:41 AM, Dan Tenenbaum wrote:
>>>
>>>
>>> On Tue, Mar 5, 2013 at 12:21 AM, Nikolas Pontikos <n.pontikos at gmail.com>
>>> wrote:
>>>
>>> From your R error message, system is calling /bin/sh not /bin/bash (which
>>>
>>> should be the same program but i don't think sh reads the .bashrc config
>>>
>>> file).
>>>
>>> Maybe the convert command is not available from /bin/sh?
>>>
>>>
>>>
>>> In that case the file to be edited is ~/.profile
>>>
>>>
>>> Dan
>>>
>>>
>>>
>>>
>>> On 5 March 2013 06:42, Chandra Jack <chanj at rice.edu> wrote:
>>>
>>>
>>> Yes. I've been restarting R after everytime I changed bash_profile. I also
>>>
>>> just tried reinstalling R but that didn't help either.
>>>
>>>
>>> On Mar 5, 2013, at 12:20 AM, Dan Tenenbaum wrote:
>>>
>>>
>>> On Mon, Mar 4, 2013 at 10:06 PM, Chandra Jack <chanj at rice.edu> wrote:
>>>
>>>
>>> On Mar 4, 2013, at 11:57 PM, Dan Tenenbaum wrote:
>>>
>>>
>>> On Mon, Mar 4, 2013 at 9:53 PM, Chandra Jack <chanj at rice.edu> wrote:
>>>
>>> Thank you so much for your help.
>>>
>>>
>>> Chandra-Jacks-MacBook:~ chanj$ 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 Œplot‚ when loading Œgraphics‚
>>>
>>>
>>> 2: replacing previous import Œas‚ when loading Œmethods‚
>>>
>>>
>>> Error: package/namespace load failed for ŒflowQ‚.
>>>
>>>
>>>
>>>
>>> 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]]
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>>
>>> 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
>>>
>>>
>>>
>>>
>>>
>>> [[alternative HTML version deleted]]
>>>
>>>
>>> _______________________________________________
>>>
>>> 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
>
>
>



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