[BioC] flowQ loading error after installing ImageMagick

Tue Mar 5 19:01:08 CET 2013

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?

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