[BioC] flowQ loading error after installing ImageMagick
Chandra Jack
chanj at rice.edu
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
>>
>>
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>>
>>
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>>
>>
>> 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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