[BioC] flowQ loading error after installing ImageMagick
Dan Tenenbaum
dtenenba at fhcrc.org
Tue Mar 5 18:26:05 CET 2013
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
>
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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
>
>
>
>
>
> [[alternative HTML version deleted]]
>
>
> _______________________________________________
>
> Bioconductor mailing list
>
> Bioconductor at r-project.org
>
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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
>
>
>
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