[BioC] flowQ loading error after installing ImageMagick

Dan Tenenbaum dtenenba at fhcrc.org
Tue Mar 5 06:45:41 CET 2013


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.
>
>
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>
>
>
> 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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