[BioC] flowQ loading error after installing ImageMagick

Dan Tenenbaum dtenenba at fhcrc.org
Mon Mar 4 23:15:23 CET 2013


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
>
> --
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>
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