[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
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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