[BioC] flowQ loading error after installing ImageMagick

Mon Mar 4 23:09:26 CET 2013

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
In addition: Warning messages:
1: replacing previous import â€˜plotâ€™ when loading â€˜graphicsâ€™ 
2: replacing previous import â€˜asâ€™ when loading â€˜methodsâ€™ 
Error: package/namespace load failed for â€˜flowQâ€™.

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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