Thank you for the reply. I reinstalled ImageMagick per their instructions (that is, as I am using a Mac I installed via MacPorts), and when I run the convert command I get the attached output. However, R gives me the same error. Any help is appreciated. Thank you, Kipper convert -list configure Path: /opt/local/lib/ImageMagick-6.7.8/config/configure.xml Name Value ---------------------------------------------------------------------- ----- ---- CC /usr/bin/clang CFLAGS -D_THREAD_SAFE -D_THREAD_SAFE -pthread -pipe -O2 -arch x86_64 -Wall -D_THREAD_SAFE -pthread CODER_PATH /opt/local/lib/ImageMagick-6.7.8/modules-Q16/coders CONFIGURE ./configure '--prefix=/opt/local' '--enable-shared' '--enable-static' '--disable-ltdl-install' '--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/clang' 'CFLAGS=-pipe -O2 -arch x86_64' 'LDFLAGS=-L/opt/local/lib -arch x86_64' 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/clang++' '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/clang++ CXXFLAGS -pipe -O2 -arch x86_64 -D_THREAD_SAFE -pthread DEFS -DHAVE_CONFIG_H DELEGATES bzlib fontconfig freetype gs jpeg jng lcms2 lzma png tiff x11 xml zlib DISTCHECK_CONFIG_FLAGS 'CC=/usr/bin/clang' 'CFLAGS=-pipe -O2 -arch x86_64' 'CPPFLAGS=-I/opt/local/include' 'CXX=/usr/bin/clang++' '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-6.7.8 EXEC-PREFIX /opt/local EXECUTABLE_PATH /opt/local/bin FEATURES OpenCL FILTER_PATH /opt/local/lib/ImageMagick-6.7.8/modules-Q16/filters HOST x86_64-apple-darwin11.4.0 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 0x678 LIB_VERSION_NUMBER 6,7,8,0 LIBRARY_PATH /opt/local/lib/ImageMagick-6.7.8 LIBS -lMagickCore -llcms2 -ltiff -lfreetype -ljpeg -L/opt/local/lib -lfontconfig -lXext -lSM -lICE -lX11 -lXt -L/opt/local/lib -llzma -lbz2 -lz -lm -Wl,-framework,OpenCL -lm -lpthread -lltdl NAME ImageMagick PCFLAGS PREFIX /opt/local QuantumDepth 16 RELEASE_DATE 2012-07-12 SHARE_PATH /opt/local/share/ImageMagick-6.7.8 SVN_REVISION 8563 TARGET_CPU x86_64 TARGET_OS darwin11.4.0 TARGET_VENDOR apple VERSION 6.7.8 WEBSITE http://www.imagemagick.org Path: [built-in] Name Value ---------------------------------------------------------------------- ----- ---- NAME ImageMagick > sessionInfo() R version 2.15.0 (2012-03-30) 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_0.6-19 parody_1.14.0 bioDist_1.28.0 KernSmooth_2.23-8 mvoutlier_1.9.7 sgeostat_1.0-24 robCompositions_1.6.0 [8] car_2.0-12 nnet_7.3-4 compositions_1.10-2 energy_1.4-0 MASS_7.3-19 boot_1.3-5 tensorA_0.36 [15] rgl_0.92.880 outliers_0.14 HTqPCR_1.10.0 limma_3.12.1 RColorBrewer_1.0-5 flowViz_1.20.0 lattice_0.20-6 [22] flowCore_1.22.1 rrcov_1.3-02 pcaPP_1.9-47 mvtnorm_0.9-9992 robustbase_0.9-2 Biobase_2.16.0 BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] affy_1.34.0 affyio_1.24.0 annotate_1.34.1 AnnotationDbi_1.18.1 BiocInstaller_1.4.7 DBI_0.2-5 feature_1.2.8 [8] flowQ_1.16.0 gdata_2.11.0 geneplotter_1.34.0 gplots_2.11.0 graph_1.34.0 grid_2.15.0 gtools_2.7.0 [15] IRanges_1.14.4 ks_1.8.8 preprocessCore_1.18.0 RSQLite_0.11.1 stats4_2.15.0 XML_3.9-4 xtable_1.7-0 [22] zlibbioc_1.2.0 On 7/13/12 11:39 AM, "Finak, Greg" <gfinak at="" fhcrc.org=""> wrote: >Hi, Christopher >Yes, it's related. >It appears that your ImageMagick installation is not set up correctly. >From the look of it, flowQ tries to run the 'convert' command and it >fails for the same reasons you see runnung it from the command line. > >Greg Finak > > >> ------------------------------ >> >> Message: 4 >> Date: Thu, 12 Jul 2012 08:28:49 -0400 >> From: "Fletez-Brant, Christopher (NIH/VRC) [C]" >> <christopher.fletez-brant at="" nih.gov=""> >> To: "bioconductor at r-project.org" <bioconductor at="" r-project.org=""> >> Subject: [BioC] flowQ loading issue >> Message-ID: <cc243b41.674%christopher.fletez-brant at="" nih.gov=""> >> Content-Type: text/plain; charset="Windows-1252" >> >> Dear List, >> >> I am attempting to load flowQ and am getting the error message listed >>at the end of this message. It is similar to errors reported here: >> >> https://stat.ethz.ch/pipermail/bioconductor/2011-June/039962.html >> >> and here: >> >> https://stat.ethz.ch/pipermail/bioconductor/2011-August/040806.html >> >> However, I have ImageMagick installed already. On a whim I decided to >>run the ImageMagick command listed in the error message and got the >>following output: >> >> ~ $ convert -list configure >> >> Path: [built-in] >> >> Name Value >> >>-------------------------------------------------------------------- ----- >>------ >> NAME ImageMagick >> convert: unable to access configure file `configure.xml' @ >>warning/configure.c/GetConfigureOptions/591. >> >> Is this related? R Errors, version info after signature. >> >> Thank you, >> Kipper Fletez-Brant >> >> R information: >> >> $platform >> >> [1] "x86_64-apple-darwin9.8.0" >> >> >> $version.string >> >> [1] "R version 2.15.0 (2012-03-30)" >> >> Error Message: >> >> >> Attaching package: ?latticeExtra? >> >> >> The following object(s) are masked from ?package:flowViz?: >> >> >> ecdfplot >> >> >> 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: package ?boot? was built under R version 2.15.1 >> >> 2: package ?MASS? was built under R version 2.15.1 >> >> 3: package ?nnet? was built under R version 2.15.1 >> >> 4: package ?KernSmooth? was built under R version 2.15.1 >> >> Error: package/namespace load failed for ?flowQ? >> >> >> >> ------------------------------ > > > [[alternative HTML version deleted]] > >_______________________________________________ >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