[BioC] flowQ loading issue
Fletez-Brant, Christopher (NIH/VRC) [C]
christopher.fletez-brant at nih.gov
Fri Jul 13 21:22:12 CEST 2012
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]]
>
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