[BioC] flowClust installation on OS X
Patrick Aboyoun
paboyoun at fhcrc.org
Wed May 6 00:35:41 CEST 2009
Noah,
This fits in with a discussion we had earlier on this mailing list
concerning the Rredland Mac OS X binary package:
http://article.gmane.org/gmane.science.biology.informatics.conductor/22936
Mac OS X binary packages that link to 3rd party libraries can be
difficult to use because these 3rd libraries may be installed in a
different location or the versions may differ between the build machine
and the machine you wish to install it on. As a general rule BioC build
machines do not use MacPorts or DarwinPorts because these tools do not
facilitate the creation of universal binaries for the libraries they
install. Lacking pre-built universal binaries for the 3rd party
libraries, we build the universal binaries ourselves and install them in
/usr/local/lib.
In your situation, I'd first try installing flowClust from source:
source("http://bioconductor.org/biocLite.R")
biocLite("flowClust", type = "source")
If that causes you difficulties, you could try building GSL from source
and install it at /usr/local/lib. We have GSL version 1.12 on the Mac
build machines.
Patrick
Noah Zimmerman wrote:
> Hello,
>
> I get the following errors when I try to install flowClust on Mac OS X
> 10.5.6 with R 2.8.
> I installed gsl using Macports (located in /opt/loca/lib) and set my
> library path accordingly
>
> noah at insight~> echo $LD_LIBRARY_PATH
> /opt/local/lib:
>
> Any advice?
>
> Best,
> Noah
>
> Installing directly from bioconductor:
> > source("http://bioconductor.org/biocLite.R")
> > biocLite("flowClust")
> Running biocinstall version 2.3.13 with R version 2.8.0
> Your version of R requires version 2.3 of Bioconductor.
> trying URL 'http://bioconductor.org/packages/2.3/bioc/bin/macosx/universal/contrib/2.8/flowClust_1.8.1.tgz'
> Content type 'application/x-gzip' length 423564 bytes (413 Kb)
> opened URL
> ==================================================
> downloaded 413 Kb
> The downloaded packages are in
> /var/folders/vO/vOrIx2YWEoG2aXlhfq7ZpE+++TI/-Tmp-//RtmpLadWOr/
> downloaded_packages
> > library(flowClust)
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
> unable to load shared library '/Library/Frameworks/R.framework/
> Resources/library/flowClust/libs/i386/flowClust.so':
> dlopen(/Library/Frameworks/R.framework/Resources/library/flowClust/
> libs/i386/flowClust.so, 6): Library not loaded: /usr/local/lib/libgsl.
> 0.dylib
> Referenced from: /Library/Frameworks/R.framework/Resources/library/
> flowClust/libs/i386/flowClust.so
> Reason: image not found
> In addition: Warning message:
> package 'flowClust' was built under R version 2.8.1
> Error: package/namespace load failed for 'flowClust'
>
> Trying to install from source (note: I had to modify the Makevars file
> to point to my gsl installation):
> noah at insight~/Desktop/installfail> R CMD BUILD flowClust/
> * checking for file 'flowClust/DESCRIPTION' ... OK
> * preparing 'flowClust':
> * checking DESCRIPTION meta-information ... OK
> * cleaning src
> * running cleanup
> * installing the package to re-build vignettes
> * Installing *source* package 'flowClust' ...
> checking for gcc... gcc -arch i386 -std=gnu99
> checking for C compiler default output file name... rm: a.out.dSYM: is
> a directory
> a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc -arch i386 -std=gnu99 accepts -g... yes
> checking for gcc -arch i386 -std=gnu99 option to accept ISO C89...
> none needed
> checking for gsl-config... /opt/local/bin/gsl-config
> checking for GSL - version >= 1.6... yes
> configure: creating ./config.status
> config.status: creating src/Makevars
> ** libs
> ** arch - i386
> gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/
> include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/
> opt/local/include -I/usr/local/include -fPIC -g -O2 -c BoxCox.c -o
> BoxCox.o
> gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/
> include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/
> opt/local/include -I/usr/local/include -fPIC -g -O2 -c flowClust.c
> -o flowClust.o
> gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/
> include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/
> opt/local/include -I/usr/local/include -fPIC -g -O2 -c ranMVNT.c -
> o ranMVNT.o
> gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names
> -mmacosx-version-min=10.4 -undefined dynamic_lookup -single_module -
> multiply_defined suppress -L/usr/local/lib -o flowClust.so BoxCox.o
> flowClust.o ranMVNT.o -L/opt/local/lib -F/Library/Frameworks/
> R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
> ** R
> ** data
> ** inst
> ** preparing package for lazy loading
> Loading required package: mnormt
> Loading required package: mclust
> by using mclust, you accept the license agreement in the LICENSE file
> and at http://www.stat.washington.edu/mclust/license.txt
> Loading required package: ellipse
> Loading required package: flowCore
> Loading required package: rrcov
> Loading required package: robustbase
> Scalable Robust Estimators with High Breakdown Point (version 0.4-07)
> Loading required package: feature
> Loading required package: KernSmooth
> KernSmooth 2.22 installed
> Copyright M. P. Wand 1997
> Loading required package: Biobase
> Loading required package: tools
>
> Welcome to Bioconductor
>
> Vignettes contain introductory material. To view, type
> 'openVignette()'. To cite Bioconductor, see
> 'citation("Biobase")' and for packages 'citation(pkgname)'.
>
>
> Attaching package: 'flowCore'
>
>
> The following object(s) are masked from package:stats :
>
> alias,
> filter
>
> ** help
> >>> Building/Updating help pages for package 'flowClust'
> Formats: text html latex example
> Map text html latex example
> SimulateMixture text html latex example
> Subset text html latex
> box text html latex example
> density text html latex example
> dmvt text html latex
> flowClust-internal text html latex
> flowClust-package text html latex
> flowClust text html latex example
> hist text html latex example
> plot.flowClust text html latex example
> plot.flowCore text html latex
> plot.flowDens text html latex
> posterior text html latex example
> rbox text html latex
> rituximab text html latex
> ruleOutliers text html latex example
> show.flowClust text html latex
> show.tmixFilter text html latex
> split text html latex
> summary text html latex
> tmixFilter text html latex example
> ** building package indices ...
> * DONE (flowClust)
> * creating vignettes ... ERROR
> Loading required package: mnormt
> Loading required package: mclust
> Loading required package: ellipse
> Loading required package: flowCore
> Loading required package: rrcov
> Loading required package: robustbase
> Loading required package: feature
> Loading required package: KernSmooth
> KernSmooth 2.22 installed
> Copyright M. P. Wand 1997
> Loading required package: Biobase
>
> Welcome to Bioconductor
>
> Vignettes contain introductory material. To view, type
> 'openVignette()'. To cite Bioconductor, see
> 'citation("Biobase")' and for packages 'citation(pkgname)'.
>
>
> Attaching package: 'flowCore'
>
>
> The following object(s) are masked from package:stats :
>
> alias,
> filter
>
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
> unable to load shared library '/var/folders/vO/
> vOrIx2YWEoG2aXlhfq7ZpE+++TI/-Tmp-//Rinst2151656065/flowClust/libs/i386/
> flowClust.so':
> dlopen(/var/folders/vO/vOrIx2YWEoG2aXlhfq7ZpE+++TI/-Tmp-//
> Rinst2151656065/flowClust/libs/i386/flowClust.so, 6): Symbol not
> found: _gsl_root_fsolver_brent
> Referenced from: /var/folders/vO/vOrIx2YWEoG2aXlhfq7ZpE+++TI/-Tmp-//
> Rinst2151656065/flowClust/libs/i386/flowClust.so
> Expected in: dynamic lookup
>
>
> Error: processing vignette 'flowClust.Rnw' failed with diagnostics:
> chunk 1 (label=stage0)
> Error : package/namespace load failed for 'flowClust'
> Execution halted
>
>
>
> [[alternative HTML version deleted]]
>
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