[BioC] flowClust installation on OS X
Kenneth Lo
c.lo at stat.ubc.ca
Wed May 6 01:59:30 CEST 2009
Hi Noah,
In addition to Patrick's suggestions, please note the following:
To narrow down the possible sources of errors, please clear all the
object files in the /src directory first and see what goes wrong
again. There should be four source files, and flowClustGaussian.c
seems to be missing / not compiled properly, according to your output.
As a first attempt, you may try if it helps by setting the environment
variable PKG_CFLAGS to point to the include directory of your gsl
installation, for example:
# to locate gsl header files for gcc
export PKG_CFLAGS='-I/usr/local/include'
In the example above, the header files are located in a sub-directory
named "gsl" under the "include" directory.
Kenneth
On 5-May-09, at 3:35 PM, Patrick Aboyoun wrote:
> 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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