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/un iversal/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]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >