Sean Davis wrote: > On Fri, May 29, 2009 at 11:01 PM, Mark Kimpel <mwkimpel at="" gmail.com=""> wrote: >> Thanks Sean, that fixed it. I didn't get any errors when I installed R >> (Linux from source) so I don't know what could have happened. Fixed anyway, >> good pick up! Mark > > You will want to be sure to do tools/rsync-recommended when installing > from source, I think. I'm not sure exactly which tarballs are > supposed to include what, but doing the rsync first won't hurt. This is the important part. Very recently a decision was made to abandon the notion of package bundles, and MASS was in one. With that gone, the whole install process changed and updating requires not just the code, but also getting all required packages. Robert > > Sean > > >> On Fri, May 29, 2009 at 10:53 PM, Sean Davis <seandavi at="" gmail.com=""> wrote: >>> On Fri, May 29, 2009 at 10:43 PM, Mark Kimpel <mwkimpel at="" gmail.com=""> wrote: >>>> I went to update packages and discovered multiple packages that import >>>> or >>>> depend on MASS to have non-zero exit status. An example is the BioC >>>> package >>>> "multtest". I must confess that I don't remember what MASS does/did but >>>> I >>>> believe it was a CRAN package. When I went there, it wasn't there, nor >>>> is it >>>> listed as a BioC package. What could be the problem? My output and >>>> sessionInfo() follows. Mark >>>> >>>>> biocLite("multtest") >>>> Running biocinstall version 2.4.10 with R version 2.9.0 >>>> Your version of R requires version 2.4 of Bioconductor. >>>> Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = >>>> dependencies, : >>>> argument 'lib' is missing: using >>>> '/home/mkimpel/R_HOME/site-library-2.9.0' >>>> Warning: dependency ?MASS? is not available >>> MASS is a recommended package, so it is usually installed when you >>> install R. It appears that it was not for some reason, so you can get >>> it as part of the VR bundle, I believe. Doing biocLite('VR') should >>> get you what you need. I'm not sure how biocLite() is supposed to >>> behave with "bundles", but it appears to not pick up the fact that >>> MASS is in the VR bundle. >>> >>> Sean >>> >>>> trying URL ' >>>> >>>> http://bioconductor.org/packages/2.4/bioc/src/contrib/multtest_2. 0.0.tar.gz' >>>> Content type 'application/x-gzip' length 1446401 bytes (1.4 Mb) >>>> opened URL >>>> ================================================== >>>> downloaded 1.4 Mb >>>> >>>> * Installing *source* package ?multtest? ... >>>> ** libs >>>> gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-2.9.0/R-build/lib64/R/include >>>> -I/usr/local/include -DUSEDOUBLE -fpic -g -O2 -c Rpack.c -o Rpack.o >>>> gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-2.9.0/R-build/lib64/R/include >>>> -I/usr/local/include -DUSEDOUBLE -fpic -g -O2 -c VScount.c -o >>>> VScount.o >>>> gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-2.9.0/R-build/lib64/R/include >>>> -I/usr/local/include -DUSEDOUBLE -fpic -g -O2 -c >>>> block_sampling_fixed.c >>>> -o block_sampling_fixed.o >>>> gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-2.9.0/R-build/lib64/R/include >>>> -I/usr/local/include -DUSEDOUBLE -fpic -g -O2 -c bootloop.c -o >>>> bootloop.o >>>> gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-2.9.0/R-build/lib64/R/include >>>> -I/usr/local/include -DUSEDOUBLE -fpic -g -O2 -c mt.c -o mt.o >>>> gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-2.9.0/R-build/lib64/R/include >>>> -I/usr/local/include -DUSEDOUBLE -fpic -g -O2 -c pairt_sampling.c -o >>>> pairt_sampling.o >>>> gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-2.9.0/R-build/lib64/R/include >>>> -I/usr/local/include -DUSEDOUBLE -fpic -g -O2 -c >>>> pairt_sampling_fixed.c >>>> -o pairt_sampling_fixed.o >>>> gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-2.9.0/R-build/lib64/R/include >>>> -I/usr/local/include -DUSEDOUBLE -fpic -g -O2 -c random.c -o random.o >>>> gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-2.9.0/R-build/lib64/R/include >>>> -I/usr/local/include -DUSEDOUBLE -fpic -g -O2 -c sampling.c -o >>>> sampling.o >>>> gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-2.9.0/R-build/lib64/R/include >>>> -I/usr/local/include -DUSEDOUBLE -fpic -g -O2 -c sampling_fixed.c -o >>>> sampling_fixed.o >>>> gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-2.9.0/R-build/lib64/R/include >>>> -I/usr/local/include -DUSEDOUBLE -fpic -g -O2 -c stat_func.c -o >>>> stat_func.o >>>> gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-2.9.0/R-build/lib64/R/include >>>> -I/usr/local/include -DUSEDOUBLE -fpic -g -O2 -c stat_order.c -o >>>> stat_order.o >>>> gcc -std=gnu99 -shared -L/usr/local/lib64 -o multtest.so Rpack.o >>>> VScount.o >>>> block_sampling_fixed.o bootloop.o mt.o pairt_sampling.o >>>> pairt_sampling_fixed.o random.o sampling.o sampling_fixed.o stat_func.o >>>> stat_order.o -lm >>>> ** R >>>> ** data >>>> ** inst >>>> ** preparing package for lazy loading >>>> >>>> Welcome to Bioconductor >>>> >>>> Vignettes contain introductory material. To view, type >>>> 'openVignette()'. To cite Bioconductor, see >>>> 'citation("Biobase")' and for packages 'citation(pkgname)'. >>>> >>>> Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) : >>>> there is no package called 'MASS' >>>> ERROR: lazy loading failed for package ?multtest? >>>> * Removing ?/home/mkimpel/R_HOME/site-library-2.9.0/multtest? >>>> >>>> The downloaded packages are in >>>> ?/tmp/RtmphnsZE8/downloaded_packages? >>>> Warning message: >>>> In install.packages(pkgs = pkgs, repos = repos, dependencies = >>>> dependencies, : >>>> installation of package 'multtest' had non-zero exit status >>>>> sessionInfo() >>>> R version 2.9.0 (2009-04-17) >>>> x86_64-unknown-linux-gnu >>>> >>>> locale: >>>> >>>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE= en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8 ;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_I DENTIFICATION=C >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> >>>> loaded via a namespace (and not attached): >>>> [1] tcltk_2.9.0 tools_2.9.0 >>>> ------------------------------------------------------------ >>>> Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry >>>> Indiana University School of Medicine >>>> >>>> 15032 Hunter Court, Westfield, IN 46074 >>>> >>>> (317) 490-5129 Work, & Mobile & VoiceMail >>>> (317) 399-1219 Home >>>> Skype: mkimpel >>>> >>>> "The real problem is not whether machines think but whether men do." -- >>>> B. >>>> F. Skinner >>>> ****************************************************************** >>>> >>>> [[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 >>>> >> > > _______________________________________________ > 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 -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org