This question should probably go on the support site as it is not about package development.
You should update to Mavericks or higher. Earlier versions of Mac OS X are no longer officially supported by R or Bioconductor (that's why a binary is not available). Dan ----- Original Message ----- > From: "Jianhong Ou" <jianhong...@umassmed.edu> > To: "bioc-devel" <bioc-devel@r-project.org> > Sent: Monday, May 2, 2016 12:00:09 PM > Subject: [Bioc-devel] could not install S4Vectors in Mac OS 10.8.5 > Hi, > > I got error when I update S4Vectors in R 3.3 RC r70564 today. I also tried > r70549, same error like this > >> biocLite() > BioC_mirror: https://bioconductor.org > Using Bioconductor 3.3 (BiocInstaller 1.21.6), R 3.3.0 RC (2016-04-28 r70564). > Old packages: 'S4Vectors' > Update all/some/none? [a/s/n]: > a > trying URL > 'https://bioconductor.org/packages/3.3/bioc/src/contrib/S4Vectors_0.9.52.tar.gz' > Content type 'application/x-gzip' length 225431 bytes (220 KB) > ================================================== > downloaded 220 KB > > * installing *source* package �S4Vectors� ... > ** libs > gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG > -I/usr/local/include -fPIC -g -O2 -c AEbufs.c -o AEbufs.o > gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG > -I/usr/local/include -fPIC -g -O2 -c DataFrame_class.c -o > DataFrame_class.o > gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG > -I/usr/local/include -fPIC -g -O2 -c Hits_class.c -o Hits_class.o > gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG > -I/usr/local/include -fPIC -g -O2 -c List_class.c -o List_class.o > gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG > -I/usr/local/include -fPIC -g -O2 -c R_init_S4Vectors.c -o > R_init_S4Vectors.o > gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG > -I/usr/local/include -fPIC -g -O2 -c Rle_class.c -o Rle_class.o > gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG > -I/usr/local/include -fPIC -g -O2 -c Rle_utils.c -o Rle_utils.o > gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG > -I/usr/local/include -fPIC -g -O2 -c SEXP_utils.c -o SEXP_utils.o > gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG > -I/usr/local/include -fPIC -g -O2 -c SimpleList_class.c -o > SimpleList_class.o > gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG > -I/usr/local/include -fPIC -g -O2 -c anyMissing.c -o anyMissing.o > gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG > -I/usr/local/include -fPIC -g -O2 -c eval_utils.c -o eval_utils.o > gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG > -I/usr/local/include -fPIC -g -O2 -c hash_utils.c -o hash_utils.o > gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG > -I/usr/local/include -fPIC -g -O2 -c int_utils.c -o int_utils.o > gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG > -I/usr/local/include -fPIC -g -O2 -c logical_utils.c -o logical_utils.o > gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG > -I/usr/local/include -fPIC -g -O2 -c safe_arithm.c -o safe_arithm.o > gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG > -I/usr/local/include -fPIC -g -O2 -c sort_utils.c -o sort_utils.o > gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG > -I/usr/local/include -fPIC -g -O2 -c str_utils.c -o str_utils.o > gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG > -I/usr/local/include -fPIC -g -O2 -c vector_utils.c -o vector_utils.o > gcc -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup > -single_module -multiply_defined suppress > -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o > S4Vectors.so AEbufs.o DataFrame_class.o Hits_class.o List_class.o > R_init_S4Vectors.o Rle_class.o Rle_utils.o SEXP_utils.o SimpleList_class.o > anyMissing.o eval_utils.o hash_utils.o int_utils.o logical_utils.o > safe_arithm.o sort_utils.o str_utils.o vector_utils.o > -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework > -Wl,CoreFoundation > installing to > /Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/libs > ** R > ** inst > ** preparing package for lazy loading > Creating a generic function for �head� from package �utils� in package > �S4Vectors� > Creating a generic function for �tail� from package �utils� in package > �S4Vectors� > Creating a generic function for �na.omit� from package �stats� in package > �S4Vectors� > Creating a generic function for �na.exclude� from package �stats� in package > �S4Vectors� > Creating a generic function for �complete.cases� from package �stats� in > package > �S4Vectors� > Creating a generic function for �transform� from package �base� in package > �S4Vectors� > Creating a generic function for �merge� from package �base� in package > �S4Vectors� > Creating a new generic function for �rowSums� in package �S4Vectors� > Creating a new generic function for �colSums� in package �S4Vectors� > Creating a new generic function for �rowMeans� in package �S4Vectors� > Creating a new generic function for �colMeans� in package �S4Vectors� > Creating a generic function for �as.matrix� from package �base� in package > �S4Vectors� > Creating a generic function for �window� from package �stats� in package > �S4Vectors� > Creating a generic function for �with� from package �base� in package > �S4Vectors� > Creating a new generic function for �expand.grid� in package �S4Vectors� > Creating a generic function for �by� from package �base� in package > �S4Vectors� > Creating a generic function for �%in%� from package �base� in package > �S4Vectors� > Creating a new generic function for �findMatches� in package �S4Vectors� > Creating a generic function for �as.table� from package �base� in package > �S4Vectors� > Creating a generic function for �t� from package �base� in package �S4Vectors� > Error in rematchDefinition(definition, fdef, mnames, fnames, signature) : > arguments (na.last, decreasing) after '...' in the generic must appear in the > method, in the same place at the end of the argument list > Error : unable to load R code in package �S4Vectors� > ERROR: lazy loading failed for package �S4Vectors� > * removing > �/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors� > * restoring previous > �/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors� > > The downloaded source packages are in > �/private/var/folders/n4/11sc2xz13k56hl85z_h2rgq00000gn/T/RtmpjkynR7/downloaded_packages� > Warning message: > In install.packages(update[instlib == l, "Package"], l, contriburl = > contriburl, > : > installation of package �S4Vectors� had non-zero exit status >> sessionInfo() > R version 3.3.0 RC (2016-04-28 r70564) > Platform: x86_64-apple-darwin12.5.0 (64-bit) > Running under: OS X 10.8.5 (Mountain Lion) > > 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] parallel stats4 methods stats graphics grDevices datasets > utils > base > > other attached packages: > [1] S4Vectors_0.9.41 BiocGenerics_0.17.5 BiocInstaller_1.21.6 > > loaded via a namespace (and not attached): > [1] tools_3.3.0 > > > Yours Sincerely, > > Jianhong Ou > > TEL: 508-856-5379 > LRB 608 > Bioinformatician of Bioinformatics core at > Department of Molecular, Cell and Cancer Biology > 364 Plantation Street Worcester, > MA 01605 > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
