Hi Dan, Thank you for your answer. I hope I can update to Mavericks but our help desk just ask me to hold on current OS.
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 On 5/2/16 3:04 PM, "Dan Tenenbaum" <dtene...@fredhutch.org> wrote: >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/down >>loaded_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]] >> >> >> 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