Well, you can tell your helpdesk that this is going to impact people's work as the OS you are using will no longer be supported by R/Bioconductor starting with the release this week.
Mavericks was released 3 years ago. It seems reasonable to support it now. Dan ----- Original Message ----- > From: "Jianhong Ou" <jianhong...@umassmed.edu> > To: "Dan Tenenbaum" <dtene...@fredhutch.org> > Cc: "bioc-devel" <bioc-devel@r-project.org> > Sent: Monday, May 2, 2016 12:34:47 PM > Subject: Re: [Bioc-devel] could not install S4Vectors in Mac OS 10.8.5 > 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]] >>> >>> >>> _______________________________________________ >>> 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
