Thanks Herve, that solved the problem. It installed correctly now. Regards, Charles
On Thu, Aug 27, 2015 at 4:14 PM, Hervé Pagès <hpa...@fredhutch.org> wrote: > On 08/27/2015 10:21 AM, Charles Determan wrote: > >> I am simply using gcc-4.8 >> >> Here is the full output: >> >> BioC_mirror: http://bioconductor.org >> Using Bioconductor version 3.1 (BiocInstaller 1.18.4), R version 3.2.2. >> Installing package(s) ‘S4Vectors’ >> trying URL >> ' >> http://bioconductor.org/packages/3.1/bioc/src/contrib/S4Vectors_0.6.3.tar.gz >> ' >> Content type 'application/x-gzip' length 187491 bytes (183 KB) >> ================================================== >> downloaded 183 KB >> >> * installing *source* package ‘S4Vectors’ ... >> ** libs >> ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3 >> -std=c99 -c AEbufs.c -o AEbufs.o >> ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3 >> -std=c99 -c DataFrame_class.c -o DataFrame_class.o >> ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3 >> -std=c99 -c Hits_class.c -o Hits_class.o >> Hits_class.c: In function ‘Hits_new’: >> Hits_class.c:157:13: warning: ‘q_hits2’ may be used uninitialized in >> this function [-Wmaybe-uninitialized] >> tsort_hits(q_hits2, s_hits, qh_out, sh_out, nhit, >> ^ >> Hits_class.c:144:7: note: ‘q_hits2’ was declared here >> int *q_hits2, *qh_out, *sh_out; >> ^ >> Hits_class.c:233:14: warning: ‘revmap’ may be used uninitialized in this >> function [-Wmaybe-uninitialized] >> defineVar(install(translateChar(symbol)), revmap, revmap_envir); >> ^ >> ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3 >> -std=c99 -c List_class.c -o List_class.o >> ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3 >> -std=c99 -c R_init_S4Vectors.c -o R_init_S4Vectors.o >> ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3 >> -std=c99 -c Rle_class.c -o Rle_class.o >> ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3 >> -std=c99 -c Rle_utils.c -o Rle_utils.o >> ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3 >> -std=c99 -c SEXP_utils.c -o SEXP_utils.o >> ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3 >> -std=c99 -c SimpleList_class.c -o SimpleList_class.o >> ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3 >> -std=c99 -c anyMissing.c -o anyMissing.o >> ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3 >> -std=c99 -c eval_utils.c -o eval_utils.o >> ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3 >> -std=c99 -c hash_utils.c -o hash_utils.o >> ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3 >> -std=c99 -c int_utils.c -o int_utils.o >> ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3 >> -std=c99 -c logical_utils.c -o logical_utils.o >> ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3 >> -std=c99 -c safe_arithm.c -o safe_arithm.o >> ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3 >> -std=c99 -c sort_utils.c -o sort_utils.o >> ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3 >> -std=c99 -c str_utils.c -o str_utils.o >> str_utils.c: In function ‘get_svn_time’: >> str_utils.c:259:2: warning: implicit declaration of function ‘tzset’ >> [-Wimplicit-function-declaration] >> tzset(); >> ^ >> str_utils.c:261:18: error: ‘timezone’ undeclared (first use in this >> function) >> utc_offset = - (timezone / 3600); >> ^ >> str_utils.c:261:18: note: each undeclared identifier is reported only >> once for each function it appears in >> make: *** [str_utils.o] Error 1 >> ERROR: compilation failed for package ‘S4Vectors’ >> * removing ‘/home/cdeterman/R/x86_64-pc-linux-gnu-library/3.2/S4Vectors’ >> > > The -std=c99 compilation flag seems to be causing this. On our build > machines that use gcc (i.e. Linux, Windows, and Snow Leopard), we use > -std=gnu99. Check what flag your R is using by running: > > R CMD config CC > > in your terminal. My understanding is that gcc doesn't fully support > c99 yet, and that R packages are only required to support gnu99. > AFAIK the standard procedure for configuring/compiling/installing > R should set this to gnu99 when gcc is the default compiler. > So I'm not not sure why R is configured to use -std=c99 on your > system. > > Anyway I just made a change to S4Vectors so now it should compile > with -std=c99. The change is in versions 0.6.4 (release) and 0.7.14 > (devel) which should become available in the next 24 hours or less. > You might run into compilation problems with other packages that > don't support -std=c99 though so I would still encourage you to change > that setting (just edit R_HOME/etc/Makeconf if you know what you are > doing or ask a system admin to look into this). > > Cheers, > H. > > > >> On Thu, Aug 27, 2015 at 12:04 PM, Hervé Pagès <hpa...@fredhutch.org >> <mailto:hpa...@fredhutch.org>> wrote: >> >> Hi Charles, >> >> What compiler do you use? Please show the entire output of >> biocLite("S4Vectors") plus your sessionInfo(). Thanks! >> >> H. >> >> >> On 08/27/2015 06:19 AM, Charles Determan wrote: >> >> I am trying to run the basic install with biocLite. I am >> running R 3.2.2 >> on Ubuntu 14.04. >> >> I install the BiocInstaller package with >> >> source("http://bioconductor.org/biocLite.R";) >> >> I then try again to just install S4Vectors but it errors out on >> the >> src_utils file with the following error: >> >> str_utils.c: In function ‘get_svn_time’: >> str_utils.c:259:2: warning: implicit declaration of function >> ‘tzset’ >> [-Wimplicit-function-declaration] >> tzset(); >> ^ >> str_utils.c:261:18: error: ‘timezone’ undeclared (first use in >> this >> function) >> utc_offset = - (timezone / 3600); >> ^ >> str_utils.c:261:18: note: each undeclared identifier is reported >> only once >> for each function it appears in >> make: *** [str_utils.o] Error 1 >> ERROR: compilation failed for package ‘S4Vectors’ >> >> Did I miss something? >> >> Thanks, >> Charles >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> >> mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> >> -- >> Hervé Pagès >> >> Program in Computational Biology >> Division of Public Health Sciences >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N, M1-B514 >> P.O. Box 19024 >> Seattle, WA 98109-1024 >> >> E-mail: hpa...@fredhutch.org <mailto:hpa...@fredhutch.org> >> Phone: (206) 667-5791 <tel:%28206%29%20667-5791> >> Fax: (206) 667-1319 <tel:%28206%29%20667-1319> >> >> >> > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpa...@fredhutch.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
