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’ On Thu, Aug 27, 2015 at 12:04 PM, Hervé Pagès <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 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 > 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
