Re: [Bioc-devel] Trouble installing S4Vectors?
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().
[Bioc-devel] Trouble installing S4Vectors?
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
Re: [Bioc-devel] Trouble installing S4Vectors?
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
Re: [Bioc-devel] Trouble installing S4Vectors?
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 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
