[Bioc-devel] Trouble installing S4Vectors?
Charles Determan
cdetermanjr at gmail.com
Fri Aug 28 16:12:45 CEST 2015
Thanks Herve, that solved the problem. It installed correctly now.
Regards,
Charles
On Thu, Aug 27, 2015 at 4:14 PM, Hervé Pagès <hpages at 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 <hpages at fredhutch.org
>> <mailto:hpages at 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 at r-project.org <mailto:Bioc-devel at 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: hpages at fredhutch.org <mailto:hpages at 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: hpages at fredhutch.org
> Phone: (206) 667-5791
> Fax: (206) 667-1319
>
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