[Bioc-devel] Trouble installing S4Vectors?

[Charles Determan]

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 <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 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
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>

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