[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, Herv? Pag?s <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

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