BioC 3.5: INSTALL report for GenomicAlignments on tokay2

Package: GenomicAlignments

Version: 1.12.1

Command: rm -rf GenomicAlignments.buildbin-libdir && mkdir GenomicAlignments.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.5/bioc/src/contrib/GenomicAlignments_1.12.1.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --library=GenomicAlignments.buildbin-libdir --merge-multiarch GenomicAlignments_1.12.1.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL GenomicAlignments_1.12.1.zip && rm GenomicAlignments_1.12.1.tar.gz GenomicAlignments_1.12.1.zip

StartedAt: 2017-08-15 18:29:18 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 18:30:27 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 69.1 seconds

RetCode: 0

Status:  OK

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### Running command:
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###   rm -rf GenomicAlignments.buildbin-libdir && mkdir GenomicAlignments.buildbin-libdir  && C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.5/bioc/src/contrib/GenomicAlignments_1.12.1.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --library=GenomicAlignments.buildbin-libdir --merge-multiarch GenomicAlignments_1.12.1.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL GenomicAlignments_1.12.1.zip  && rm GenomicAlignments_1.12.1.tar.gz GenomicAlignments_1.12.1.zip
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install for i386

* installing *source* package 'GenomicAlignments' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c cigar_utils.c -o cigar_utils.o
cigar_utils.c: In function 'cigar_ranges':
cigar_utils.c:676:9: warning: 'f_elt' may be used uninitialized in this function [-Wmaybe-uninitialized]
    f_elt++;
         ^
cigar_utils.c:658:27: warning: 'range_buf2' may be used uninitialized in this function [-Wmaybe-uninitialized]
    range_buf1 = range_buf2->elts[*f_elt - 1];
                           ^
cigar_utils.c:674:22: warning: 'range_buf1' may be used uninitialized in this function [-Wmaybe-uninitialized]
    *(breakpoint++) = IntPairAE_get_nelt(range_buf1);
                      ^
cigar_utils.c:674:16: warning: 'breakpoint' may be used uninitialized in this function [-Wmaybe-uninitialized]
    *(breakpoint++) = IntPairAE_get_nelt(range_buf1);
                ^
cigar_utils.c:670:12: warning: 'flag_elt' may be used uninitialized in this function [-Wmaybe-uninitialized]
    flag_elt++;
            ^
cigar_utils.c: In function 'cigar_width':
cigar_utils.c:708:8: warning: 'flag_elt' may be used uninitialized in this function [-Wmaybe-uninitialized]
    if (*flag_elt == NA_INTEGER) {
        ^
cigar_utils.c: In function 'cigar_narrow':
cigar_utils.c:887:17: warning: 'OP' may be used uninitialized in this function [-Wmaybe-uninitialized]
   buf_offset += sprintf(cigar_buf + buf_offset,
                 ^
cigar_utils.c:855:7: note: 'OP' was declared here
  char OP /* Operation */;
       ^
cigar_utils.c:879:8: warning: 'OPL' may be used uninitialized in this function [-Wmaybe-uninitialized]
    OPL -= Lwidth;
        ^
cigar_utils.c:854:17: note: 'OPL' was declared here
  int offset, n, OPL /* Operation Length */;
                 ^
cigar_utils.c: In function 'cigar_qnarrow':
cigar_utils.c:1071:17: warning: 'OP' may be used uninitialized in this function [-Wmaybe-uninitialized]
   buf_offset += sprintf(cigar_buf + buf_offset,
                 ^
cigar_utils.c:1039:7: note: 'OP' was declared here
  char OP /* Operation */;
       ^
cigar_utils.c:1063:8: warning: 'OPL' may be used uninitialized in this function [-Wmaybe-uninitialized]
    OPL -= Lqwidth;
        ^
cigar_utils.c:1038:17: note: 'OPL' was declared here
  int offset, n, OPL /* Operation Length */;
                 ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o
encodeOverlaps_methods.c: In function 'overlap_encoding':
encodeOverlaps_methods.c:182:2: warning: 'out_nelt0' may be used uninitialized in this function [-Wmaybe-uninitialized]
  CharAE_delete_at(out, out_nelt0, j1 * nrow);
  ^
encodeOverlaps_methods.c:99:6: note: 'out_nelt0' was declared here
  int out_nelt0, i, starti, widthi, spacei, j, startj, widthj, spacej,
      ^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o GenomicAlignments.dll tmp.def IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o coordinate_mapping_methods.o encodeOverlaps_methods.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/GenomicAlignments.buildbin-libdir/GenomicAlignments/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'GenomicAlignments' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c cigar_utils.c -o cigar_utils.o
cigar_utils.c: In function 'cigar_ranges':
cigar_utils.c:676:9: warning: 'f_elt' may be used uninitialized in this function [-Wmaybe-uninitialized]
    f_elt++;
         ^
cigar_utils.c:658:27: warning: 'range_buf2' may be used uninitialized in this function [-Wmaybe-uninitialized]
    range_buf1 = range_buf2->elts[*f_elt - 1];
                           ^
cigar_utils.c:674:22: warning: 'range_buf1' may be used uninitialized in this function [-Wmaybe-uninitialized]
    *(breakpoint++) = IntPairAE_get_nelt(range_buf1);
                      ^
cigar_utils.c:674:16: warning: 'breakpoint' may be used uninitialized in this function [-Wmaybe-uninitialized]
    *(breakpoint++) = IntPairAE_get_nelt(range_buf1);
                ^
cigar_utils.c:670:12: warning: 'flag_elt' may be used uninitialized in this function [-Wmaybe-uninitialized]
    flag_elt++;
            ^
cigar_utils.c: In function 'cigar_width':
cigar_utils.c:708:8: warning: 'flag_elt' may be used uninitialized in this function [-Wmaybe-uninitialized]
    if (*flag_elt == NA_INTEGER) {
        ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o
encodeOverlaps_methods.c: In function 'overlap_encoding':
encodeOverlaps_methods.c:182:2: warning: 'out_nelt0' may be used uninitialized in this function [-Wmaybe-uninitialized]
  CharAE_delete_at(out, out_nelt0, j1 * nrow);
  ^
encodeOverlaps_methods.c:99:6: note: 'out_nelt0' was declared here
  int out_nelt0, i, starti, widthi, spacei, j, startj, widthj, spacej,
      ^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o GenomicAlignments.dll tmp.def IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o coordinate_mapping_methods.o encodeOverlaps_methods.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/GenomicAlignments.buildbin-libdir/GenomicAlignments/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicAlignments' as GenomicAlignments_1.12.1.zip
* DONE (GenomicAlignments)
* installing to library 'C:/Users/biocbuild/bbs-3.5-bioc/R/library'
package 'GenomicAlignments' successfully unpacked and MD5 sums checked