BioC 3.3: INSTALL report for IRanges on moscato2

Package: IRanges

Version: 2.6.1

Command: rm -rf IRanges.buildbin-libdir && mkdir IRanges.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://zin2/BBS/3.3/bioc/src/contrib/IRanges_2.6.1.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --library=IRanges.buildbin-libdir --merge-multiarch IRanges_2.6.1.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL IRanges_2.6.1.zip && rm IRanges_2.6.1.tar.gz IRanges_2.6.1.zip

StartedAt: 2016-10-12 18:37:27 -0700 (Wed, 12 Oct 2016)

EndedAt: 2016-10-12 18:39:18 -0700 (Wed, 12 Oct 2016)

EllapsedTime: 110.2 seconds

RetCode: 0

Status:  OK

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### Running command:
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###   rm -rf IRanges.buildbin-libdir && mkdir IRanges.buildbin-libdir  && C:\cygwin\bin\curl.exe -O http://zin2/BBS/3.3/bioc/src/contrib/IRanges_2.6.1.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --library=IRanges.buildbin-libdir --merge-multiarch IRanges_2.6.1.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL IRanges_2.6.1.zip  && rm IRanges_2.6.1.tar.gz IRanges_2.6.1.zip
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install for i386

* installing *source* package 'IRanges' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c CompressedList_class.c -o CompressedList_class.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c GappedRanges_class.c -o GappedRanges_class.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c Grouping_class.c -o Grouping_class.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c IRanges_class.c -o IRanges_class.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c IRanges_constructor.c -o IRanges_constructor.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c NCList.c -o NCList.o
NCList.c:202:22: warning: 'next_top_down' defined but not used [-Wunused-function]
 static const NCList *next_top_down(const NCList *nclist)
                      ^
NCList.c:1184:13: warning: 'NCList_get_y_overlaps_rec' defined but not used [-Wunused-function]
 static void NCList_get_y_overlaps_rec(const NCList *x_nclist,
             ^
NCList.c: In function 'NCList_find_overlaps':
NCList.c:1473:7: warning: 'ans' may be used uninitialized in this function [-Wmaybe-uninitialized]
  SEXP ans;
       ^
NCList.c: In function 'NCList_find_overlaps_in_groups':
NCList.c:1553:7: warning: 'ans' may be used uninitialized in this function [-Wmaybe-uninitialized]
  SEXP ans;
       ^
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_IRanges.c -o R_init_IRanges.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c Ranges_class.c -o Ranges_class.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c Ranges_comparison.c -o Ranges_comparison.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c RleViews_utils.c -o RleViews_utils.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/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"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c SimpleRangesList_class.c -o SimpleRangesList_class.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c coverage_methods.c -o coverage_methods.o
coverage_methods.c: In function 'compute_coverage_from_IRanges_holder':
coverage_methods.c:503:28: warning: 'x_end' may be used uninitialized in this function [-Wmaybe-uninitialized]
  if (*out_ranges_are_tiles && x_end != cvg_len)
                            ^
coverage_methods.c:419:21: note: 'x_end' was declared here
      i, j, x_start, x_end, shift_elt, tmp;
                     ^
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c inter_range_methods.c -o inter_range_methods.o
inter_range_methods.c: In function 'Ranges_reduce':
inter_range_methods.c:154:11: warning: 'gapwidth' may be used uninitialized in this function [-Wmaybe-uninitialized]
     delta += gapwidth;
           ^
inter_range_methods.c:102:31: note: 'gapwidth' was declared here
      append_or_drop, max_end, gapwidth, delta, width_inc;
                               ^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o IRanges.dll tmp.def CompressedAtomicList_utils.o CompressedIRangesList_class.o CompressedList_class.o GappedRanges_class.o Grouping_class.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o Ranges_class.o Ranges_comparison.o RleViews_utils.o S4Vectors_stubs.o SimpleRangesList_class.o coverage_methods.o inter_range_methods.o -Lc:/local323/lib/i386 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.3-bioc/meat/IRanges.buildbin-libdir/IRanges/libs/i386
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'window<-' from package 'stats' in package 'IRanges'
Creating a generic function for 'rev' from package 'base' in package 'IRanges'
Creating a generic function for 'stack' from package 'utils' in package 'IRanges'
Creating a generic function for 'mean' from package 'base' in package 'IRanges'
Creating a generic function for 'which.max' from package 'base' in package 'IRanges'
Creating a generic function for 'which.min' from package 'base' in package 'IRanges'
Creating a generic function for 'split<-' from package 'base' in package 'IRanges'
Creating a generic function for 'drop' from package 'base' in package 'IRanges'
Creating a generic function for 'which' from package 'base' in package 'IRanges'
Creating a generic function for 'diff' from package 'base' in package 'IRanges'
Creating a generic function for 'median' from package 'stats' in package 'IRanges'
Creating a generic function for 'quantile' from package 'stats' in package 'IRanges'
Creating a generic function for 'smoothEnds' from package 'stats' in package 'IRanges'
Creating a generic function for 'runmed' from package 'stats' in package 'IRanges'
Creating a generic function for 'chartr' from package 'base' in package 'IRanges'
Creating a generic function for 'tolower' from package 'base' in package 'IRanges'
Creating a generic function for 'toupper' from package 'base' in package 'IRanges'
Creating a generic function for 'sub' from package 'base' in package 'IRanges'
Creating a generic function for 'gsub' from package 'base' in package 'IRanges'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'IRanges' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c CompressedList_class.c -o CompressedList_class.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c GappedRanges_class.c -o GappedRanges_class.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c Grouping_class.c -o Grouping_class.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c IRanges_class.c -o IRanges_class.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c IRanges_constructor.c -o IRanges_constructor.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c NCList.c -o NCList.o
NCList.c:202:22: warning: 'next_top_down' defined but not used [-Wunused-function]
 static const NCList *next_top_down(const NCList *nclist)
                      ^
NCList.c:1184:13: warning: 'NCList_get_y_overlaps_rec' defined but not used [-Wunused-function]
 static void NCList_get_y_overlaps_rec(const NCList *x_nclist,
             ^
NCList.c: In function 'NCList_find_overlaps_in_groups':
NCList.c:1553:7: warning: 'ans' may be used uninitialized in this function [-Wmaybe-uninitialized]
  SEXP ans;
       ^
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_IRanges.c -o R_init_IRanges.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c Ranges_class.c -o Ranges_class.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c Ranges_comparison.c -o Ranges_comparison.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c RleViews_utils.c -o RleViews_utils.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/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"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c SimpleRangesList_class.c -o SimpleRangesList_class.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c coverage_methods.c -o coverage_methods.o
coverage_methods.c: In function 'compute_coverage_from_IRanges_holder':
coverage_methods.c:503:28: warning: 'x_end' may be used uninitialized in this function [-Wmaybe-uninitialized]
  if (*out_ranges_are_tiles && x_end != cvg_len)
                            ^
coverage_methods.c:419:21: note: 'x_end' was declared here
      i, j, x_start, x_end, shift_elt, tmp;
                     ^
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c inter_range_methods.c -o inter_range_methods.o
inter_range_methods.c: In function 'reduce_ranges':
inter_range_methods.c:165:5: warning: 'revmap_elt' may be used uninitialized in this function [-Wmaybe-uninitialized]
     IntAE_insert_at(revmap_elt,
     ^
inter_range_methods.c:154:11: warning: 'delta' may be used uninitialized in this function [-Wmaybe-uninitialized]
     delta += gapwidth;
           ^
inter_range_methods.c:154:11: warning: 'gapwidth' may be used uninitialized in this function [-Wmaybe-uninitialized]
inter_range_methods.c:156:14: warning: 'max_end' may be used uninitialized in this function [-Wmaybe-uninitialized]
    width_inc = end_j - max_end;
              ^
inter_range_methods.c:131:6: warning: 'append_or_drop' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (append_or_drop) {
      ^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o IRanges.dll tmp.def CompressedAtomicList_utils.o CompressedIRangesList_class.o CompressedList_class.o GappedRanges_class.o Grouping_class.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o Ranges_class.o Ranges_comparison.o RleViews_utils.o S4Vectors_stubs.o SimpleRangesList_class.o coverage_methods.o inter_range_methods.o -Lc:/local323/lib/x64 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.3-bioc/meat/IRanges.buildbin-libdir/IRanges/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IRanges' as IRanges_2.6.1.zip
* DONE (IRanges)
* installing to library 'E:/biocbld/bbs-3.3-bioc/R/library'
package 'IRanges' successfully unpacked and MD5 sums checked