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BioC 3.5: INSTALL report for IRanges on tokay2

This page was generated on 2017-08-16 13:18:39 -0400 (Wed, 16 Aug 2017).

Package 685/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IRanges 2.10.2
Bioconductor Package Maintainer
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/IRanges
Last Changed Rev: 129836 / Revision: 131943
Last Changed Date: 2017-05-24 14:22:03 -0400 (Wed, 24 May 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: IRanges
Version: 2.10.2
Command: rm -rf IRanges.buildbin-libdir && mkdir IRanges.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.5/bioc/src/contrib/IRanges_2.10.2.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --library=IRanges.buildbin-libdir --merge-multiarch IRanges_2.10.2.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL IRanges_2.10.2.zip && rm IRanges_2.10.2.tar.gz IRanges_2.10.2.zip
StartedAt: 2017-08-15 18:14:20 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 18:15:53 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 92.9 seconds
RetCode: 0
Status:  OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf IRanges.buildbin-libdir && mkdir IRanges.buildbin-libdir  && C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.5/bioc/src/contrib/IRanges_2.10.2.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --library=IRanges.buildbin-libdir --merge-multiarch IRanges_2.10.2.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL IRanges_2.10.2.zip  && rm IRanges_2.10.2.tar.gz IRanges_2.10.2.zip
###
##############################################################################
##############################################################################


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install for i386

* installing *source* package 'IRanges' ...
** 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:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.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:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c CompressedIRangesList_class.c -o CompressedIRangesList_class.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:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c CompressedList_class.c -o CompressedList_class.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:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c Grouping_class.c -o Grouping_class.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:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c IRanges_class.c -o IRanges_class.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:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c IRanges_constructor.c -o IRanges_constructor.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:/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:1163:13: 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:1452:7: warning: 'ans' may be used uninitialized in this function [-Wmaybe-uninitialized]
  SEXP ans;
       ^
NCList.c: In function 'NCList_find_overlaps_in_groups':
NCList.c:1532:7: warning: 'ans' may be used uninitialized in this function [-Wmaybe-uninitialized]
  SEXP ans;
       ^
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:/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"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:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c Ranges_class.c -o Ranges_class.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:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c Ranges_comparison.c -o Ranges_comparison.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:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c RleViews_utils.c -o RleViews_utils.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:/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:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c SimpleRangesList_class.c -o SimpleRangesList_class.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:/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"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:/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 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 -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/IRanges.buildbin-libdir/IRanges/libs/i386
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'drop' from package 'base' in package 'IRanges'
Creating a generic function for 'ifelse' from package 'base' 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"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:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.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:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c CompressedIRangesList_class.c -o CompressedIRangesList_class.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:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c CompressedList_class.c -o CompressedList_class.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:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c Grouping_class.c -o Grouping_class.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:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c IRanges_class.c -o IRanges_class.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:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c IRanges_constructor.c -o IRanges_constructor.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:/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:1163:13: 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:1532:7: warning: 'ans' may be used uninitialized in this function [-Wmaybe-uninitialized]
  SEXP ans;
       ^
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:/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"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:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c Ranges_class.c -o Ranges_class.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:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c Ranges_comparison.c -o Ranges_comparison.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:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c RleViews_utils.c -o RleViews_utils.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:/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:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c SimpleRangesList_class.c -o SimpleRangesList_class.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:/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"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:/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 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 -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/IRanges.buildbin-libdir/IRanges/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IRanges' as IRanges_2.10.2.zip
* DONE (IRanges)
* installing to library 'C:/Users/biocbuild/bbs-3.5-bioc/R/library'
package 'IRanges' successfully unpacked and MD5 sums checked