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INSTALL report for IRanges on tokay2

This page was generated on 2018-10-17 08:32:02 -0400 (Wed, 17 Oct 2018).

Package 750/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IRanges 2.14.12
Bioconductor Package Maintainer
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/IRanges
Branch: RELEASE_3_7
Last Commit: 00af027
Last Changed Date: 2018-09-19 23:34:20 -0400 (Wed, 19 Sep 2018)
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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: IRanges
Version: 2.14.12
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/IRanges_2.14.12.tar.gz && rm -rf IRanges.buildbin-libdir && mkdir IRanges.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=IRanges.buildbin-libdir IRanges_2.14.12.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL IRanges_2.14.12.zip && rm IRanges_2.14.12.tar.gz IRanges_2.14.12.zip
StartedAt: 2018-10-16 18:48:38 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 18:50:48 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 129.5 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/IRanges_2.14.12.tar.gz && rm -rf IRanges.buildbin-libdir && mkdir IRanges.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=IRanges.buildbin-libdir IRanges_2.14.12.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL IRanges_2.14.12.zip && rm IRanges_2.14.12.tar.gz IRanges_2.14.12.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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100  260k  100  260k    0     0  4120k      0 --:--:-- --:--:-- --:--:-- 4653k

install for i386

* installing *source* package 'IRanges' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c CompressedList_class.c -o CompressedList_class.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c Grouping_class.c -o Grouping_class.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c IPosRanges_comparison.c -o IPosRanges_comparison.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c IRanges_class.c -o IRanges_class.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c IRanges_constructor.c -o IRanges_constructor.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -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:1173:13: 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:1465:7: warning: 'ans' may be used uninitialized in this function [-Wmaybe-uninitialized]
  SEXP ans;
       ^
NCList.c: In function 'NCList_find_overlaps_in_groups':
NCList.c:1546:7: 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˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c R_init_IRanges.c -o R_init_IRanges.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c Ranges_class.c -o Ranges_class.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c RleViews_utils.c -o RleViews_utils.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c SimpleIRangesList_class.c -o SimpleIRangesList_class.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -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˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c extractListFragments.c -o extractListFragments.o
extractListFragments.c: In function 'find_partition_overlaps':
extractListFragments.c:85:4: warning: 'split_partitions_buf' may be used uninitialized in this function [-Wmaybe-uninitialized]
    IntAE_insert_at(split_partitions_buf,
    ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c inter_range_methods.c -o inter_range_methods.o
inter_range_methods.c: In function 'IntegerRanges_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 IPosRanges_comparison.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o Ranges_class.o RleViews_utils.o S4Vectors_stubs.o SimpleIRangesList_class.o coverage_methods.o extractListFragments.o inter_range_methods.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/IRanges.buildbin-libdir/IRanges/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'drop' from package 'base' in package 'IRanges'
Creating a generic function for 'runmed' from package 'stats' in package 'IRanges'
Creating a generic function for 'smoothEnds' 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'
Creating a new generic function for 'windows' in package 'IRanges'
** help
*** installing help indices
  converting help for package 'IRanges'
    finding HTML links ... done
    AtomicList-class                        html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaouRr6/R.INSTALLb2c47af1342/IRanges/man/AtomicList-class.Rd:307: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
    AtomicList-utils                        html  
    CompressedHitsList-class                html  
    CompressedList-class                    html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaouRr6/R.INSTALLb2c47af1342/IRanges/man/CompressedList-class.Rd:38: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaouRr6/R.INSTALLb2c47af1342/IRanges/man/CompressedList-class.Rd:39: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaouRr6/R.INSTALLb2c47af1342/IRanges/man/CompressedList-class.Rd:44: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaouRr6/R.INSTALLb2c47af1342/IRanges/man/CompressedList-class.Rd:49: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaouRr6/R.INSTALLb2c47af1342/IRanges/man/CompressedList-class.Rd:50: file link 'GAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaouRr6/R.INSTALLb2c47af1342/IRanges/man/CompressedList-class.Rd:60: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaouRr6/R.INSTALLb2c47af1342/IRanges/man/CompressedList-class.Rd:66: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaouRr6/R.INSTALLb2c47af1342/IRanges/man/CompressedList-class.Rd:81: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaouRr6/R.INSTALLb2c47af1342/IRanges/man/CompressedList-class.Rd:84: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaouRr6/R.INSTALLb2c47af1342/IRanges/man/CompressedList-class.Rd:87: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaouRr6/R.INSTALLb2c47af1342/IRanges/man/CompressedList-class.Rd:89: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaouRr6/R.INSTALLb2c47af1342/IRanges/man/CompressedList-class.Rd:95: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaouRr6/R.INSTALLb2c47af1342/IRanges/man/CompressedList-class.Rd:100: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaouRr6/R.INSTALLb2c47af1342/IRanges/man/CompressedList-class.Rd:105: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaouRr6/R.INSTALLb2c47af1342/IRanges/man/CompressedList-class.Rd:110: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaouRr6/R.INSTALLb2c47af1342/IRanges/man/CompressedList-class.Rd:118: file link 'classNameForDisplay' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaouRr6/R.INSTALLb2c47af1342/IRanges/man/CompressedList-class.Rd:124: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaouRr6/R.INSTALLb2c47af1342/IRanges/man/CompressedList-class.Rd:127: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
    DataFrame-utils                         html  
    DataFrameList-class                     html  
    Grouping-class                          html  
    Hits-class-leftovers                    html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaouRr6/R.INSTALLb2c47af1342/IRanges/man/Hits-class-leftovers.Rd:31: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaouRr6/R.INSTALLb2c47af1342/IRanges/man/Hits-class-leftovers.Rd:68: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
    IPos-class                              html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaouRr6/R.INSTALLb2c47af1342/IRanges/man/IPos-class.Rd:96: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaouRr6/R.INSTALLb2c47af1342/IRanges/man/IPos-class.Rd:106: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaouRr6/R.INSTALLb2c47af1342/IRanges/man/IPos-class.Rd:120: file link 'GPos' in package 'GenomicRanges' does not exist and so has been treated as a topic
    IPosRanges-class                        html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaouRr6/R.INSTALLb2c47af1342/IRanges/man/IPosRanges-class.Rd:200: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaouRr6/R.INSTALLb2c47af1342/IRanges/man/IPosRanges-class.Rd:225: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaouRr6/R.INSTALLb2c47af1342/IRanges/man/IPosRanges-class.Rd:225: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaouRr6/R.INSTALLb2c47af1342/IRanges/man/IPosRanges-class.Rd:226: file link 'GPos' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaouRr6/R.INSTALLb2c47af1342/IRanges/man/IPosRanges-class.Rd:226: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaouRr6/R.INSTALLb2c47af1342/IRanges/man/IPosRanges-class.Rd:227: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
    IPosRanges-comparison                   html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaouRr6/R.INSTALLb2c47af1342/IRanges/man/IPosRanges-comparison.Rd:164: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    IRanges-class                           html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaouRr6/R.INSTALLb2c47af1342/IRanges/man/IRanges-class.Rd:97: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic
    IRanges-constructor                     html  
    IRanges-internals                       html  
    IRanges-utils                           html  
    IRangesList-class                       html  
    IntegerRanges-class                     html  
    IntegerRangesList-class                 html  
    List-class-leftovers                    html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaouRr6/R.INSTALLb2c47af1342/IRanges/man/List-class-leftovers.Rd:11: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaouRr6/R.INSTALLb2c47af1342/IRanges/man/List-class-leftovers.Rd:35: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
    MaskCollection-class                    html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaouRr6/R.INSTALLb2c47af1342/IRanges/man/MaskCollection-class.Rd:206: file link 'alphabetFrequency' in package 'Biostrings' does not exist and so has been treated as a topic
    NCList-class                            html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaouRr6/R.INSTALLb2c47af1342/IRanges/man/NCList-class.Rd:81: file link 'GNCList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaouRr6/R.INSTALLb2c47af1342/IRanges/man/NCList-class.Rd:101: file link 'GNCList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaouRr6/R.INSTALLb2c47af1342/IRanges/man/NCList-class.Rd:102: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaouRr6/R.INSTALLb2c47af1342/IRanges/man/NCList-class.Rd:110: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaouRr6/R.INSTALLb2c47af1342/IRanges/man/NCList-class.Rd:126: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaouRr6/R.INSTALLb2c47af1342/IRanges/man/NCList-class.Rd:128: file link 'GNCList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaouRr6/R.INSTALLb2c47af1342/IRanges/man/NCList-class.Rd:131: file link 'GNCList' in package 'GenomicRanges' does not exist and so has been treated as a topic
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    setops-methods                          html  
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** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'IRanges' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c CompressedList_class.c -o CompressedList_class.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c Grouping_class.c -o Grouping_class.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c IPosRanges_comparison.c -o IPosRanges_comparison.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c IRanges_class.c -o IRanges_class.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c IRanges_constructor.c -o IRanges_constructor.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -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:1173:13: 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:1546:7: 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˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c R_init_IRanges.c -o R_init_IRanges.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c Ranges_class.c -o Ranges_class.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c RleViews_utils.c -o RleViews_utils.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c SimpleIRangesList_class.c -o SimpleIRangesList_class.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -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˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c extractListFragments.c -o extractListFragments.o
extractListFragments.c: In function 'find_partition_overlaps':
extractListFragments.c:85:4: warning: 'split_partitions_buf' may be used uninitialized in this function [-Wmaybe-uninitialized]
    IntAE_insert_at(split_partitions_buf,
    ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -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 IPosRanges_comparison.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o Ranges_class.o RleViews_utils.o S4Vectors_stubs.o SimpleIRangesList_class.o coverage_methods.o extractListFragments.o inter_range_methods.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/IRanges.buildbin-libdir/IRanges/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IRanges' as IRanges_2.14.12.zip
* DONE (IRanges)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'IRanges' successfully unpacked and MD5 sums checked
In R CMD INSTALL