Bioconductor Package Maintainer
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/IRanges |
| Branch: RELEASE_3_6 |
| Last Commit: 1b17486 |
| Last Changed Date: 2017-10-30 12:39:00 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:17:24 -0400 (Thu, 12 Apr 2018).
| Package 712/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| IRanges 2.12.0 Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: IRanges |
| Version: 2.12.0 |
| Command: rm -rf IRanges.buildbin-libdir && mkdir IRanges.buildbin-libdir && C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.6/bioc/src/contrib/IRanges_2.12.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=IRanges.buildbin-libdir --merge-multiarch IRanges_2.12.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL IRanges_2.12.0.zip && rm IRanges_2.12.0.tar.gz IRanges_2.12.0.zip |
| StartedAt: 2018-04-11 18:17:13 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 18:20:22 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 188.5 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
###
### rm -rf IRanges.buildbin-libdir && mkdir IRanges.buildbin-libdir && C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.6/bioc/src/contrib/IRanges_2.12.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=IRanges.buildbin-libdir --merge-multiarch IRanges_2.12.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL IRanges_2.12.0.zip && rm IRanges_2.12.0.tar.gz IRanges_2.12.0.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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/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:1545:7: 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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c Ranges_comparison.c -o Ranges_comparison.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c SimpleRangesList_class.c -o SimpleRangesList_class.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -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/g++ -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˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-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 '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
converting help for package 'IRanges'
finding HTML links ... done
AtomicList-class html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/AtomicList-class.Rd:307: missing file link 'List'
AtomicList-utils html
CompressedHitsList-class html
CompressedList-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/CompressedList-class.Rd:42: missing file link 'SimpleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/CompressedList-class.Rd:43: missing file link 'List'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/CompressedList-class.Rd:48: missing file link 'SimpleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/CompressedList-class.Rd:53: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/CompressedList-class.Rd:54: missing file link 'GAlignmentsList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/CompressedList-class.Rd:64: missing file link 'SimpleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/CompressedList-class.Rd:70: missing file link 'SimpleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/CompressedList-class.Rd:85: missing file link 'List'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/CompressedList-class.Rd:88: missing file link 'SimpleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/CompressedList-class.Rd:91: missing file link 'List'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/CompressedList-class.Rd:93: missing file link 'SimpleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/CompressedList-class.Rd:99: missing file link 'List'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/CompressedList-class.Rd:104: missing file link 'List'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/CompressedList-class.Rd:109: missing file link 'List'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/CompressedList-class.Rd:114: missing file link 'List'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/CompressedList-class.Rd:122: missing file link 'classNameForDisplay'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/CompressedList-class.Rd:128: missing file link 'List'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/CompressedList-class.Rd:131: missing file link 'SimpleList'
DataFrame-utils html
DataFrameList-class html
Grouping-class html
Hits-class-leftovers html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/Hits-class-leftovers.Rd:31: missing file link 'Hits'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/Hits-class-leftovers.Rd:68: missing file link 'Hits'
IPos-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/IPos-class.Rd:109: missing file link 'Vector'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/IPos-class.Rd:123: missing file link 'GPos'
IRanges-class html
IRanges-constructor html
IRanges-internals html
IRanges-utils html
IRangesList-class html
List-class-leftovers html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/List-class-leftovers.Rd:11: missing file link 'List'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/List-class-leftovers.Rd:35: missing file link 'List'
MaskCollection-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/MaskCollection-class.Rd:206: missing file link 'alphabetFrequency'
NCList-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/NCList-class.Rd:77: missing file link 'GNCList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/NCList-class.Rd:97: missing file link 'GNCList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/NCList-class.Rd:98: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/NCList-class.Rd:106: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/NCList-class.Rd:121: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/NCList-class.Rd:123: missing file link 'GNCList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/NCList-class.Rd:126: missing file link 'GNCList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/NCList-class.Rd:150: missing file link 'GNCList'
RangedData-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/RangedData-class.Rd:78: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/RangedData-class.Rd:78: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/RangedData-class.Rd:80: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/RangedData-class.Rd:80: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/RangedData-class.Rd:84: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/RangedData-class.Rd:85: missing file link 'GRangesList'
RangedSelection-class html
Ranges-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/Ranges-class.Rd:243: missing file link 'Hits'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/Ranges-class.Rd:243: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/Ranges-class.Rd:244: missing file link 'GPos'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/Ranges-class.Rd:244: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/Ranges-class.Rd:245: missing file link 'XStringSet'
Ranges-comparison html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/Ranges-comparison.Rd:161: missing file link 'GenomicRanges'
RangesList-class html
Rle-class-leftovers html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/Rle-class-leftovers.Rd:22: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/Rle-class-leftovers.Rd:71: missing file link 'Rle'
RleViews-class html
RleViewsList-class html
Vector-class-leftovers html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/Vector-class-leftovers.Rd:34: missing file link 'Vector'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/Vector-class-leftovers.Rd:159: missing file link 'Vector'
Views-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/Views-class.Rd:45: missing file link 'XIntegerViews'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/Views-class.Rd:46: missing file link 'XStringViews'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/Views-class.Rd:155: missing file link 'XVector'
ViewsList-class html
coverage-methods html
extractList html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/extractList.Rd:24: missing file link 'split'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/extractList.Rd:95: missing file link 'relistToClass'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/extractList.Rd:149: missing file link 'relistToClass'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/extractList.Rd:160: missing file link 'unsplit'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/extractList.Rd:163: missing file link 'split'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/extractList.Rd:166: missing file link 'Vector'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/extractList.Rd:166: missing file link 'List'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/extractList.Rd:167: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/extractList.Rd:167: missing file link 'DataFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/extractList.Rd:169: missing file link 'relistToClass'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/extractList.Rd:170: missing file link 'List'
findOverlaps-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/findOverlaps-methods.Rd:82: missing file link 'findOverlaps,GenomicRanges,GenomicRanges-method'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/findOverlaps-methods.Rd:84: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/findOverlaps-methods.Rd:84: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/findOverlaps-methods.Rd:193: missing file link 'Hits'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/findOverlaps-methods.Rd:201: missing file link 'HitsList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/findOverlaps-methods.Rd:213: missing file link 'Hits'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/findOverlaps-methods.Rd:213: missing file link 'HitsList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/findOverlaps-methods.Rd:270: missing file link 'Hits'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/findOverlaps-methods.Rd:270: missing file link 'HitsList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/findOverlaps-methods.Rd:278: missing file link 'Hits'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/findOverlaps-methods.Rd:279: missing file link 'HitsList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/findOverlaps-methods.Rd:310: missing file link 'Hits'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/findOverlaps-methods.Rd:310: missing file link 'HitsList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/findOverlaps-methods.Rd:314: missing file link 'findOverlaps,GenomicRanges,GenomicRanges-method'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/findOverlaps-methods.Rd:316: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/findOverlaps-methods.Rd:316: missing file link 'GRangesList'
inter-range-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/inter-range-methods.Rd:266: missing file link 'endoapply'
intra-range-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/intra-range-methods.Rd:281: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/intra-range-methods.Rd:282: missing file link 'promoters,GenomicRanges-method'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/intra-range-methods.Rd:337: missing file link 'endoapply'
multisplit html
nearest-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/nearest-methods.Rd:147: missing file link 'breakTies'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/nearest-methods.Rd:173: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/nearest-methods.Rd:174: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/nearest-methods.Rd:187: missing file link 'precede,GenomicRanges,GenomicRanges-method'
range-squeezers html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/range-squeezers.Rd:15: missing file link 'granges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/range-squeezers.Rd:16: missing file link 'grglist'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/range-squeezers.Rd:18: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/range-squeezers.Rd:19: missing file link 'granges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/range-squeezers.Rd:20: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/range-squeezers.Rd:21: missing file link 'grglist'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/range-squeezers.Rd:32: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/range-squeezers.Rd:33: missing file link 'RangedSummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/range-squeezers.Rd:34: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/range-squeezers.Rd:35: missing file link 'GAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/range-squeezers.Rd:36: missing file link 'GAlignmentsList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/range-squeezers.Rd:37: missing file link 'Pairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/range-squeezers.Rd:63: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/range-squeezers.Rd:64: missing file link 'GAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/range-squeezers.Rd:77: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/range-squeezers.Rd:93: missing file link 'RangedSummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/range-squeezers.Rd:96: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/range-squeezers.Rd:97: missing file link 'GAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/range-squeezers.Rd:98: missing file link 'GAlignmentsList'
read.Mask html
reverse-methods html
seqapply html
setops-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/setops-methods.Rd:90: missing file link 'Pairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/setops-methods.Rd:115: missing file link 'Pairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2XIvps/R.INSTALL13243ebe5df1/IRanges/man/setops-methods.Rd:165: missing file link 'mendoapply'
slice-methods html
view-summarization-methods html
** 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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/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:1545:7: 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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c Ranges_comparison.c -o Ranges_comparison.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c SimpleRangesList_class.c -o SimpleRangesList_class.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/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/g++ -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˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/IRanges.buildbin-libdir/IRanges/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IRanges' as IRanges_2.12.0.zip
* DONE (IRanges)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.6-bioc/R/library'
package 'IRanges' successfully unpacked and MD5 sums checked
In R CMD INSTALL