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This page was generated on 2021-05-06 12:31:28 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the GenomicRanges package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 720/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GenomicRanges 1.42.0 (landing page) Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: GenomicRanges |
| Version: 1.42.0 |
| Command: C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/GenomicRanges_1.42.0.tar.gz && rm -rf GenomicRanges.buildbin-libdir && mkdir GenomicRanges.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomicRanges.buildbin-libdir GenomicRanges_1.42.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL GenomicRanges_1.42.0.zip && rm GenomicRanges_1.42.0.tar.gz GenomicRanges_1.42.0.zip |
| StartedAt: 2021-05-05 17:02:17 -0400 (Wed, 05 May 2021) |
| EndedAt: 2021-05-05 17:03:30 -0400 (Wed, 05 May 2021) |
| EllapsedTime: 72.7 seconds |
| RetCode: 0 |
| Status: OK |
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/GenomicRanges_1.42.0.tar.gz && rm -rf GenomicRanges.buildbin-libdir && mkdir GenomicRanges.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomicRanges.buildbin-libdir GenomicRanges_1.42.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL GenomicRanges_1.42.0.zip && rm GenomicRanges_1.42.0.tar.gz GenomicRanges_1.42.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 157k 100 157k 0 0 3137k 0 --:--:-- --:--:-- --:--:-- 3217k
install for i386
* installing *source* package 'GenomicRanges' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c transcript_utils.c -o transcript_utils.o
transcript_utils.c: In function 'tlocs2rlocs':
transcript_utils.c:143:38: warning: 'end' may be used uninitialized in this function [-Wmaybe-uninitialized]
return on_minus_strand ? end - tloc : start + tloc;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
transcript_utils.c:120:24: note: 'end' was declared here
int nexons, j, start, end, width;
^~~
transcript_utils.c:143:38: warning: 'start' may be used uninitialized in this function [-Wmaybe-uninitialized]
return on_minus_strand ? end - tloc : start + tloc;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
transcript_utils.c:120:17: note: 'start' was declared here
int nexons, j, start, end, width;
^~~~~
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o GenomicRanges.dll tmp.def IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/GenomicRanges.buildbin-libdir/00LOCK-GenomicRanges/00new/GenomicRanges/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'GenomicRanges'
finding HTML links ... done
DelegatingGenomicRanges-class html
GNCList-class html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GNCList-class.Rd:46: file link 'NCList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GNCList-class.Rd:47: file link 'NCLists' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GNCList-class.Rd:48: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GNCList-class.Rd:49: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GNCList-class.Rd:55: file link 'NCList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GNCList-class.Rd:79: file link 'NCList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GNCList-class.Rd:79: file link 'NCLists' in package 'IRanges' does not exist and so has been treated as a topic
GPos-class html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GPos-class.Rd:78: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GPos-class.Rd:79: file link 'IPos' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GPos-class.Rd:79: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GPos-class.Rd:82: file link 'IPos' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GPos-class.Rd:97: file link 'IPos' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GPos-class.Rd:99: file link 'UnstitchedIPos' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GPos-class.Rd:100: file link 'StitchedIPos' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GPos-class.Rd:117: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GPos-class.Rd:137: file link 'IPos' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GPos-class.Rd:138: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GPos-class.Rd:139: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GPos-class.Rd:141: file link 'IPos' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GPos-class.Rd:153: file link 'seqlevels' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GPos-class.Rd:155: file link 'seqlengths' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GPos-class.Rd:156: file link 'isCircular' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GPos-class.Rd:157: file link 'genome' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GPos-class.Rd:207: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GPos-class.Rd:230: file link 'IPos' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GPos-class.Rd:259: file link 'snpsBySeqname' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GPos-class.Rd:260: file link 'snpsByOverlaps' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GPos-class.Rd:261: file link 'snpsById' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GPos-class.Rd:262: file link 'SNPlocs' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GPos-class.Rd:265: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
GRanges-class html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GRanges-class.Rd:97: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GRanges-class.Rd:99: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GRanges-class.Rd:101: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GRanges-class.Rd:103: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GRanges-class.Rd:121: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GRanges-class.Rd:125: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GRanges-class.Rd:129: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GRanges-class.Rd:180: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GRanges-class.Rd:186: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GRanges-class.Rd:286: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GRanges-class.Rd:302: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GRanges-class.Rd:345: file link 'ManyToOneGrouping' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GRanges-class.Rd:360: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GRanges-class.Rd:397: file link '[' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GRanges-class.Rd:425: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GRanges-class.Rd:461: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GRanges-class.Rd:462: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GRanges-class.Rd:465: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GRanges-class.Rd:465: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GRanges-class.Rd:474: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GRanges-class.Rd:482: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GRanges-class.Rd:519: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GRanges-class.Rd:519: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GRanges-class.Rd:520: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
GRangesFactor-class html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GRangesFactor-class.Rd:28: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GRangesFactor-class.Rd:31: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GRangesFactor-class.Rd:32: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GRangesFactor-class.Rd:41: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GRangesFactor-class.Rd:66: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GRangesFactor-class.Rd:69: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GRangesFactor-class.Rd:78: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GRangesFactor-class.Rd:88: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GRangesFactor-class.Rd:93: file link 'unfactor' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GRangesFactor-class.Rd:98: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GRangesFactor-class.Rd:107: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GRangesFactor-class.Rd:114: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GRangesFactor-class.Rd:118: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GRangesFactor-class.Rd:127: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic
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GRangesList-class html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GRangesList-class.Rd:200: file link 'IRangesList' in package 'IRanges' does not exist and so has been treated as a topic
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Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GRangesList-class.Rd:359: file link 'DataFrameList' in package 'IRanges' does not exist and so has been treated as a topic
GenomicRanges-comparison html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GenomicRanges-comparison.Rd:115: file link 'reduce' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GenomicRanges-comparison.Rd:115: file link 'disjoin' in package 'GenomicRanges' does not exist and so has been treated as a topic
GenomicRangesList-class html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GenomicRangesList-class.Rd:91: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GenomicRangesList-class.Rd:91: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GenomicRangesList-class.Rd:92: file link 'IRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/GenomicRangesList-class.Rd:92: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
absoluteRanges html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/absoluteRanges.Rd:39: file link 'seqlengths' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/absoluteRanges.Rd:41: file link 'seqlengths' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/absoluteRanges.Rd:50: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/absoluteRanges.Rd:65: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/absoluteRanges.Rd:86: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
constraint html
coverage-methods html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/coverage-methods.Rd:13: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/coverage-methods.Rd:16: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/coverage-methods.Rd:17: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/coverage-methods.Rd:17: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/coverage-methods.Rd:19: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/coverage-methods.Rd:20: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/coverage-methods.Rd:46: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/coverage-methods.Rd:58: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/coverage-methods.Rd:62: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/coverage-methods.Rd:73: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/coverage-methods.Rd:81: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/coverage-methods.Rd:86: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
findOverlaps-methods html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/findOverlaps-methods.Rd:25: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/findOverlaps-methods.Rd:26: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/findOverlaps-methods.Rd:27: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/findOverlaps-methods.Rd:29: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/findOverlaps-methods.Rd:30: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/findOverlaps-methods.Rd:31: file link 'GAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/findOverlaps-methods.Rd:59: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/findOverlaps-methods.Rd:103: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/findOverlaps-methods.Rd:117: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
genomic-range-squeezers html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/genomic-range-squeezers.Rd:16: file link 'ranges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/genomic-range-squeezers.Rd:17: file link 'rglist' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/genomic-range-squeezers.Rd:19: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/genomic-range-squeezers.Rd:19: file link 'ranges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/genomic-range-squeezers.Rd:21: file link 'IRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/genomic-range-squeezers.Rd:21: file link 'rglist' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/genomic-range-squeezers.Rd:32: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/genomic-range-squeezers.Rd:33: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/genomic-range-squeezers.Rd:34: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/genomic-range-squeezers.Rd:35: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/genomic-range-squeezers.Rd:36: file link 'GAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/genomic-range-squeezers.Rd:37: file link 'Pairs' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/genomic-range-squeezers.Rd:40: file link 'ranges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/genomic-range-squeezers.Rd:46: file link 'ranges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/genomic-range-squeezers.Rd:49: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/genomic-range-squeezers.Rd:50: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/genomic-range-squeezers.Rd:63: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/genomic-range-squeezers.Rd:79: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/genomic-range-squeezers.Rd:82: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/genomic-range-squeezers.Rd:83: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/genomic-range-squeezers.Rd:84: file link 'GAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic
genomicvars html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/genomicvars.Rd:20: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/genomicvars.Rd:49: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/genomicvars.Rd:60: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/genomicvars.Rd:80: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/genomicvars.Rd:91: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/genomicvars.Rd:105: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
inter-range-methods html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/inter-range-methods.Rd:95: file link 'reduce' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/inter-range-methods.Rd:103: file link 'gaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/inter-range-methods.Rd:112: file link 'disjoin' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/inter-range-methods.Rd:136: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/inter-range-methods.Rd:144: file link 'endoapply' in package 'S4Vectors' does not exist and so has been treated as a topic
intra-range-methods html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/intra-range-methods.Rd:40: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/intra-range-methods.Rd:41: file link 'GAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/intra-range-methods.Rd:81: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/intra-range-methods.Rd:85: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/intra-range-methods.Rd:89: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/intra-range-methods.Rd:158: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
makeGRangesFromDataFrame html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/makeGRangesFromDataFrame.Rd:16: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/makeGRangesFromDataFrame.Rd:37: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/makeGRangesFromDataFrame.Rd:122: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/makeGRangesFromDataFrame.Rd:144: file link 'getTable' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/makeGRangesFromDataFrame.Rd:148: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
makeGRangesListFromDataFrame html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/makeGRangesListFromDataFrame.Rd:15: file link 'split' in package 'S4Vectors' does not exist and so has been treated as a topic
nearest-methods html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/nearest-methods.Rd:80: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/nearest-methods.Rd:114: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/nearest-methods.Rd:118: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/nearest-methods.Rd:161: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/nearest-methods.Rd:164: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/nearest-methods.Rd:167: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/nearest-methods.Rd:180: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/nearest-methods.Rd:181: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
phicoef html
setops-methods html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/setops-methods.Rd:45: file link 'punion' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/setops-methods.Rd:45: file link 'pintersect' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/setops-methods.Rd:46: file link 'psetdiff' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/setops-methods.Rd:46: file link 'pgap' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/setops-methods.Rd:47: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/setops-methods.Rd:155: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/setops-methods.Rd:156: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/setops-methods.Rd:167: file link 'mendoapply' in package 'S4Vectors' does not exist and so has been treated as a topic
strand-utils html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/strand-utils.Rd:52: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/strand-utils.Rd:64: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/strand-utils.Rd:65: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/strand-utils.Rd:73: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/strand-utils.Rd:96: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
tile-methods html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/tile-methods.Rd:12: file link 'tile' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/tile-methods.Rd:12: file link 'slidingWindows' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/tile-methods.Rd:30: file link 'tile' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/tile-methods.Rd:35: file link 'tile' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/tile-methods.Rd:65: file link 'tile' in package 'IRanges' does not exist and so has been treated as a topic
tileGenome html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/tileGenome.Rd:68: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8wQmZx/R.INSTALLe283bc64b67/GenomicRanges/man/tileGenome.Rd:70: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'GenomicRanges' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c transcript_utils.c -o transcript_utils.o
transcript_utils.c: In function 'tlocs2rlocs':
transcript_utils.c:143:38: warning: 'end' may be used uninitialized in this function [-Wmaybe-uninitialized]
return on_minus_strand ? end - tloc : start + tloc;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
transcript_utils.c:120:24: note: 'end' was declared here
int nexons, j, start, end, width;
^~~
transcript_utils.c:143:38: warning: 'start' may be used uninitialized in this function [-Wmaybe-uninitialized]
return on_minus_strand ? end - tloc : start + tloc;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
transcript_utils.c:120:17: note: 'start' was declared here
int nexons, j, start, end, width;
^~~~~
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o GenomicRanges.dll tmp.def IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/GenomicRanges.buildbin-libdir/GenomicRanges/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicRanges' as GenomicRanges_1.42.0.zip
* DONE (GenomicRanges)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'GenomicRanges' successfully unpacked and MD5 sums checked