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This page was generated on 2019-04-09 12:14:37 -0400 (Tue, 09 Apr 2019).
Package 645/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
GenomicAlignments 1.19.1 Bioconductor Package Maintainer
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | [ OK ] | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
Package: GenomicAlignments |
Version: 1.19.1 |
Command: rm -rf GenomicAlignments.buildbin-libdir && mkdir GenomicAlignments.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomicAlignments.buildbin-libdir GenomicAlignments_1.19.1.tar.gz |
StartedAt: 2019-04-09 08:00:25 -0400 (Tue, 09 Apr 2019) |
EndedAt: 2019-04-09 08:01:18 -0400 (Tue, 09 Apr 2019) |
EllapsedTime: 52.9 seconds |
RetCode: 0 |
Status: OK |
PackageFile: GenomicAlignments_1.19.1.zip |
PackageFileSize: 2.328 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf GenomicAlignments.buildbin-libdir && mkdir GenomicAlignments.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomicAlignments.buildbin-libdir GenomicAlignments_1.19.1.tar.gz ### ############################################################################## ############################################################################## install for i386 * installing *source* package 'GenomicAlignments' ... ** libs C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c IRanges_stubs.c -o IRanges_stubs.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/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˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c cigar_utils.c -o cigar_utils.o cigar_utils.c: In function 'cigar_ranges': cigar_utils.c:676:9: warning: 'f_elt' may be used uninitialized in this function [-Wmaybe-uninitialized] f_elt++; ^ cigar_utils.c:658:27: warning: 'range_buf2' may be used uninitialized in this function [-Wmaybe-uninitialized] range_buf1 = range_buf2->elts[*f_elt - 1]; ^ cigar_utils.c:674:22: warning: 'range_buf1' may be used uninitialized in this function [-Wmaybe-uninitialized] *(breakpoint++) = IntPairAE_get_nelt(range_buf1); ^ cigar_utils.c:674:16: warning: 'breakpoint' may be used uninitialized in this function [-Wmaybe-uninitialized] *(breakpoint++) = IntPairAE_get_nelt(range_buf1); ^ cigar_utils.c:670:12: warning: 'flag_elt' may be used uninitialized in this function [-Wmaybe-uninitialized] flag_elt++; ^ cigar_utils.c: In function 'cigar_width': cigar_utils.c:708:8: warning: 'flag_elt' may be used uninitialized in this function [-Wmaybe-uninitialized] if (*flag_elt == NA_INTEGER) { ^ cigar_utils.c: In function 'cigar_narrow': cigar_utils.c:887:17: warning: 'OP' may be used uninitialized in this function [-Wmaybe-uninitialized] buf_offset += sprintf(cigar_buf + buf_offset, ^ cigar_utils.c:855:7: note: 'OP' was declared here char OP /* Operation */; ^ cigar_utils.c:879:8: warning: 'OPL' may be used uninitialized in this function [-Wmaybe-uninitialized] OPL -= Lwidth; ^ cigar_utils.c:854:17: note: 'OPL' was declared here int offset, n, OPL /* Operation Length */; ^ cigar_utils.c: In function 'cigar_qnarrow': cigar_utils.c:1071:17: warning: 'OP' may be used uninitialized in this function [-Wmaybe-uninitialized] buf_offset += sprintf(cigar_buf + buf_offset, ^ cigar_utils.c:1039:7: note: 'OP' was declared here char OP /* Operation */; ^ cigar_utils.c:1063:8: warning: 'OPL' may be used uninitialized in this function [-Wmaybe-uninitialized] OPL -= Lqwidth; ^ cigar_utils.c:1038:17: note: 'OPL' was declared here int offset, n, OPL /* Operation Length */; ^ C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o encodeOverlaps_methods.c: In function 'overlap_encoding': encodeOverlaps_methods.c:182:2: warning: 'out_nelt0' may be used uninitialized in this function [-Wmaybe-uninitialized] CharAE_delete_at(out, out_nelt0, j1 * nrow); ^ encodeOverlaps_methods.c:99:6: note: 'out_nelt0' was declared here int out_nelt0, i, starti, widthi, spacei, j, startj, widthj, spacej, ^ C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o GenomicAlignments.dll tmp.def IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o coordinate_mapping_methods.o encodeOverlaps_methods.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/GenomicAlignments.buildbin-libdir/00LOCK-GenomicAlignments/00new/GenomicAlignments/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'GenomicAlignments' finding HTML links ... done GAlignmentPairs-class html finding level-2 HTML links ... done Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/GAlignmentPairs-class.Rd:168: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/GAlignmentPairs-class.Rd:278: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/GAlignmentPairs-class.Rd:355: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/GAlignmentPairs-class.Rd:357: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/GAlignmentPairs-class.Rd:357: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/GAlignmentPairs-class.Rd:389: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/GAlignmentPairs-class.Rd:390: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic GAlignments-class html Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/GAlignments-class.Rd:173: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/GAlignments-class.Rd:185: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/GAlignments-class.Rd:279: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/GAlignments-class.Rd:295: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/GAlignments-class.Rd:300: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/GAlignments-class.Rd:301: file link 'CompressedIRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/GAlignments-class.Rd:343: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/GAlignments-class.Rd:349: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/GAlignments-class.Rd:375: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/GAlignments-class.Rd:394: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/GAlignments-class.Rd:394: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/GAlignments-class.Rd:427: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/GAlignments-class.Rd:428: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/GAlignments-class.Rd:431: file link 'CompressedIRangesList' in package 'IRanges' does not exist and so has been treated as a topic GAlignmentsList-class html Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/GAlignmentsList-class.Rd:174: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/GAlignmentsList-class.Rd:192: file link 'IRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/GAlignmentsList-class.Rd:260: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/GAlignmentsList-class.Rd:291: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/GAlignmentsList-class.Rd:292: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic GappedReads-class html Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/GappedReads-class.Rd:43: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic OverlapEncodings-class html Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/OverlapEncodings-class.Rd:112: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/OverlapEncodings-class.Rd:273: file link 'pcompare' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/OverlapEncodings-class.Rd:277: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic cigar-utils html Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/cigar-utils.Rd:133: file link 'IRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/cigar-utils.Rd:135: file link 'IRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/cigar-utils.Rd:139: file link 'IRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/cigar-utils.Rd:189: file link 'solveUserSEW' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/cigar-utils.Rd:221: file link 'CompressedRleList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/cigar-utils.Rd:229: file link 'IRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/cigar-utils.Rd:230: file link 'CompressedIRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/cigar-utils.Rd:233: file link 'IRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/cigar-utils.Rd:233: file link 'SimpleIRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/cigar-utils.Rd:234: file link 'CompressedIRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/cigar-utils.Rd:289: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/cigar-utils.Rd:289: file link 'IRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/cigar-utils.Rd:290: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/cigar-utils.Rd:292: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic coordinate-mapping-methods html Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/coordinate-mapping-methods.Rd:25: file link 'mapToTranscripts' in package 'GenomicFeatures' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/coordinate-mapping-methods.Rd:144: file link 'mapToTranscripts' in package 'GenomicFeatures' does not exist and so has been treated as a topic coverage-methods html Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/coverage-methods.Rd:15: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/coverage-methods.Rd:17: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/coverage-methods.Rd:19: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/coverage-methods.Rd:20: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/coverage-methods.Rd:20: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/coverage-methods.Rd:22: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/coverage-methods.Rd:23: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/coverage-methods.Rd:46: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/coverage-methods.Rd:49: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/coverage-methods.Rd:53: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/coverage-methods.Rd:65: file link 'ScanBamParam' in package 'Rsamtools' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/coverage-methods.Rd:70: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/coverage-methods.Rd:84: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/coverage-methods.Rd:92: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/coverage-methods.Rd:97: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/coverage-methods.Rd:103: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/coverage-methods.Rd:108: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: 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C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/setops-methods.Rd:18: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/setops-methods.Rd:29: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic stackStringsFromBam html Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/stackStringsFromBam.Rd:40: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/stackStringsFromBam.Rd:41: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/stackStringsFromBam.Rd:43: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/stackStringsFromBam.Rd:63: file link 'stackStrings' in package 'Biostrings' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/stackStringsFromBam.Rd:65: file link 'stackStrings' in package 'Biostrings' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/stackStringsFromBam.Rd:69: file link 'alphabetFrequency' in package 'Biostrings' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/stackStringsFromBam.Rd:86: file link 'stackStrings' in package 'Biostrings' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/stackStringsFromBam.Rd:97: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/stackStringsFromBam.Rd:98: file link 'BStringSet' in package 'Biostrings' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/stackStringsFromBam.Rd:101: file link 'alphabetFrequency' in package 'Biostrings' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/stackStringsFromBam.Rd:131: file link 'stackStrings' in package 'Biostrings' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/stackStringsFromBam.Rd:133: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/stackStringsFromBam.Rd:135: file link 'alphabetFrequency' in package 'Biostrings' does not exist and so has been treated as a topic summarizeOverlaps-methods html Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/summarizeOverlaps-methods.Rd:83: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/summarizeOverlaps-methods.Rd:83: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/summarizeOverlaps-methods.Rd:84: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/summarizeOverlaps-methods.Rd:86: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/summarizeOverlaps-methods.Rd:90: file link 'BamViews' in package 'Rsamtools' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/summarizeOverlaps-methods.Rd:94: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/summarizeOverlaps-methods.Rd:98: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/summarizeOverlaps-methods.Rd:98: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/summarizeOverlaps-methods.Rd:100: file link 'BamViews' in package 'Rsamtools' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/summarizeOverlaps-methods.Rd:101: file link 'BamFileList' in package 'Rsamtools' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/summarizeOverlaps-methods.Rd:104: file link 'BamViews' in package 'Rsamtools' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/summarizeOverlaps-methods.Rd:107: file link 'BamViews' in package 'Rsamtools' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/summarizeOverlaps-methods.Rd:215: file link 'ScanBamParam' in package 'Rsamtools' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/summarizeOverlaps-methods.Rd:250: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/summarizeOverlaps-methods.Rd:251: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/summarizeOverlaps-methods.Rd:252: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/summarizeOverlaps-methods.Rd:254: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/summarizeOverlaps-methods.Rd:259: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/summarizeOverlaps-methods.Rd:261: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/summarizeOverlaps-methods.Rd:284: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/summarizeOverlaps-methods.Rd:315: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/summarizeOverlaps-methods.Rd:320: file link 'BamFileList' in package 'Rsamtools' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpag2hfQ/R.INSTALL4a4364b61d0/GenomicAlignments/man/summarizeOverlaps-methods.Rd:320: file link 'BamViews' in package 'Rsamtools' 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 'GenomicAlignments' ... ** libs C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c IRanges_stubs.c -o IRanges_stubs.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/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˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c cigar_utils.c -o cigar_utils.o cigar_utils.c: In function 'cigar_ranges': cigar_utils.c:676:9: warning: 'f_elt' may be used uninitialized in this function [-Wmaybe-uninitialized] f_elt++; ^ cigar_utils.c:658:27: warning: 'range_buf2' may be used uninitialized in this function [-Wmaybe-uninitialized] range_buf1 = range_buf2->elts[*f_elt - 1]; ^ cigar_utils.c:674:22: warning: 'range_buf1' may be used uninitialized in this function [-Wmaybe-uninitialized] *(breakpoint++) = IntPairAE_get_nelt(range_buf1); ^ cigar_utils.c:674:16: warning: 'breakpoint' may be used uninitialized in this function [-Wmaybe-uninitialized] *(breakpoint++) = IntPairAE_get_nelt(range_buf1); ^ cigar_utils.c:670:12: warning: 'flag_elt' may be used uninitialized in this function [-Wmaybe-uninitialized] flag_elt++; ^ cigar_utils.c: In function 'cigar_width': cigar_utils.c:708:8: warning: 'flag_elt' may be used uninitialized in this function [-Wmaybe-uninitialized] if (*flag_elt == NA_INTEGER) { ^ C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o encodeOverlaps_methods.c: In function 'overlap_encoding': encodeOverlaps_methods.c:182:2: warning: 'out_nelt0' may be used uninitialized in this function [-Wmaybe-uninitialized] CharAE_delete_at(out, out_nelt0, j1 * nrow); ^ encodeOverlaps_methods.c:99:6: note: 'out_nelt0' was declared here int out_nelt0, i, starti, widthi, spacei, j, startj, widthj, spacej, ^ C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o GenomicAlignments.dll tmp.def IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o coordinate_mapping_methods.o encodeOverlaps_methods.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/GenomicAlignments.buildbin-libdir/GenomicAlignments/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'GenomicAlignments' as GenomicAlignments_1.19.1.zip * DONE (GenomicAlignments)