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BUILD BIN report for GenomicAlignments on tokay2

This page was generated on 2018-10-17 08:37:59 -0400 (Wed, 17 Oct 2018).

Package 592/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicAlignments 1.16.0
Bioconductor Package Maintainer
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/GenomicAlignments
Branch: RELEASE_3_7
Last Commit: db032a4
Last Changed Date: 2018-04-30 10:35:32 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS [ OK ]UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: GenomicAlignments
Version: 1.16.0
Command: rm -rf GenomicAlignments.buildbin-libdir && mkdir GenomicAlignments.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomicAlignments.buildbin-libdir GenomicAlignments_1.16.0.tar.gz
StartedAt: 2018-10-17 06:23:03 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 06:23:48 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 45.3 seconds
RetCode: 0
Status:  OK  
PackageFile: GenomicAlignments_1.16.0.zip
PackageFileSize: 2.31 MiB

Command output

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###
### Running command:
###
###   rm -rf GenomicAlignments.buildbin-libdir && mkdir GenomicAlignments.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomicAlignments.buildbin-libdir GenomicAlignments_1.16.0.tar.gz
###
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install for i386

* installing *source* package 'GenomicAlignments' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-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˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-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˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-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˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-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˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-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˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-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˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/GenomicAlignments.buildbin-libdir/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/GenomicAlignments/man/coverage-methods.Rd:65: file link 'ScanBamParam' in package 'Rsamtools' does not exist and so has been treated as a topic
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    encodeOverlaps-methods                  html  
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    findCompatibleOverlaps-methods          html  
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    findMateAlignment                       html  
    findOverlaps-methods                    html  
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    findSpliceOverlaps-methods              html  
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    intra-range-methods                     html  
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    junctions-methods                       html  
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    pileLettersAt                           html  
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    readGAlignments                         html  
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Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/GenomicAlignments/man/readGAlignments.Rd:208: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/GenomicAlignments/man/readGAlignments.Rd:252: file link 'ScanBamParam' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/GenomicAlignments/man/readGAlignments.Rd:258: file link 'IRangesList' in package 'IRanges' does not exist and so has been treated as a topic
    sequenceLayer                           html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/GenomicAlignments/man/sequenceLayer.Rd:120: file link 'extractAt' in package 'Biostrings' does not exist and so has been treated as a topic
    setops-methods                          html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/GenomicAlignments/man/setops-methods.Rd:14: file link 'pintersect' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/GenomicAlignments/man/setops-methods.Rd:15: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/GenomicAlignments/man/setops-methods.Rd:17: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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-3.7-bioc/tmpdir/Rtmp29YXsV/R.INSTALL1fbc7c6927b1/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
In R CMD INSTALL

install for x64

* installing *source* package 'GenomicAlignments' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-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˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-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˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-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˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-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˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-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˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-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˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/GenomicAlignments.buildbin-libdir/GenomicAlignments/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicAlignments' as GenomicAlignments_1.16.0.zip
* DONE (GenomicAlignments)
In R CMD INSTALL
In R CMD INSTALL