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INSTALL report for GenomicAlignments on tokay1

This page was generated on 2018-04-12 13:23:36 -0400 (Thu, 12 Apr 2018).

Package 562/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicAlignments 1.14.2
Bioconductor Package Maintainer
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/GenomicAlignments
Branch: RELEASE_3_6
Last Commit: 57b0b35
Last Changed Date: 2018-03-26 21:49:57 -0400 (Mon, 26 Mar 2018)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64 [ OK ] OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GenomicAlignments
Version: 1.14.2
Command: rm -rf GenomicAlignments.buildbin-libdir && mkdir GenomicAlignments.buildbin-libdir && C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.6/bioc/src/contrib/GenomicAlignments_1.14.2.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=GenomicAlignments.buildbin-libdir --merge-multiarch GenomicAlignments_1.14.2.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL GenomicAlignments_1.14.2.zip && rm GenomicAlignments_1.14.2.tar.gz GenomicAlignments_1.14.2.zip
StartedAt: 2018-04-11 18:43:00 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 18:44:36 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 95.7 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   rm -rf GenomicAlignments.buildbin-libdir && mkdir GenomicAlignments.buildbin-libdir  && C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.6/bioc/src/contrib/GenomicAlignments_1.14.2.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=GenomicAlignments.buildbin-libdir --merge-multiarch GenomicAlignments_1.14.2.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL GenomicAlignments_1.14.2.zip  && rm GenomicAlignments_1.14.2.tar.gz GenomicAlignments_1.14.2.zip
###
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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˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include"   -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include"   -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include"   -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include"   -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include"   -I"C:/local323/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/g++ -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:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomicAlignments.buildbin-libdir/GenomicAlignments/libs/i386
** R
** inst
** preparing 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-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/GAlignmentPairs-class.Rd:164: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/GAlignmentPairs-class.Rd:274: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/GAlignmentPairs-class.Rd:352: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/GAlignmentPairs-class.Rd:353: missing file link 'XStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/GAlignmentPairs-class.Rd:385: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/GAlignmentPairs-class.Rd:386: missing file link 'GRangesList'
    GAlignments-class                       html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/GAlignments-class.Rd:171: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/GAlignments-class.Rd:183: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/GAlignments-class.Rd:277: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/GAlignments-class.Rd:293: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/GAlignments-class.Rd:298: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/GAlignments-class.Rd:299: missing file link 'CompressedIRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/GAlignments-class.Rd:341: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/GAlignments-class.Rd:347: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/GAlignments-class.Rd:389: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/GAlignments-class.Rd:389: missing file link 'DNAStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/GAlignments-class.Rd:422: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/GAlignments-class.Rd:423: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/GAlignments-class.Rd:426: missing file link 'CompressedIRangesList'
    GAlignmentsList-class                   html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/GAlignmentsList-class.Rd:178: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/GAlignmentsList-class.Rd:196: missing file link 'IRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/GAlignmentsList-class.Rd:292: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/GAlignmentsList-class.Rd:293: missing file link 'GRangesList'
    GappedReads-class                       html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/GappedReads-class.Rd:43: missing file link 'DNAStringSet'
    OverlapEncodings-class                  html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/OverlapEncodings-class.Rd:111: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/OverlapEncodings-class.Rd:272: missing file link 'pcompare'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/OverlapEncodings-class.Rd:276: missing file link 'GRangesList'
    cigar-utils                             html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/cigar-utils.Rd:133: missing file link 'IRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/cigar-utils.Rd:135: missing file link 'IRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/cigar-utils.Rd:139: missing file link 'IRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/cigar-utils.Rd:189: missing file link 'solveUserSEW'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/cigar-utils.Rd:221: missing file link 'CompressedRleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/cigar-utils.Rd:229: missing file link 'IRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/cigar-utils.Rd:230: missing file link 'CompressedIRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/cigar-utils.Rd:233: missing file link 'IRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/cigar-utils.Rd:233: missing file link 'SimpleIRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/cigar-utils.Rd:234: missing file link 'CompressedIRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/cigar-utils.Rd:289: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/cigar-utils.Rd:289: missing file link 'IRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/cigar-utils.Rd:290: missing file link 'RleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/cigar-utils.Rd:292: missing file link 'coverage'
    coordinate-mapping-methods              html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/coordinate-mapping-methods.Rd:25: missing file link 'mapToTranscripts'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/coordinate-mapping-methods.Rd:144: missing file link 'mapToTranscripts'
    coverage-methods                        html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/coverage-methods.Rd:15: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/coverage-methods.Rd:17: missing file link 'BamFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/coverage-methods.Rd:19: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/coverage-methods.Rd:20: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/coverage-methods.Rd:20: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/coverage-methods.Rd:22: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/coverage-methods.Rd:23: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/coverage-methods.Rd:46: missing file link 'BamFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/coverage-methods.Rd:49: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/coverage-methods.Rd:53: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/coverage-methods.Rd:65: missing file link 'ScanBamParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/coverage-methods.Rd:70: missing file link 'BamFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/coverage-methods.Rd:84: missing file link 'BamFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/coverage-methods.Rd:92: missing file link 'BamFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/coverage-methods.Rd:97: missing file link 'RleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/coverage-methods.Rd:103: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/coverage-methods.Rd:108: missing file link 'RleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/coverage-methods.Rd:114: missing file link 'BamFile'
    encodeOverlaps-methods                  html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/encodeOverlaps-methods.Rd:50: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/encodeOverlaps-methods.Rd:83: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/encodeOverlaps-methods.Rd:91: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/encodeOverlaps-methods.Rd:91: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/encodeOverlaps-methods.Rd:94: missing file link 'Hits'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/encodeOverlaps-methods.Rd:95: missing file link 'findOverlaps'
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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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Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/junctions-methods.Rd:261: missing file link 'List'
    pileLettersAt                           html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/pileLettersAt.Rd:13: missing file link 'XStringSet'
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    readGAlignments                         html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/readGAlignments.Rd:45: missing file link 'BamFile'
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Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/readGAlignments.Rd:63: missing file link 'ScanBamParam'
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Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/readGAlignments.Rd:258: missing file link 'RangesList'
    sequenceLayer                           html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/sequenceLayer.Rd:120: missing file link 'extractAt'
    setops-methods                          html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/setops-methods.Rd:14: missing file link 'pintersect'
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    stackStringsFromBam                     html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/stackStringsFromBam.Rd:40: missing file link 'GRanges'
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Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/stackStringsFromBam.Rd:97: missing file link 'DNAStringSet'
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    summarizeOverlaps-methods               html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/summarizeOverlaps-methods.Rd:83: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/summarizeOverlaps-methods.Rd:83: missing file link 'GRangesList'
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Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/summarizeOverlaps-methods.Rd:90: missing file link 'BamViews'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/summarizeOverlaps-methods.Rd:94: missing file link 'RangedSummarizedExperiment'
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Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/summarizeOverlaps-methods.Rd:101: missing file link 'BamFileList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/summarizeOverlaps-methods.Rd:104: missing file link 'BamViews'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/summarizeOverlaps-methods.Rd:107: missing file link 'BamViews'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/summarizeOverlaps-methods.Rd:215: missing file link 'ScanBamParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/summarizeOverlaps-methods.Rd:250: missing file link 'GRanges'
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Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/summarizeOverlaps-methods.Rd:252: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/summarizeOverlaps-methods.Rd:254: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/summarizeOverlaps-methods.Rd:259: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/summarizeOverlaps-methods.Rd:261: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/summarizeOverlaps-methods.Rd:284: missing file link 'RangedSummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/summarizeOverlaps-methods.Rd:315: missing file link 'RangedSummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/summarizeOverlaps-methods.Rd:320: missing file link 'BamFileList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp2LK4bp/R.INSTALL86c8a433ab/GenomicAlignments/man/summarizeOverlaps-methods.Rd:320: missing file link 'BamViews'
** 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˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include"   -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include"   -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include"   -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include"   -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include"   -I"C:/local323/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/g++ -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:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomicAlignments.buildbin-libdir/GenomicAlignments/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicAlignments' as GenomicAlignments_1.14.2.zip
* DONE (GenomicAlignments)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.6-bioc/R/library'
package 'GenomicAlignments' successfully unpacked and MD5 sums checked
In R CMD INSTALL