Back to "Blame Jeroen" build/check report for BioC 3.11

INSTALL report for GenomicAlignments on tokay2

This page was generated on 2020-04-15 03:20:10 -0400 (Wed, 15 Apr 2020).

These builds are using Rtools40 and R-testing by Jeroen Ooms (available at https://cran.r-project.org/bin/windows/testing/rtools40.html)
TO THE DEVELOPERS/MAINTAINERS OF THE GenomicAlignments PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 41/89HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicAlignments 1.23.2
Bioconductor Package Maintainer
Snapshot Date: 2020-04-14 17:00:05 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/GenomicAlignments
Branch: master
Last Commit: e7002a6
Last Changed Date: 2020-03-24 01:20:27 -0400 (Tue, 24 Mar 2020)
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] OK  WARNINGS  OK 

Summary

Package: GenomicAlignments
Version: 1.23.2
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc-testing/src/contrib/GenomicAlignments_1.23.2.tar.gz && rm -rf GenomicAlignments.buildbin-libdir && mkdir GenomicAlignments.buildbin-libdir && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomicAlignments.buildbin-libdir GenomicAlignments_1.23.2.tar.gz && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL GenomicAlignments_1.23.2.zip && rm GenomicAlignments_1.23.2.tar.gz GenomicAlignments_1.23.2.zip
StartedAt: 2020-04-14 18:10:24 -0400 (Tue, 14 Apr 2020)
EndedAt: 2020-04-14 18:11:20 -0400 (Tue, 14 Apr 2020)
EllapsedTime: 55.8 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc-testing/src/contrib/GenomicAlignments_1.23.2.tar.gz && rm -rf GenomicAlignments.buildbin-libdir && mkdir GenomicAlignments.buildbin-libdir && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomicAlignments.buildbin-libdir GenomicAlignments_1.23.2.tar.gz && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL GenomicAlignments_1.23.2.zip && rm GenomicAlignments_1.23.2.tar.gz GenomicAlignments_1.23.2.zip
###
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100 1372k  100 1372k    0     0  14.4M      0 --:--:-- --:--:-- --:--:-- 15.4M

install for i386

* installing *source* package 'GenomicAlignments' ...
** using staged installation
** libs
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cigar_utils.c -o cigar_utils.o
cigar_utils.c: In function 'cigar_ranges':
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];
                 ~~~~~~~~~~^~~~~~
In file included from C:/Users/BIOCTE~1/BBS-3~1.11-/R/include/Rdefines.h:40,
                 from GenomicAlignments.h:1,
                 from cigar_utils.c:1:
C:/Users/BIOCTE~1/BBS-3~1.11-/R/include/Rinternals.h:1548:20: warning: 'f_levels' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define duplicate  Rf_duplicate
                    ^~~~~~~~~~~~
cigar_utils.c:587:29: note: 'f_levels' was declared here
  SEXP ans, ans_breakpoints, f_levels, cigar_elt;
                             ^~~~~~~~
cigar_utils.c:542:4: warning: 'ans_breakpoints' may be used uninitialized in this function [-Wmaybe-uninitialized]
    new_PartitioningByEnd("PartitioningByEnd",
    ^~~~~~~~~~~~~~~~~~~~~
cigar_utils.c:587:12: note: 'ans_breakpoints' was declared here
  SEXP ans, ans_breakpoints, f_levels, cigar_elt;
            ^~~~~~~~~~~~~~~
cigar_utils.c:676:9: warning: 'f_elt' may be used uninitialized in this function [-Wmaybe-uninitialized]
    f_elt++;
    ~~~~~^~
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:626:8: warning: 'flag_elt' may be used uninitialized in this function [-Wmaybe-uninitialized]
    if (*flag_elt == NA_INTEGER) {
        ^~~~~~~~~
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) {
        ^~~~~~~~~
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o
/mingw32/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/BIOCTE~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/bioctesting/bbs-3.11-bioc-testing/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/GenomicAlignments/man/GAlignments-class.Rd:177: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/GenomicAlignments/man/GAlignments-class.Rd:189: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/GenomicAlignments/man/GAlignments-class.Rd:283: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/GenomicAlignments/man/GAlignments-class.Rd:299: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/GenomicAlignments/man/GAlignments-class.Rd:304: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/GenomicAlignments/man/GAlignments-class.Rd:305: file link 'CompressedIRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/GenomicAlignments/man/GAlignments-class.Rd:347: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/GenomicAlignments/man/GAlignments-class.Rd:353: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/GenomicAlignments/man/GAlignments-class.Rd:379: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/GenomicAlignments/man/GAlignments-class.Rd:398: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/GenomicAlignments/man/GAlignments-class.Rd:398: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/GenomicAlignments/man/GAlignments-class.Rd:431: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/GenomicAlignments/man/GAlignments-class.Rd:432: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/GenomicAlignments/man/GAlignments-class.Rd:435: file link 'CompressedIRangesList' in package 'IRanges' does not exist and so has been treated as a topic
    GAlignmentsList-class                   html  
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/GenomicAlignments/man/coverage-methods.Rd:53: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
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    findOverlaps-methods                    html  
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    findSpliceOverlaps-methods              html  
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    intra-range-methods                     html  
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    pileLettersAt                           html  
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    readGAlignments                         html  
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    sequenceLayer                           html  
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    setops-methods                          html  
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/GenomicAlignments/man/setops-methods.Rd:29: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    stackStringsFromGAlignments             html  
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/GenomicAlignments/man/stackStringsFromGAlignments.Rd:48: file link 'ScanBamParam' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/GenomicAlignments/man/stackStringsFromGAlignments.Rd:52: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/GenomicAlignments/man/stackStringsFromGAlignments.Rd:69: file link 'stackStrings' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/GenomicAlignments/man/stackStringsFromGAlignments.Rd:71: file link 'stackStrings' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/GenomicAlignments/man/stackStringsFromGAlignments.Rd:82: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/GenomicAlignments/man/stackStringsFromGAlignments.Rd:83: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/GenomicAlignments/man/stackStringsFromGAlignments.Rd:85: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/GenomicAlignments/man/stackStringsFromGAlignments.Rd:93: file link 'alphabetFrequency' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/GenomicAlignments/man/stackStringsFromGAlignments.Rd:108: file link 'stackStrings' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/GenomicAlignments/man/stackStringsFromGAlignments.Rd:132: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/GenomicAlignments/man/stackStringsFromGAlignments.Rd:133: file link 'BStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/GenomicAlignments/man/stackStringsFromGAlignments.Rd:136: file link 'alphabetFrequency' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/GenomicAlignments/man/stackStringsFromGAlignments.Rd:167: file link 'stackStrings' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/GenomicAlignments/man/stackStringsFromGAlignments.Rd:169: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/GenomicAlignments/man/stackStringsFromGAlignments.Rd:171: file link 'alphabetFrequency' in package 'Biostrings' does not exist and so has been treated as a topic
    summarizeOverlaps-methods               html  
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp40PhEe/R.INSTALLcdc26776491/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
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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: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:626:8: warning: 'flag_elt' may be used uninitialized in this function [-Wmaybe-uninitialized]
    if (*flag_elt == NA_INTEGER) {
        ^~~~~~~~~
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) {
        ^~~~~~~~~
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o
encodeOverlaps_methods.c: In function 'overlap_encoding':
encodeOverlaps_methods.c:180:33: warning: 'out_nelt0' may be used uninitialized in this function [-Wmaybe-uninitialized]
  CharAE_set_nelt(out, out_nelt0 + j2 * nrow);
                       ~~~~~~~~~~^~~~~~~~~~~
encodeOverlaps_methods.c:99:6: note: 'out_nelt0' was declared here
  int out_nelt0, i, starti, widthi, spacei, j, startj, widthj, spacej,
      ^~~~~~~~~
/mingw64/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/BIOCTE~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/bioctesting/bbs-3.11-bioc-testing/meat/GenomicAlignments.buildbin-libdir/GenomicAlignments/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicAlignments' as GenomicAlignments_1.23.2.zip
* DONE (GenomicAlignments)
* installing to library 'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library'
package 'GenomicAlignments' successfully unpacked and MD5 sums checked