| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:19:12 -0400 (Wed, 15 Apr 2020).
| Package 1481/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Rsamtools 2.2.3 Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: Rsamtools |
| Version: 2.2.3 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Rsamtools.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings Rsamtools_2.2.3.tar.gz |
| StartedAt: 2020-04-15 06:17:49 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 06:23:16 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 326.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: Rsamtools.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Rsamtools.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings Rsamtools_2.2.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/Rsamtools.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Rsamtools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Rsamtools' version '2.2.3'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'Rsamtools' can be installed ... WARNING
Found the following significant warnings:
BamRangeIterator.h:138:39: warning: ignoring return value of 'int64_t bgzf_seek(BGZF*, int64_t, int)', declared with attribute warn_unused_result [-Wunused-result]
BamIterator.h:87:30: warning: ignoring return value of 'int64_t bgzf_seek(BGZF*, int64_t, int)', declared with attribute warn_unused_result [-Wunused-result]
C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/bam_sort.c:2263:13: warning: too many arguments for format [-Wformat-extra-args]
bamfile.c:168:13: warning: ignoring return value of 'bgzf_seek', declared with attribute warn_unused_result [-Wunused-result]
C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/bam.h:57:32: warning: ignoring return value of 'bgzf_seek', declared with attribute warn_unused_result [-Wunused-result]
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmp8GiokM/R.INSTALL18cc615d4152/Rsamtools/man/BamFile-class.Rd:350: file link 'readGAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmp8GiokM/R.INSTALL18cc615d4152/Rsamtools/man/BamFile-class.Rd:351: file link 'readGAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmp8GiokM/R.INSTALL18cc615d4152/Rsamtools/man/BamFile-class.Rd:354: file link 'summarizeOverlaps' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmp8GiokM/R.INSTALL18cc615d4152/Rsamtools/man/ScanBcfParam-class.Rd:62: file link 'scanVcfHeader' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmp8GiokM/R.INSTALL18cc615d4152/Rsamtools/man/ScanBcfParam-class.Rd:65: file link 'scanVcfHeader' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmp8GiokM/R.INSTALL18cc615d4152/Rsamtools/man/ScanBcfParam-class.Rd:69: file link 'scanVcfHeader' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmp8GiokM/R.INSTALL18cc615d4152/Rsamtools/man/ScanBcfParam-class.Rd:138: file link 'scanVcf' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmp8GiokM/R.INSTALL18cc615d4152/Rsamtools/man/ScanBcfParam-class.Rd:139: file link 'ScanVcfParam' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmp8GiokM/R.INSTALL18cc615d4152/Rsamtools/man/readPileup.Rd:34: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/Rsamtools.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 11.5Mb
sub-directories of 1Mb or more:
extdata 2.6Mb
libs 6.9Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Versioned 'LinkingTo' value for 'Rhtslib' is only usable in R >= 3.0.2
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
'S4Vectors:::explodeIntBits' 'S4Vectors:::implodeIntBits'
'S4Vectors:::makePowersOfTwo' 'S4Vectors:::quick_unlist'
'S4Vectors:::selectSome'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rsamtools/libs/i386/Rsamtools.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Found 'putchar', possibly from 'putchar' (C)
Found 'puts', possibly from 'printf' (C), 'puts' (C)
Found 'rand', possibly from 'rand' (C)
File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rsamtools/libs/x64/Rsamtools.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Found 'putchar', possibly from 'putchar' (C)
Found 'puts', possibly from 'printf' (C), 'puts' (C)
Found 'rand', possibly from 'rand' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
pileup 53.02 0.44 53.45
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
pileup 40.75 0.62 41.39
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'Rsamtools_unit_tests.R'
OK
** running tests for arch 'x64' ...
Running 'Rsamtools_unit_tests.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 5 NOTEs
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/Rsamtools.Rcheck/00check.log'
for details.
Rsamtools.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/Rsamtools_2.2.3.tar.gz && rm -rf Rsamtools.buildbin-libdir && mkdir Rsamtools.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rsamtools.buildbin-libdir Rsamtools_2.2.3.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL Rsamtools_2.2.3.zip && rm Rsamtools_2.2.3.tar.gz Rsamtools_2.2.3.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 2659k 100 2659k 0 0 26.7M 0 --:--:-- --:--:-- --:--:-- 27.6M
install for i386
* installing *source* package 'Rsamtools' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c COMPAT_bcf_hdr_read.c -o COMPAT_bcf_hdr_read.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c PileupBuffer.cpp -o PileupBuffer.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c PosCacheColl.cpp -o PosCacheColl.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c R_init_Rsamtools.c -o R_init_Rsamtools.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c ResultManager.cpp -o ResultManager.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c as_bam.c -o as_bam.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c bam.c -o bam.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c bam_data.c -o bam_data.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c bam_mate_iter.cpp -o bam_mate_iter.o
In file included from bam_mate_iter.cpp:2:0:
BamRangeIterator.h: In member function 'virtual void BamRangeIterator::finalize_inprogress(bamFile)':
BamRangeIterator.h:138:39: warning: ignoring return value of 'int64_t bgzf_seek(BGZF*, int64_t, int)', declared with attribute warn_unused_result [-Wunused-result]
bam_seek(bfile, pos, SEEK_SET);
^
In file included from BamRangeIterator.h:7:0,
from bam_mate_iter.cpp:2:
BamIterator.h: In constructor 'BamIterator::BamIterator(bamFile, const bam_index_t*)':
BamIterator.h:87:30: warning: ignoring return value of 'int64_t bgzf_seek(BGZF*, int64_t, int)', declared with attribute warn_unused_result [-Wunused-result]
bam_seek(bfile, 0, 0);
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c bam_plbuf.c -o bam_plbuf.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c bam_sort.c -o bam_sort.o
In file included from bam_sort.c:1:0:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/bam_sort.c: In function 'complain_about_memory_setting':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/bam_sort.c:2263:13: warning: unknown conversion type character 'z' in format [-Wformat=]
max_mem, suffix, SORT_MIN_MEGS_PER_THREAD);
^
C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/bam_sort.c:2263:13: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'size_t' [-Wformat=]
C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/bam_sort.c:2263:13: warning: unknown conversion type character 'z' in format [-Wformat=]
C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/bam_sort.c:2263:13: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c bambuffer.c -o bambuffer.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c bamfile.c -o bamfile.o
bamfile.c: In function 'bamfile_isincomplete':
bamfile.c:168:13: warning: ignoring return value of 'bgzf_seek', declared with attribute warn_unused_result [-Wunused-result]
bgzf_seek(bfile->file->x.bam, offset, SEEK_SET);
^
bamfile.c: In function 'bamfile_open':
bamfile.c:29:15: warning: 'cfile' may be used uninitialized in this function [-Wmaybe-uninitialized]
index = hts_idx_load2(file, indexname);
^
bamfile.c:73:17: note: 'cfile' was declared here
const char *cfile;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c bcffile.c -o bcffile.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c encode.c -o encode.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c fafile.c -o fafile.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c idxstats.c -o idxstats.o
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/sam.h:29:0,
from bamfile.h:5,
from idxstats.c:1:
idxstats.c: In function 'idxstats_bamfile':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/bam.h:57:32: warning: ignoring return value of 'bgzf_seek', declared with attribute warn_unused_result [-Wunused-result]
#define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
^
idxstats.c:20:5: note: in expansion of macro 'bam_seek'
bam_seek(fp, 0, 0);
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c io_sam.c -o io_sam.o
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/sam.h:29:0,
from io_sam.c:2:
io_sam.c: In function '_scan_bam_all':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/bam.h:57:32: warning: ignoring return value of 'bgzf_seek', declared with attribute warn_unused_result [-Wunused-result]
#define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
^
io_sam.c:304:5: note: in expansion of macro 'bam_seek'
bam_seek(bfile->file->x.bam, bfile->pos0, SEEK_SET);
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c pileup.cpp -o pileup.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c pileupbam.c -o pileupbam.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c sam.c -o sam.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c sam_opts.c -o sam_opts.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c sam_utils.c -o sam_utils.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c samtools_patch.c -o samtools_patch.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c scan_bam_data.c -o scan_bam_data.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c tabixfile.c -o tabixfile.o
tabixfile.c: In function 'index_tabix':
tabixfile.c:190:5: warning: 'bgzf_is_bgzf' is deprecated (declared at C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/htslib/bgzf.h:243): Use bgzf_compression() or hts_detect_format() instead [-Wdeprecated-declarations]
if (bgzf_is_bgzf(fn) != 1)
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c tagfilter.c -o tagfilter.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c utilities.c -o utilities.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c zip_compression.c -o zip_compression.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o Rsamtools.dll tmp.def Biostrings_stubs.o COMPAT_bcf_hdr_read.o IRanges_stubs.o PileupBuffer.o PosCacheColl.o R_init_Rsamtools.o ResultManager.o S4Vectors_stubs.o XVector_stubs.o as_bam.o bam.o bam_data.o bam_mate_iter.o bam_plbuf.o bam_sort.o bambuffer.o bamfile.o bcffile.o encode.o fafile.o idxstats.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.o sam.o sam_opts.o sam_utils.o samtools_patch.o scan_bam_data.o tabixfile.o tagfilter.o utilities.o zip_compression.o C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/usrlib/i386/libhts.a -LC:/extsoft/lib/i386 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -lidn -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/Rsamtools.buildbin-libdir/00LOCK-Rsamtools/00new/Rsamtools/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'Rsamtools'
finding HTML links ... done
ApplyPileupsParam-class html
BamFile-class html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmp8GiokM/R.INSTALL18cc615d4152/Rsamtools/man/BamFile-class.Rd:350: file link 'readGAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmp8GiokM/R.INSTALL18cc615d4152/Rsamtools/man/BamFile-class.Rd:351: file link 'readGAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmp8GiokM/R.INSTALL18cc615d4152/Rsamtools/man/BamFile-class.Rd:354: file link 'summarizeOverlaps' in package 'GenomicAlignments' does not exist and so has been treated as a topic
BamViews-class html
BcfFile-class html
FaFile-class html
PileupFiles-class html
Rsamtools-package html
RsamtoolsFile-class html
RsamtoolsFileList-class html
ScanBamParam-class html
ScanBcfParam-class html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmp8GiokM/R.INSTALL18cc615d4152/Rsamtools/man/ScanBcfParam-class.Rd:62: file link 'scanVcfHeader' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmp8GiokM/R.INSTALL18cc615d4152/Rsamtools/man/ScanBcfParam-class.Rd:65: file link 'scanVcfHeader' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmp8GiokM/R.INSTALL18cc615d4152/Rsamtools/man/ScanBcfParam-class.Rd:69: file link 'scanVcfHeader' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmp8GiokM/R.INSTALL18cc615d4152/Rsamtools/man/ScanBcfParam-class.Rd:138: file link 'scanVcf' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmp8GiokM/R.INSTALL18cc615d4152/Rsamtools/man/ScanBcfParam-class.Rd:139: file link 'ScanVcfParam' in package 'VariantAnnotation' does not exist and so has been treated as a topic
TabixFile-class html
applyPileups html
defunct html
deprecated html
headerTabix html
indexTabix html
pileup html
quickBamFlagSummary html
readPileup html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmp8GiokM/R.INSTALL18cc615d4152/Rsamtools/man/readPileup.Rd:34: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
scanBam html
scanBcf html
scanFa html
scanTabix html
seqnamesTabix html
testPairedEndBam html
zip html
** 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 'Rsamtools' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c COMPAT_bcf_hdr_read.c -o COMPAT_bcf_hdr_read.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c PileupBuffer.cpp -o PileupBuffer.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c PosCacheColl.cpp -o PosCacheColl.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c R_init_Rsamtools.c -o R_init_Rsamtools.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c ResultManager.cpp -o ResultManager.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c as_bam.c -o as_bam.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c bam.c -o bam.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c bam_data.c -o bam_data.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c bam_mate_iter.cpp -o bam_mate_iter.o
In file included from bam_mate_iter.cpp:2:0:
BamRangeIterator.h: In member function 'virtual void BamRangeIterator::finalize_inprogress(bamFile)':
BamRangeIterator.h:138:39: warning: ignoring return value of 'int64_t bgzf_seek(BGZF*, int64_t, int)', declared with attribute warn_unused_result [-Wunused-result]
bam_seek(bfile, pos, SEEK_SET);
^
In file included from BamRangeIterator.h:7:0,
from bam_mate_iter.cpp:2:
BamIterator.h: In constructor 'BamIterator::BamIterator(bamFile, const bam_index_t*)':
BamIterator.h:87:30: warning: ignoring return value of 'int64_t bgzf_seek(BGZF*, int64_t, int)', declared with attribute warn_unused_result [-Wunused-result]
bam_seek(bfile, 0, 0);
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c bam_plbuf.c -o bam_plbuf.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c bam_sort.c -o bam_sort.o
In file included from bam_sort.c:1:0:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/bam_sort.c: In function 'complain_about_memory_setting':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/bam_sort.c:2263:13: warning: unknown conversion type character 'z' in format [-Wformat=]
max_mem, suffix, SORT_MIN_MEGS_PER_THREAD);
^
C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/bam_sort.c:2263:13: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'size_t' [-Wformat=]
C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/bam_sort.c:2263:13: warning: unknown conversion type character 'z' in format [-Wformat=]
C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/bam_sort.c:2263:13: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c bambuffer.c -o bambuffer.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c bamfile.c -o bamfile.o
bamfile.c: In function 'bamfile_isincomplete':
bamfile.c:168:13: warning: ignoring return value of 'bgzf_seek', declared with attribute warn_unused_result [-Wunused-result]
bgzf_seek(bfile->file->x.bam, offset, SEEK_SET);
^
bamfile.c: In function 'bamfile_open':
bamfile.c:29:15: warning: 'cfile' may be used uninitialized in this function [-Wmaybe-uninitialized]
index = hts_idx_load2(file, indexname);
^
bamfile.c:73:17: note: 'cfile' was declared here
const char *cfile;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c bcffile.c -o bcffile.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c encode.c -o encode.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c fafile.c -o fafile.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c idxstats.c -o idxstats.o
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/sam.h:29:0,
from bamfile.h:5,
from idxstats.c:1:
idxstats.c: In function 'idxstats_bamfile':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/bam.h:57:32: warning: ignoring return value of 'bgzf_seek', declared with attribute warn_unused_result [-Wunused-result]
#define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
^
idxstats.c:20:5: note: in expansion of macro 'bam_seek'
bam_seek(fp, 0, 0);
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c io_sam.c -o io_sam.o
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/sam.h:29:0,
from io_sam.c:2:
io_sam.c: In function '_scan_bam_all':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/bam.h:57:32: warning: ignoring return value of 'bgzf_seek', declared with attribute warn_unused_result [-Wunused-result]
#define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
^
io_sam.c:304:5: note: in expansion of macro 'bam_seek'
bam_seek(bfile->file->x.bam, bfile->pos0, SEEK_SET);
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c pileup.cpp -o pileup.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c pileupbam.c -o pileupbam.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c sam.c -o sam.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c sam_opts.c -o sam_opts.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c sam_utils.c -o sam_utils.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c samtools_patch.c -o samtools_patch.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c scan_bam_data.c -o scan_bam_data.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c tabixfile.c -o tabixfile.o
tabixfile.c: In function 'index_tabix':
tabixfile.c:190:5: warning: 'bgzf_is_bgzf' is deprecated (declared at C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/htslib/bgzf.h:243): Use bgzf_compression() or hts_detect_format() instead [-Wdeprecated-declarations]
if (bgzf_is_bgzf(fn) != 1)
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c tagfilter.c -o tagfilter.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c utilities.c -o utilities.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c zip_compression.c -o zip_compression.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o Rsamtools.dll tmp.def Biostrings_stubs.o COMPAT_bcf_hdr_read.o IRanges_stubs.o PileupBuffer.o PosCacheColl.o R_init_Rsamtools.o ResultManager.o S4Vectors_stubs.o XVector_stubs.o as_bam.o bam.o bam_data.o bam_mate_iter.o bam_plbuf.o bam_sort.o bambuffer.o bamfile.o bcffile.o encode.o fafile.o idxstats.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.o sam.o sam_opts.o sam_utils.o samtools_patch.o scan_bam_data.o tabixfile.o tagfilter.o utilities.o zip_compression.o C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -LC:/extsoft/lib/x64 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rsamtools' as Rsamtools_2.2.3.zip
* DONE (Rsamtools)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'Rsamtools' successfully unpacked and MD5 sums checked
|
Rsamtools.Rcheck/tests_i386/Rsamtools_unit_tests.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage('Rsamtools')
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
[E::COMPAT_bcf_hdr_read] Input is not detected as bcf or vcf format
Timing stopped at: 0 0 0
Error in DEACTIVATED("remote tabix not supported on Windows") :
remote tabix not supported on Windows
RUNIT TEST PROTOCOL -- Wed Apr 15 06:22:28 2020
***********************************************
Number of test functions: 179
Number of deactivated test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
Rsamtools RUnit Tests - 179 test functions, 0 errors, 0 failures
Number of test functions: 179
Number of deactivated test functions: 1
Number of errors: 0
Number of failures: 0
[E::hts_idx_push] Chromosome blocks not continuous
[E::hts_open_format] Failed to open file http://httpbin.org/status/504
Warning messages:
1: In read.table(conn, colClasses = colClasses, col.names = names(colClasses), :
not all columns named in 'colClasses' exist
2: In read.table(conn, colClasses = colClasses, col.names = names(colClasses), :
not all columns named in 'colClasses' exist
3: In read.table(conn, colClasses = colClasses, col.names = names(colClasses), :
not all columns named in 'colClasses' exist
4: In read.table(conn, colClasses = colClasses, col.names = names(colClasses), :
not all columns named in 'colClasses' exist
>
> proc.time()
user system elapsed
18.15 0.71 36.96
|
Rsamtools.Rcheck/tests_x64/Rsamtools_unit_tests.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage('Rsamtools')
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
[E::COMPAT_bcf_hdr_read] Input is not detected as bcf or vcf format
Timing stopped at: 0 0 0
Error in DEACTIVATED("remote tabix not supported on Windows") :
remote tabix not supported on Windows
RUNIT TEST PROTOCOL -- Wed Apr 15 06:23:08 2020
***********************************************
Number of test functions: 179
Number of deactivated test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
Rsamtools RUnit Tests - 179 test functions, 0 errors, 0 failures
Number of test functions: 179
Number of deactivated test functions: 1
Number of errors: 0
Number of failures: 0
[E::hts_idx_push] Chromosome blocks not continuous
[E::hts_open_format] Failed to open file http://httpbin.org/status/504
Warning messages:
1: In read.table(conn, colClasses = colClasses, col.names = names(colClasses), :
not all columns named in 'colClasses' exist
2: In read.table(conn, colClasses = colClasses, col.names = names(colClasses), :
not all columns named in 'colClasses' exist
3: In read.table(conn, colClasses = colClasses, col.names = names(colClasses), :
not all columns named in 'colClasses' exist
4: In read.table(conn, colClasses = colClasses, col.names = names(colClasses), :
not all columns named in 'colClasses' exist
>
> proc.time()
user system elapsed
17.79 0.59 39.26
|
|
Rsamtools.Rcheck/examples_i386/Rsamtools-Ex.timings
|
Rsamtools.Rcheck/examples_x64/Rsamtools-Ex.timings
|