Rhtslib 1.5.4
Bioconductor Package Maintainer
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rhtslib | | Last Changed Rev: 119330 / Revision: 121152 | | Last Changed Date: 2016-07-12 14:42:14 -0700 (Tue, 12 Jul 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | OK | OK | [ WARNINGS ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### rm -rf Rhtslib.buildbin-libdir Rhtslib.Rcheck && mkdir Rhtslib.buildbin-libdir Rhtslib.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Rhtslib.buildbin-libdir Rhtslib_1.5.4.tar.gz >Rhtslib.Rcheck\00install.out 2>&1 && cp Rhtslib.Rcheck\00install.out Rhtslib-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=Rhtslib.buildbin-libdir --install="check:Rhtslib-install.out" --force-multiarch --no-vignettes --timings Rhtslib_1.5.4.tar.gz
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/Rhtslib.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Rhtslib/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Rhtslib' version '1.5.4'
* 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 ... NOTE
Found the following hidden files and directories:
src/htslib/.travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... WARNING
Found the following file with a non-portable file name:
src/htslib/m4/lt˜obsolete.m4
These are not fully portable file names.
See section 'Package structure' in the 'Writing R Extensions' manual.
* checking whether package 'Rhtslib' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
* 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 ... OK
* 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 'D:/biocbld/bbs-3.4-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/libs/i386/Rhtslib.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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, 2 NOTEs
See
'D:/biocbld/bbs-3.4-bioc/meat/Rhtslib.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'Rhtslib' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
cp "winlib/i386/libhts.a" "D:/biocbld/bbs-3.4-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/lib/i386"/libhts.a
cp ./htslib/htslib/bgzf.h ./htslib/htslib/faidx.h ./htslib/htslib/hfile.h ./htslib/htslib/hts.h ./htslib/htslib/hts_defs.h ./htslib/htslib/kfunc.h ./htslib/htslib/khash.h ./htslib/htslib/khash_str2int.h ./htslib/htslib/klist.h ./htslib/htslib/knetfile.h ./htslib/htslib/kseq.h ./htslib/htslib/ksort.h ./htslib/htslib/kstring.h ./htslib/htslib/regidx.h ./htslib/htslib/sam.h ./htslib/htslib/synced_bcf_reader.h ./htslib/htslib/tbx.h ./htslib/htslib/vcf.h ./htslib/htslib/vcf_sweep.h ./htslib/htslib/vcfutils.h ""D:/biocbld/bbs-3.4-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/include""
C:/Rtools/mingw_32/bin/gcc -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c Rhtslib.c -o Rhtslib.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o Rhtslib.dll tmp.def Rhtslib.o -Lc:/local323/lib/i386 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'Rhtslib' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
cp "winlib/x64/libhts.a" "D:/biocbld/bbs-3.4-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/lib/x64"/libhts.a
cp ./htslib/htslib/bgzf.h ./htslib/htslib/faidx.h ./htslib/htslib/hfile.h ./htslib/htslib/hts.h ./htslib/htslib/hts_defs.h ./htslib/htslib/kfunc.h ./htslib/htslib/khash.h ./htslib/htslib/khash_str2int.h ./htslib/htslib/klist.h ./htslib/htslib/knetfile.h ./htslib/htslib/kseq.h ./htslib/htslib/ksort.h ./htslib/htslib/kstring.h ./htslib/htslib/regidx.h ./htslib/htslib/sam.h ./htslib/htslib/synced_bcf_reader.h ./htslib/htslib/tbx.h ./htslib/htslib/vcf.h ./htslib/htslib/vcf_sweep.h ./htslib/htslib/vcfutils.h ""D:/biocbld/bbs-3.4-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/include""
C:/Rtools/mingw_64/bin/gcc -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c Rhtslib.c -o Rhtslib.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o Rhtslib.dll tmp.def Rhtslib.o -Lc:/local323/lib/x64 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rhtslib' as Rhtslib_1.5.4.zip
* DONE (Rhtslib)