ChIPseqR 1.30.0
Peter Humburg
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/ChIPseqR | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ WARNINGS ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | WARNINGS | OK | |
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### Running command:
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### rm -rf ChIPseqR.buildbin-libdir ChIPseqR.Rcheck && mkdir ChIPseqR.buildbin-libdir ChIPseqR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChIPseqR.buildbin-libdir ChIPseqR_1.30.0.tar.gz >ChIPseqR.Rcheck\00install.out 2>&1 && cp ChIPseqR.Rcheck\00install.out ChIPseqR-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=ChIPseqR.buildbin-libdir --install="check:ChIPseqR-install.out" --force-multiarch --no-vignettes --timings ChIPseqR_1.30.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/ChIPseqR.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ChIPseqR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChIPseqR' version '1.30.0'
* 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 'ChIPseqR' can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import 'BiocGenerics::image' by 'graphics::image' when loading 'ChIPseqR'
Warning: replacing previous import 'S4Vectors::head' by 'utils::head' when loading 'ChIPseqR'
Warning: replacing previous import 'S4Vectors::tail' by 'utils::tail' when loading 'ChIPseqR'
See 'C:/Users/biocbuild/bbs-3.5-bioc/meat/ChIPseqR.Rcheck/00install.out' for details.
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 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-3.5-bioc/meat/ChIPseqR.buildbin-libdir/ChIPseqR/libs/i386/ChIPseqR.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
Examples with CPU or elapsed time > 5s
user system elapsed
BindScore 15.51 0.44 15.96
RLEBindScore-class 12.70 0.26 12.97
simpleNucCall 11.86 0.20 12.06
callBindingSites 10.39 0.26 10.66
alignFeature 6.45 2.58 9.03
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
callBindingSites 13.53 0.33 13.86
BindScore 13.48 0.19 13.67
alignFeature 9.84 3.25 13.09
simpleNucCall 12.76 0.28 13.04
RLEBindScore-class 11.80 0.26 12.07
* 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, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.5-bioc/meat/ChIPseqR.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'ChIPseqR' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c startScore.c -o startScore.o
startScore.c: In function '_ratioStat_pois':
startScore.c:66:15: warning: unused variable 'tmp_stat' [-Wunused-variable]
double stat, tmp_stat;
^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o ChIPseqR.dll tmp.def startScore.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/ChIPseqR.buildbin-libdir/ChIPseqR/libs/i386
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import 'BiocGenerics::image' by 'graphics::image' when loading 'ChIPseqR'
Warning: replacing previous import 'S4Vectors::head' by 'utils::head' when loading 'ChIPseqR'
Warning: replacing previous import 'S4Vectors::tail' by 'utils::tail' when loading 'ChIPseqR'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'BiocGenerics::image' by 'graphics::image' when loading 'ChIPseqR'
Warning: replacing previous import 'S4Vectors::head' by 'utils::head' when loading 'ChIPseqR'
Warning: replacing previous import 'S4Vectors::tail' by 'utils::tail' when loading 'ChIPseqR'
install for x64
* installing *source* package 'ChIPseqR' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c startScore.c -o startScore.o
startScore.c: In function '_ratioStat_pois':
startScore.c:66:15: warning: unused variable 'tmp_stat' [-Wunused-variable]
double stat, tmp_stat;
^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o ChIPseqR.dll tmp.def startScore.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/ChIPseqR.buildbin-libdir/ChIPseqR/libs/x64
** testing if installed package can be loaded
Warning: replacing previous import 'BiocGenerics::image' by 'graphics::image' when loading 'ChIPseqR'
Warning: replacing previous import 'S4Vectors::head' by 'utils::head' when loading 'ChIPseqR'
Warning: replacing previous import 'S4Vectors::tail' by 'utils::tail' when loading 'ChIPseqR'
* MD5 sums
packaged installation of 'ChIPseqR' as ChIPseqR_1.30.0.zip
* DONE (ChIPseqR)