Jose M Muino
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/CSAR |
| Branch: master |
| Last Commit: bf510c8 |
| Last Changed Date: 2018-10-30 11:54:28 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 11:57:42 -0400 (Tue, 09 Apr 2019).
| Package 362/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CSAR 1.35.0 Jose M Muino
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: CSAR |
| Version: 1.35.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CSAR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings CSAR_1.35.0.tar.gz |
| StartedAt: 2019-04-09 02:04:56 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 02:09:20 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 264.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CSAR.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CSAR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings CSAR_1.35.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/CSAR.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CSAR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CSAR' version '1.35.0'
* 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 'CSAR' 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 ... NOTE
mappedReads2Nhits: no visible global function definition for
'chromosome'
mappedReads2Nhits: no visible global function definition for 'position'
Undefined global functions or variables:
chromosome position
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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-3.9-bioc/R/library/CSAR/libs/i386/CSAR.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/CSAR/libs/x64/CSAR.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 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
getThreshold 10.86 0.01 10.87
CSAR-package 10.41 0.00 10.41
getPermutatedWinScores 10.09 0.02 10.11
permutatedWinScores 9.15 0.04 9.17
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
getThreshold 20.00 0.01 20.03
getPermutatedWinScores 18.17 0.07 18.56
permutatedWinScores 17.70 0.05 17.77
CSAR-package 13.41 0.00 13.40
distance2Genes 5.92 0.00 5.92
genesWithPeaks 5.60 0.01 5.61
score2wig 5.22 0.00 5.22
* 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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/CSAR.Rcheck/00check.log'
for details.
CSAR.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/CSAR_1.35.0.tar.gz && rm -rf CSAR.buildbin-libdir && mkdir CSAR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CSAR.buildbin-libdir CSAR_1.35.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL CSAR_1.35.0.zip && rm CSAR_1.35.0.tar.gz CSAR_1.35.0.zip
###
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% 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 25088 100 25088 0 0 415k 0 --:--:-- --:--:-- --:--:-- 471k
install for i386
* installing *source* package 'CSAR' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c CSAR.c -o CSAR.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o CSAR.dll tmp.def CSAR.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/CSAR.buildbin-libdir/00LOCK-CSAR/00new/CSAR/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'CSAR'
finding HTML links ... done
CSAR-package html
ChIPseqScore html
distance2Genes html
genesWithPeaks html
getPermutatedWinScores html
getThreshold html
loadMappedReads html
mappedReads2Nhits html
permutatedWinScores html
sampleSEP3_test html
score2wig html
sigWin 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 'CSAR' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c CSAR.c -o CSAR.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o CSAR.dll tmp.def CSAR.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/CSAR.buildbin-libdir/CSAR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CSAR' as CSAR_1.35.0.zip
* DONE (CSAR)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'CSAR' successfully unpacked and MD5 sums checked
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CSAR.Rcheck/examples_i386/CSAR-Ex.timings
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CSAR.Rcheck/examples_x64/CSAR-Ex.timings
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