cobindR 1.4.0 Manuela Benary
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/cobindR | Last Changed Rev: 95439 / Revision: 102249 | Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | OK | |
moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK |
perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |
oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK |
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### Running command:
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### rm -rf cobindR.buildbin-libdir cobindR.Rcheck && mkdir cobindR.buildbin-libdir cobindR.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cobindR.buildbin-libdir cobindR_1.4.0.tar.gz >cobindR.Rcheck\00install.out 2>&1 && cp cobindR.Rcheck\00install.out cobindR-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=cobindR.buildbin-libdir --install="check:cobindR-install.out" --force-multiarch --no-vignettes --timings cobindR_1.4.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/cobindR.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cobindR/DESCRIPTION' ... OK
* this is package 'cobindR' version '1.4.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'genoPlotR'
* 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 'cobindR' 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
** 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 ... NOTE
'library' or 'require' calls in package code:
'MotifDb' 'parallel' 'snowfall'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
parallelize: no visible global function definition for 'mclapply'
parallelize: no visible global function definition for 'sfCpus'
parallelize: no visible global function definition for 'sfInit'
parallelize: no visible global function definition for 'sfLapply'
parallelize: no visible global function definition for 'sfStop'
query.motifDb: no visible binding for global variable 'MotifDb'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [171s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
testCpG 24.23 0.00 24.23
search.pwm 23.51 0.05 23.56
rtfbs 20.03 0.78 20.83
write.sequences 17.78 0.01 17.79
search.gadem 14.42 0.01 14.43
plot.gc 8.18 0.07 8.68
bg_binding_sites 5.85 0.20 6.41
sequences 5.69 0.00 5.69
pfm 5.46 0.01 5.47
pairs_of_interest 5.26 0.00 5.25
bg_sequences 5.23 0.00 5.23
experiment_description 5.23 0.00 5.23
bg_pairs 5.02 0.02 5.04
** running examples for arch 'x64' ... [208s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
testCpG 28.31 0.00 28.31
rtfbs 27.18 0.67 27.88
search.pwm 23.52 0.01 23.67
write.sequences 22.10 0.00 22.14
search.gadem 18.53 0.05 18.58
bg_binding_sites 8.72 0.16 8.97
plot.gc 8.33 0.06 9.17
pfm 7.41 0.00 7.41
bg_sequences 6.93 0.00 6.93
bg_pairs 6.66 0.01 6.67
sequences 6.07 0.01 6.08
binding_sites 5.62 0.02 5.63
experiment_description 5.62 0.00 5.61
pairs_of_interest 5.59 0.00 5.59
configuration 5.52 0.00 5.53
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R' [11s]
[12s] OK
** running tests for arch 'x64' ...
Running 'runTests.R' [12s]
[12s] 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
NOTE: There were 3 notes.
See
'D:/biocbld/bbs-3.0-bioc/meat/cobindR.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'cobindR' ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for 'sequence' in package 'cobindR'
Creating a generic function for 'write' from package 'base' in package 'cobindR'
Creating a generic function for 'write.fasta' from package 'seqinr' in package 'cobindR'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'cobindR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cobindR' as cobindR_1.4.0.zip
* DONE (cobindR)