baySeq 2.5.0
Thomas J. Hardcastle
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/baySeq | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] | OK | |
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### Running command:
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### rm -rf baySeq.buildbin-libdir baySeq.Rcheck && mkdir baySeq.buildbin-libdir baySeq.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=baySeq.buildbin-libdir baySeq_2.5.0.tar.gz >baySeq.Rcheck\00install.out 2>&1 && cp baySeq.Rcheck\00install.out baySeq-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=baySeq.buildbin-libdir --install="check:baySeq-install.out" --force-multiarch --no-vignettes --timings baySeq_2.5.0.tar.gz
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/baySeq.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'baySeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'baySeq' version '2.5.0'
* 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 'baySeq' 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 ... NOTE
'library' or 'require' call to 'edgeR' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'perm'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.posteriorWeights: no visible binding for global variable 'CDpriors'
.posteriorWeights: no visible binding for global variable 'consensus'
getLibsizes : estLibs: no visible global function definition for
'DGEList'
getLibsizes : estLibs: no visible global function definition for
'calcNormFactors'
getLikelihoods: no visible global function definition for
'clusterExport'
getLikelihoods: no visible global function definition for 'clusterCall'
getLikelihoods: no visible global function definition for 'parLapplyLB'
getLikelihoods: no visible global function definition for
'clusterEvalQ'
getPosteriors: no visible global function definition for
'clusterExport'
getPosteriors: no visible global function definition for 'clusterCall'
getPosteriors: no visible binding for global variable 'clustAssign'
getPosteriors: no visible global function definition for 'parRapply'
getPriors: no visible global function definition for 'clusterExport'
getPriors: no visible global function definition for 'parLapplyLB'
getPriors: no visible global function definition for 'clusterEvalQ'
getPriors.NB: no visible global function definition for 'parApply'
getPriors.NB: no visible global function definition for 'clusterEvalQ'
Undefined global functions or variables:
CDpriors DGEList calcNormFactors clustAssign clusterCall clusterEvalQ
clusterExport consensus parApply parLapplyLB parRapply
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [122s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
baySeq-package 59.77 0.07 59.85
getPriors 44.77 0.02 44.78
getLikelihoods 14.27 0.00 14.26
** running examples for arch 'x64' ... [155s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
baySeq-package 79.84 0.03 79.90
getPriors 56.64 0.02 56.66
getLikelihoods 14.78 0.00 14.78
* 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:/biocbld/bbs-3.3-bioc/meat/baySeq.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'baySeq' ...
** R
** data
** 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 'baySeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'baySeq' as baySeq_2.5.0.zip
* DONE (baySeq)