baySeq 1.18.0
Thomas J. Hardcastle
| Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/baySeq | | Last Changed Rev: 88838 / Revision: 95116 | | Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK |
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### Running command:
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### rm -rf baySeq.buildbin-libdir && mkdir baySeq.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=baySeq.buildbin-libdir baySeq_1.18.0.tar.gz >baySeq-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=baySeq.buildbin-libdir --install="check:baySeq-install.out" --force-multiarch --no-vignettes --timings baySeq_1.18.0.tar.gz
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* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/baySeq.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-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 '1.18.0'
* 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
Packages in Depends field not imported from:
'GenomicRanges' 'methods'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of 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
getLikelihoods : distFunctionConsensus: no visible binding for global
variable 'seglen'
getLikelihoods : LNbootStrap : PDgivenr.LNConsensus: no visible binding
for global variable 'prior'
getPosteriors: no visible binding for global variable 'clustAssign'
getPosteriors: no visible binding for global variable 'getPostsEnv'
getPriors.NB: no visible global function definition for
'newSeqCountSet'
getPriors.NB: no visible global function definition for 'estDispersion'
getTPs: no visible binding for global variable 'logsum'
* 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' ... [170s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
baySeq-package 84.82 0.01 84.84
getPriors 67.26 0.00 67.25
getLikelihoods 14.81 0.00 14.81
** running examples for arch 'x64' ... [207s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
baySeq-package 104.24 0.03 104.30
getPriors 82.00 0.00 81.99
getLikelihoods 16.37 0.00 16.36
* 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
NOTE: There were 2 notes.
See
'E:/biocbld/bbs-2.14-bioc/meat/baySeq.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'baySeq' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for 'rbind' in package 'baySeq'
** 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_1.18.0.zip
* DONE (baySeq)