msmsTests 1.9.0
Josep Gregori i Font
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msmsTests | | 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 msmsTests.buildbin-libdir msmsTests.Rcheck && mkdir msmsTests.buildbin-libdir msmsTests.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=msmsTests.buildbin-libdir msmsTests_1.9.0.tar.gz >msmsTests.Rcheck\00install.out 2>&1 && cp msmsTests.Rcheck\00install.out msmsTests-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=msmsTests.buildbin-libdir --install="check:msmsTests-install.out" --force-multiarch --no-vignettes --timings msmsTests_1.9.0.tar.gz
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/msmsTests.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 'msmsTests/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'msmsTests' version '1.9.0'
* 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 'msmsTests' 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:
'MSnbase' 'msmsEDA'
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
msms.edgeR: no visible global function definition for 'exprs'
msms.edgeR: no visible global function definition for 'pData'
msms.glm.pois: no visible global function definition for 'exprs'
msms.glm.pois: no visible global function definition for 'pData'
msms.glm.qlll: no visible global function definition for 'exprs'
msms.glm.qlll: no visible global function definition for 'pData'
test.results: no visible global function definition for 'exprs'
Undefined global functions or variables:
exprs pData
* 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' ... [38s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
res.volcanoplot 7.62 0 7.63
test.results 7.14 0 7.14
msms.glm.qlll 6.41 0 6.41
pval.by.fc 6.27 0 6.26
msms.glm.pois 6.03 0 6.03
** running examples for arch 'x64' ... [46s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
test.results 8.70 0.02 8.72
res.volcanoplot 8.55 0.00 8.54
msms.glm.qlll 8.35 0.00 8.36
msms.glm.pois 8.02 0.00 8.03
pval.by.fc 6.52 0.02 6.54
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: 'xtable'
* 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: 3 NOTEs
See
'c:/biocbld/bbs-3.3-bioc/meat/msmsTests.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'msmsTests' ...
** 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 'msmsTests' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'msmsTests' as msmsTests_1.9.0.zip
* DONE (msmsTests)