PROPER 1.3.0
Hao Wu
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/PROPER | | 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 | NotNeeded | OK | WARNINGS | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ WARNINGS ] | OK | |
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### Running command:
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### rm -rf PROPER.buildbin-libdir PROPER.Rcheck && mkdir PROPER.buildbin-libdir PROPER.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PROPER.buildbin-libdir PROPER_1.3.0.tar.gz >PROPER.Rcheck\00install.out 2>&1 && cp PROPER.Rcheck\00install.out PROPER-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=PROPER.buildbin-libdir --install="check:PROPER-install.out" --force-multiarch --no-vignettes --timings PROPER_1.3.0.tar.gz
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/PROPER.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 'PROPER/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PROPER' version '1.3.0'
* 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 'PROPER' 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 ... WARNING
'library' or 'require' call not declared from: 'edgeR'
'library' or 'require' call to 'edgeR' in package code.
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
estParam: no visible global function definition for 'exprs'
run.DESeq: no visible global function definition for 'newCountDataSet'
run.DESeq: no visible global function definition for
'estimateSizeFactors'
run.DESeq: no visible global function definition for
'estimateDispersions'
run.DESeq: no visible global function definition for 'nbinomTest'
run.DSS: no visible global function definition for 'newSeqCountSet'
run.DSS: no visible global function definition for 'estNormFactors'
run.DSS: no visible global function definition for 'estDispersion'
run.DSS: no visible global function definition for 'waldTest'
Undefined global functions or variables:
estDispersion estNormFactors estimateDispersions estimateSizeFactors
exprs nbinomTest newCountDataSet newSeqCountSet waldTest
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'estParam':
estParam
Code: function(X, type = 1)
Docs: function(X, type = c(1, 2))
Mismatches in argument default values:
Name: 'type' Code: 1 Docs: c(1, 2)
* 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' ... [21s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
runSims 19.41 0.22 19.63
** running examples for arch 'x64' ... [20s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
runSims 18.71 0.23 18.94
* 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 WARNINGs, 1 NOTE
See
'c:/biocbld/bbs-3.3-bioc/meat/PROPER.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'PROPER' ...
** 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 'PROPER' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PROPER' as PROPER_1.3.0.zip
* DONE (PROPER)