subSeq 1.1.1
Andrew J. Bass , John D. Storey
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/subSeq | | Last Changed Rev: 109695 / Revision: 109948 | | Last Changed Date: 2015-10-16 14:11:07 -0400 (Fri, 16 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
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### Running command:
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### rm -rf subSeq.buildbin-libdir subSeq.Rcheck && mkdir subSeq.buildbin-libdir subSeq.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=subSeq.buildbin-libdir subSeq_1.1.1.tar.gz >subSeq.Rcheck\00install.out 2>&1 && cp subSeq.Rcheck\00install.out subSeq-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=subSeq.buildbin-libdir --install="check:subSeq-install.out" --force-multiarch --no-vignettes --timings subSeq_1.1.1.tar.gz
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/subSeq.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 'subSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'subSeq' version '1.1.1'
* 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 'subSeq' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plot.summary.subsamples: no visible binding for global variable
'metric'
plot.summary.subsamples: no visible binding for global variable 'value'
plot.summary.subsamples: no visible binding for global variable
'significant'
plot.summary.subsamples: no visible binding for global variable
'percent'
plot.summary.subsamples: no visible binding for global variable
'method'
plot.summary.subsamples: no visible binding for global variable 'depth'
plot.summary.subsamples: no visible binding for global variable
'average.depth'
plot.summary.subsamples: no visible binding for global variable
'average.value'
subsample: no visible binding for global variable 'proportion'
subsample: no visible binding for global variable 'replication'
subsample: no visible binding for global variable '.'
subsample: no visible binding for global variable 'pvalue'
summary.subsamples: no visible binding for global variable 'count'
summary.subsamples: no visible binding for global variable 'method'
summary.subsamples: no visible binding for global variable 'depth'
summary.subsamples: no visible binding for global variable 'pvalue'
summary.subsamples: no visible binding for global variable 'proportion'
summary.subsamples: no visible binding for global variable
'replication'
summary.subsamples: no visible binding for global variable 'ID'
summary.subsamples: no visible binding for global variable 'padj'
summary.subsamples: no visible binding for global variable
'coefficient'
summary.subsamples: no visible binding for global variable
'o.coefficient'
summary.subsamples: no visible binding for global variable 'valid'
summary.subsamples: no visible binding for global variable 'o.lfdr'
summary.subsamples: no visible binding for global variable 'o.padj'
summary.subsamples: no visible binding for global variable
'significant'
summary.subsamples: no visible binding for global variable 'estFDP'
summary.subsamples: no visible binding for global variable 'rFDP'
summary.subsamples: no visible binding for global variable 'metric'
summary.subsamples: no visible binding for global variable 'value'
summary.subsamples: no visible binding for global variable 'percent'
Undefined global functions or variables:
. ID average.depth average.value coefficient count depth estFDP
method metric o.coefficient o.lfdr o.padj padj percent proportion
pvalue rFDP replication significant valid value
* 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' ... [110s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
generateSubsampledMatrix 37.90 0.20 38.11
subsample 34.92 0.09 35.02
getSeed 33.11 0.03 33.17
** running examples for arch 'x64' ... [112s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
generateSubsampledMatrix 39.93 0.22 40.16
getSeed 33.79 0.06 33.84
subsample 33.63 0.08 33.70
* 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: 1 NOTE
See
'c:/biocbld/bbs-3.3-bioc/meat/subSeq.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'subSeq' ...
** 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 'subSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'subSeq' as subSeq_1.1.1.zip
* DONE (subSeq)