BioC 3.3: CHECK report for nucleR on moscato2

Package: nucleR

Version: 2.4.0

Command: rm -rf nucleR.buildbin-libdir nucleR.Rcheck && mkdir nucleR.buildbin-libdir nucleR.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=nucleR.buildbin-libdir nucleR_2.4.0.tar.gz >nucleR.Rcheck\00install.out 2>&1 && cp nucleR.Rcheck\00install.out nucleR-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=nucleR.buildbin-libdir --install="check:nucleR-install.out" --force-multiarch --no-vignettes --timings nucleR_2.4.0.tar.gz

StartedAt: 2016-10-13 06:51:55 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 06:56:13 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 258.5 seconds

RetCode: 0

Status:  OK

CheckDir: nucleR.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf nucleR.buildbin-libdir nucleR.Rcheck && mkdir nucleR.buildbin-libdir nucleR.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=nucleR.buildbin-libdir nucleR_2.4.0.tar.gz >nucleR.Rcheck\00install.out 2>&1 && cp nucleR.Rcheck\00install.out nucleR-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=nucleR.buildbin-libdir --install="check:nucleR-install.out" --force-multiarch --no-vignettes --timings nucleR_2.4.0.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/nucleR.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'nucleR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'nucleR' version '2.4.0'
* 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 'nucleR' 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
.buildGRSingle: no visible binding for global variable 'rname'
.buildGRSingle: no visible binding for global variable 'qwidth'
Undefined global functions or variables:
  qwidth rname
* 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' ... OK
** running examples for arch 'x64' ... OK
* 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
  'E:/biocbld/bbs-3.3-bioc/meat/nucleR.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'nucleR' ...
** 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 'nucleR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'nucleR' as nucleR_2.4.0.zip
* DONE (nucleR)

name	user	system	elapsed
controlCorrection	0.04	0.00	0.03
coverage.rpm	0.11	0.01	0.12
export.bed	0	0	0
export.wig	0	0	0
filterFFT	0.23	0.04	0.27
fragmentLenDetect	1.34	0.00	1.34
mergeCalls	0.49	0.00	0.48
nucleR-package	0.71	0.00	0.94
pcKeepCompDetect	0.30	0.03	0.32
peakDetection	0.37	0.03	0.41
peakScoring	0.13	0.00	0.12
plotPeaks	0.47	0.00	0.47
processReads	0.17	0.00	0.17
processTilingArray	0	0	0
syntheticNucMap	0.56	0.02	0.58

name	user	system	elapsed
controlCorrection	0.05	0.00	0.05
coverage.rpm	0.18	0.00	0.19
export.bed	0	0	0
export.wig	0	0	0
filterFFT	0.24	0.02	0.25
fragmentLenDetect	1.47	0.00	1.47
mergeCalls	0.54	0.00	0.55
nucleR-package	0.58	0.01	0.72
pcKeepCompDetect	0.21	0.00	0.21
peakDetection	0.75	0.02	0.76
peakScoring	0.15	0.02	0.17
plotPeaks	0.47	0.00	0.47
processReads	0.13	0.00	0.13
processTilingArray	0	0	0
syntheticNucMap	0.42	0.01	0.43