BioC 3.0: CHECK report for BiSeq on moscato1

Package: BiSeq

Version: 1.6.0

Command: rm -rf BiSeq.buildbin-libdir BiSeq.Rcheck && mkdir BiSeq.buildbin-libdir BiSeq.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiSeq.buildbin-libdir BiSeq_1.6.0.tar.gz >BiSeq.Rcheck\00install.out 2>&1 && cp BiSeq.Rcheck\00install.out BiSeq-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=BiSeq.buildbin-libdir --install="check:BiSeq-install.out" --force-multiarch --no-vignettes --timings BiSeq_1.6.0.tar.gz

StartedAt: 2015-04-09 23:08:27 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 23:17:53 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 565.5 seconds

RetCode: 0

Status:  OK

CheckDir: BiSeq.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf BiSeq.buildbin-libdir BiSeq.Rcheck && mkdir BiSeq.buildbin-libdir BiSeq.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiSeq.buildbin-libdir BiSeq_1.6.0.tar.gz >BiSeq.Rcheck\00install.out 2>&1 && cp BiSeq.Rcheck\00install.out BiSeq-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=BiSeq.buildbin-libdir --install="check:BiSeq-install.out" --force-multiarch --no-vignettes --timings BiSeq_1.6.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/BiSeq.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BiSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BiSeq' version '1.6.0'
* 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 'BiSeq' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods' 'S4Vectors' 'IRanges' 'GenomicRanges' 'Formula'
A package should be listed in only one of these fields.
* 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
Namespace in Imports field not imported from: 'Formula'
  All declared Imports should be used.
Package in Depends field not imported from: 'Formula'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': 'IRanges:::width'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.predictMeth: no visible global function definition for 'seqlevels<-'
.predictMeth: no visible global function definition for 'seqlevels'
.predictMeth : predict.cluster: no visible global function definition
  for 'seqlevels<-'
.predictMeth : predict.cluster: no visible global function definition
  for 'seqlevels'
predictMeth,BSraw-numeric-numeric-numeric: no visible global function
  definition for 'seqlevels<-'
predictMeth,BSraw-numeric-numeric-numeric: no visible global function
  definition for 'seqlevels'
predictMeth,BSraw-numeric-numeric-numeric : predict.cluster: no visible
  global function definition for 'seqlevels<-'
predictMeth,BSraw-numeric-numeric-numeric : predict.cluster: no visible
  global function definition for 'seqlevels'
* 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' ... [87s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
globalTest     29.65   0.01   29.67
betaRegression  9.61   0.02    9.98
estLocCor       8.44   0.03    8.78
makeVariogram   6.82   0.02    6.83
** running examples for arch 'x64' ... [117s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
globalTest     37.68   0.00   37.67
betaRegression 15.10   0.01   15.11
makeVariogram  12.73   0.00   12.73
estLocCor      10.69   0.06   10.75
* 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

NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-3.0-bioc/meat/BiSeq.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'BiSeq' ...
** 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 'BiSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BiSeq' as BiSeq_1.6.0.zip
* DONE (BiSeq)

name	user	system	elapsed
BSraw-class	0.12	0.02	0.14
BSrel-class	0.28	0.00	0.28
DMRs	0.10	0.00	0.09
annotateGRanges	0.29	0.00	0.30
betaRegression	9.61	0.02	9.98
betaResults	0.02	0.00	0.02
betaResultsNull	0	0	0
binomLikelihoodSmooth	0	0	0
clusterSites	0.83	0.00	0.82
clusterSitesToGR	0.47	0.00	0.47
compareTwoSamples	2.03	0.00	2.03
covBoxplots	0.10	0.00	0.36
covStatistics	0.08	0.00	0.08
estLocCor	8.44	0.03	8.78
filterByCov	0.11	0.00	0.11
filterBySharedRegions	0.11	0.00	0.11
findDMRs	0.63	0.02	0.64
globalTest	29.65	0.01	29.67
limitCov	0.93	0.00	0.94
logisticRegression	2.2	0.0	2.2
makeVariogram	6.82	0.02	6.83
plotBindingSites	3.4	0.0	3.4
plotMeth	0.42	0.01	0.44
plotMethMap	0.44	0.02	0.45
plotSmoothMeth	0.51	0.00	0.51
predictMeth	0.96	0.00	0.95
predictedMeth	0.01	0.00	0.02
promoters	0.11	0.00	0.10
rawToRel	0.06	0.00	0.07
readBismark	0.11	0.00	0.11
rrbs	0.06	0.00	0.06
smoothVariogram	0.03	0.00	0.04
summarizeRegions	2.42	0.00	2.41
testClusters	0.18	0.00	0.17
trimClusters	0.95	0.01	0.97
vario	0.01	0.00	0.01
writeBED	0.35	0.02	0.39

name	user	system	elapsed
BSraw-class	0.23	0.00	0.23
BSrel-class	0.5	0.0	0.5
DMRs	0.11	0.00	0.10
annotateGRanges	0.51	0.02	0.54
betaRegression	15.10	0.01	15.11
betaResults	0.02	0.00	0.02
betaResultsNull	0.02	0.00	0.01
binomLikelihoodSmooth	0.01	0.00	0.02
clusterSites	0.69	0.00	0.69
clusterSitesToGR	0.78	0.02	0.79
compareTwoSamples	4.09	0.00	4.09
covBoxplots	0.16	0.00	0.16
covStatistics	0.07	0.00	0.08
estLocCor	10.69	0.06	10.75
filterByCov	0.11	0.00	0.11
filterBySharedRegions	0.19	0.00	0.18
findDMRs	0.92	0.00	0.92
globalTest	37.68	0.00	37.67
limitCov	1.06	0.01	1.08
logisticRegression	3.07	0.00	3.07
makeVariogram	12.73	0.00	12.73
plotBindingSites	4.09	0.02	4.10
plotMeth	0.42	0.00	0.43
plotMethMap	0.45	0.02	0.46
plotSmoothMeth	0.27	0.00	0.27
predictMeth	0.95	0.00	0.95
predictedMeth	0.01	0.00	0.02
promoters	0.07	0.00	0.06
rawToRel	0.04	0.00	0.05
readBismark	0.08	0.00	0.07
rrbs	0.05	0.00	0.05
smoothVariogram	0.03	0.01	0.05
summarizeRegions	2.23	0.08	2.31
testClusters	0.13	0.00	0.12
trimClusters	0.73	0.01	0.75
vario	0	0	0
writeBED	0.23	0.00	0.23