BioC 2.14: CHECK report for BiSeq on zin2

Package: BiSeq

Version: 1.4.2

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings BiSeq_1.4.2.tar.gz

StartedAt: 2014-10-07 22:11:35 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 22:16:54 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 318.4 seconds

RetCode: 0

Status:  OK

CheckDir: BiSeq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings BiSeq_1.4.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/BiSeq.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BiSeq’ version ‘1.4.2’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘BiSeq’ can be installed ... [22s/22s] 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’ ‘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
* 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 ... 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.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of 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 ... OK
* 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 ... NOTE
  'BiocParallel' did not register default BiocParallelParams
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [90s/90s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
globalTest        25.533  0.008  25.596
estLocCor         11.917  0.020  12.041
makeVariogram     10.501  0.024  10.618
betaRegression     9.657  0.564  10.276
compareTwoSamples  3.876  1.196   4.685
* 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

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-2.14-bioc/meat/BiSeq.Rcheck/00check.log’
for details.

* 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
* DONE (BiSeq)

name	user	system	elapsed
BSraw-class	0.124	0.008	0.131
BSrel-class	0.076	0.000	0.079
DMRs	0.064	0.000	0.064
annotateGRanges	0.544	0.004	0.550
betaRegression	9.657	0.564	10.276
betaResults	0.008	0.000	0.007
betaResultsNull	0.008	0.000	0.006
binomLikelihoodSmooth	0.008	0.000	0.008
clusterSites	0.464	0.104	0.660
clusterSitesToGR	0.688	0.136	0.782
compareTwoSamples	3.876	1.196	4.685
covBoxplots	0.368	0.020	0.390
covStatistics	0.036	0.000	0.039
estLocCor	11.917	0.020	12.041
filterByCov	0.112	0.000	0.110
filterBySharedRegions	0.120	0.000	0.118
findDMRs	0.764	0.000	0.797
globalTest	25.533	0.008	25.596
limitCov	0.692	0.104	0.918
logisticRegression	1.816	0.012	1.832
makeVariogram	10.501	0.024	10.618
plotBindingSites	2.864	0.004	2.871
plotMeth	0.316	0.000	0.317
plotMethMap	0.576	0.008	0.583
plotSmoothMeth	0.196	0.000	0.196
predictMeth	1.264	0.344	1.461
predictedMeth	0.016	0.000	0.014
promoters	0.076	0.008	0.084
rawToRel	0.040	0.000	0.044
readBismark	0.092	0.000	0.092
rrbs	0.040	0.000	0.038
smoothVariogram	0.028	0.000	0.027
summarizeRegions	2.453	0.152	2.686
testClusters	0.112	0.004	0.118
trimClusters	0.736	0.000	0.751
vario	0.004	0.000	0.003
writeBED	0.208	0.000	0.224