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BioC 2.14: CHECK report for BiSeq on morelia

This page was generated on 2014-10-08 09:06:23 -0700 (Wed, 08 Oct 2014).

Package 103/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiSeq 1.4.2
Katja Hebestreit
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/BiSeq
Last Changed Rev: 90006 / Revision: 95116
Last Changed Date: 2014-05-06 14:34:28 -0700 (Tue, 06 May 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: BiSeq
Version: 1.4.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BiSeq_1.4.2.tar.gz
StartedAt: 2014-10-07 21:33:42 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 21:40:04 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 381.8 seconds
RetCode: 0
Status:  OK 
CheckDir: BiSeq.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BiSeq_1.4.2.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/BiSeq.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (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 ... [26s/26s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [108s/109s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
globalTest        30.080  0.051  30.154
estLocCor         14.574  0.191  14.778
makeVariogram     11.974  0.432  13.003
betaRegression    10.281  0.712  11.150
compareTwoSamples  4.876  2.277   6.770
* 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
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/BiSeq.Rcheck/00check.log’
for details.

BiSeq.Rcheck/00install.out:

* 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)

BiSeq.Rcheck/BiSeq-Ex.timings:

nameusersystemelapsed
BSraw-class0.1530.0090.161
BSrel-class0.0910.0040.096
DMRs0.0690.0010.070
annotateGRanges0.5770.0180.594
betaRegression10.281 0.71211.150
betaResults0.0080.0010.009
betaResultsNull0.0060.0000.006
binomLikelihoodSmooth0.0080.0010.008
clusterSites0.5980.2390.967
clusterSitesToGR0.8110.3511.144
compareTwoSamples4.8762.2776.770
covBoxplots0.4380.0520.498
covStatistics0.0500.0020.051
estLocCor14.574 0.19114.778
filterByCov0.1240.0020.125
filterBySharedRegions0.1340.0040.137
findDMRs0.8520.0060.859
globalTest30.080 0.05130.154
limitCov0.9190.1971.403
logisticRegression2.3060.0322.360
makeVariogram11.974 0.43213.003
plotBindingSites3.5560.0253.651
plotMeth0.3610.0020.367
plotMethMap0.3270.0050.349
plotSmoothMeth0.5300.0040.534
predictMeth1.7100.7602.244
predictedMeth0.0160.0020.017
promoters0.0980.0170.116
rawToRel0.0480.0050.053
readBismark0.0990.0050.104
rrbs0.0400.0020.042
smoothVariogram0.0220.0010.024
summarizeRegions2.8470.3603.337
testClusters0.1550.0050.161
trimClusters0.7310.0150.747
vario0.0030.0010.004
writeBED0.2570.0070.265