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BioC 2.14: CHECK report for BiSeq on zin2

This page was generated on 2014-10-08 08:49:59 -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: /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

Command output

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


* 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.

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-class0.1240.0080.131
BSrel-class0.0760.0000.079
DMRs0.0640.0000.064
annotateGRanges0.5440.0040.550
betaRegression 9.657 0.56410.276
betaResults0.0080.0000.007
betaResultsNull0.0080.0000.006
binomLikelihoodSmooth0.0080.0000.008
clusterSites0.4640.1040.660
clusterSitesToGR0.6880.1360.782
compareTwoSamples3.8761.1964.685
covBoxplots0.3680.0200.390
covStatistics0.0360.0000.039
estLocCor11.917 0.02012.041
filterByCov0.1120.0000.110
filterBySharedRegions0.1200.0000.118
findDMRs0.7640.0000.797
globalTest25.533 0.00825.596
limitCov0.6920.1040.918
logisticRegression1.8160.0121.832
makeVariogram10.501 0.02410.618
plotBindingSites2.8640.0042.871
plotMeth0.3160.0000.317
plotMethMap0.5760.0080.583
plotSmoothMeth0.1960.0000.196
predictMeth1.2640.3441.461
predictedMeth0.0160.0000.014
promoters0.0760.0080.084
rawToRel0.0400.0000.044
readBismark0.0920.0000.092
rrbs0.0400.0000.038
smoothVariogram0.0280.0000.027
summarizeRegions2.4530.1522.686
testClusters0.1120.0040.118
trimClusters0.7360.0000.751
vario0.0040.0000.003
writeBED0.2080.0000.224