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BioC 3.1: CHECK report for BiSeq on zin2

This page was generated on 2015-10-09 09:25:29 -0700 (Fri, 09 Oct 2015).

Package 110/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiSeq 1.8.0
Katja Hebestreit
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/BiSeq
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BiSeq
Version: 1.8.0
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings BiSeq_1.8.0.tar.gz
StartedAt: 2015-10-08 22:54:30 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 22:57:59 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 209.0 seconds
RetCode: 0
Status:  OK 
CheckDir: BiSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings BiSeq_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/BiSeq.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-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 ‘1.8.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘BiSeq’ can be installed ... [15s/15s] 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
* 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.
* 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 ... OK
* 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 ... [60s/59s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
globalTest     19.245  0.004  19.295
betaRegression  8.418  0.359   8.808
estLocCor       5.550  0.016   5.563
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.1-bioc/meat/BiSeq.Rcheck/00check.log’
for details.


BiSeq.Rcheck/00install.out:

* installing *source* package ‘BiSeq’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (BiSeq)

BiSeq.Rcheck/BiSeq-Ex.timings:

nameusersystemelapsed
BSraw-class0.0980.0040.102
BSrel-class0.0580.0000.058
DMRs0.0480.0000.048
annotateGRanges0.1890.0000.189
betaRegression8.4180.3598.808
betaResults0.0070.0000.007
betaResultsNull0.0080.0000.008
binomLikelihoodSmooth0.0080.0000.007
clusterSites0.270.070.37
clusterSitesToGR0.4020.0560.437
compareTwoSamples2.1390.9762.787
covBoxplots0.0850.0040.090
covStatistics0.0460.0000.046
estLocCor5.5500.0165.563
filterByCov0.0910.0000.090
filterBySharedRegions0.0930.0000.092
findDMRs0.8680.0000.867
globalTest19.245 0.00419.295
limitCov0.5700.0911.118
logisticRegression1.3100.0041.334
makeVariogram4.8150.0204.884
plotBindingSites2.0800.0042.112
plotMeth0.1640.0000.175
plotMethMap0.1800.0000.188
plotSmoothMeth0.1050.0000.106
predictMeth1.0220.3580.874
predictedMeth0.0130.0000.013
promoters0.0650.0040.069
rawToRel0.0470.0040.051
readBismark0.0440.0000.044
rrbs0.0370.0000.038
smoothVariogram0.0160.0120.028
summarizeRegions1.5010.1361.652
testClusters0.0860.0000.087
trimClusters0.4740.0040.479
vario0.0030.0000.002
writeBED0.1590.0000.159