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BioC 3.2: CHECK report for BiSeq on oaxaca

This page was generated on 2016-04-23 10:26:42 -0700 (Sat, 23 Apr 2016).

Package 115/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiSeq 1.10.0
Katja Hebestreit
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/BiSeq
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  ERROR  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BiSeq
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BiSeq_1.10.0.tar.gz
StartedAt: 2016-04-22 22:14:24 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 22:19:50 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 326.2 seconds
RetCode: 0
Status:  OK 
CheckDir: BiSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BiSeq_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/BiSeq.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.10.0’
* 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 ... [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’ ‘S4Vectors’ ‘IRanges’ ‘GenomicRanges’ ‘SummarizedExperiment’ ‘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 ... [81s/81s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
globalTest        24.593  0.095  24.700
betaRegression    12.762  0.559  13.450
estLocCor          6.100  0.514   6.632
makeVariogram      5.390  0.571   5.963
compareTwoSamples  3.275  1.969   4.927
* 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
  ‘/Users/biocbuild/bbs-3.2-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-class0.1680.0110.180
BSrel-class0.1170.0150.131
DMRs0.0670.0010.069
annotateGRanges0.2580.0180.276
betaRegression12.762 0.55913.450
betaResults0.0080.0020.009
betaResultsNull0.0070.0010.009
binomLikelihoodSmooth0.0080.0010.009
clusterSites0.5120.2530.978
clusterSitesToGR0.7290.3410.922
compareTwoSamples3.2751.9694.927
covBoxplots0.1360.0140.149
covStatistics0.1170.0060.123
estLocCor6.1000.5146.632
filterByCov0.1350.0090.145
filterBySharedRegions0.1100.0080.118
findDMRs0.5500.0110.562
globalTest24.593 0.09524.700
limitCov0.3680.1430.639
logisticRegression1.6280.0651.693
makeVariogram5.3900.5715.963
plotBindingSites2.0910.0362.130
plotMeth0.2310.0100.243
plotMethMap0.2580.0130.271
plotSmoothMeth0.1410.0060.148
predictMeth1.2310.7331.890
predictedMeth0.0200.0040.025
promoters0.0670.0070.074
rawToRel0.0640.0070.071
readBismark0.0510.0050.056
rrbs0.0510.0040.055
smoothVariogram0.0230.0030.027
summarizeRegions1.6920.3982.106
testClusters0.1020.0120.122
trimClusters1.0490.1211.170
vario0.0020.0010.003
writeBED0.2220.0070.229