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BioC 2.12: CHECK report for BiSeq on petty

This page was generated on 2013-10-09 09:40:22 -0700 (Wed, 09 Oct 2013).

Package 84/671HostnameOS / ArchBUILDCHECKBUILD BIN
BiSeq 1.0.3
Katja Hebestreit
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/BiSeq
Last Changed Rev: 79504 / Revision: 81334
Last Changed Date: 2013-08-16 07:05:57 -0700 (Fri, 16 Aug 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: BiSeq
Version: 1.0.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BiSeq_1.0.3.tar.gz
StartedAt: 2013-10-08 21:45:21 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 21:54:12 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 531.1 seconds
RetCode: 0
Status:  OK 
CheckDir: BiSeq.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/BiSeq.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'BiSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BiSeq' version '1.0.3'
* 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 ... [35s/36s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 for unstated dependencies in R code ... OK
* 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' ... NOTE
The following files should probably not be installed:
  'unsrturl.bst'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... [171s/173s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
makeVariogram     30.007  0.602  31.297
estLocCor         29.602  0.623  30.393
betaRegression    22.703  1.656  25.074
compareTwoSamples 10.555  6.206  14.930
summarizeRegions   7.701  1.315  10.654
predictMeth        5.838  2.234   6.682
plotBindingSites   7.019  0.074   7.296
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-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-class0.6320.0150.666
BSrel-class0.9790.0171.000
DMRs0.0900.0030.093
annotateGRanges0.4990.0460.552
betaRegression22.703 1.65625.074
betaResults0.0250.0040.029
betaResultsNull0.0170.0040.021
binomLikelihoodSmooth0.0390.0090.049
clusterSites1.9890.6724.188
clusterSitesToGR3.7671.0194.758
compareTwoSamples10.555 6.20614.930
covBoxplots0.2250.0220.247
covStatistics0.0910.0130.105
estLocCor29.602 0.62330.393
filterByCov0.2430.0110.258
filterBySharedRegions0.2760.0230.299
findDMRs1.9500.0211.983
limitCov1.9290.6574.145
logisticRegression3.5730.0803.691
makeVariogram30.007 0.60231.297
plotBindingSites7.0190.0747.296
plotMeth0.5030.0120.521
plotMethMap0.9980.0251.027
plotSmoothMeth0.3390.0070.349
predictMeth5.8382.2346.682
predictedMeth0.0320.0050.037
promoters0.1480.0170.165
rawToRel0.1030.0180.121
readBismark0.1480.0080.157
rrbs0.0760.0060.082
smoothVariogram0.0580.0100.080
summarizeRegions 7.701 1.31510.654
testClusters0.2070.0110.218
trimClusters1.3310.0341.368
vario0.0070.0040.010
writeBED1.2790.0231.326