Back to the "Multiple platform build/check report" A [B] C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

Package 84/671HostnameOS / ArchBUILDCHECKBUILD BIN
BiSeq 1.0.1
Katja Hebestreit
Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/BiSeq
Last Changed Rev: 75871 / Revision: 76155
Last Changed Date: 2013-04-22 07:40:58 -0700 (Mon, 22 Apr 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 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: BiSeq
Version: 1.0.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BiSeq_1.0.1.tar.gz
StartedAt: 2013-05-01 03:01:38 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 03:08:58 -0700 (Wed, 01 May 2013)
EllapsedTime: 440.5 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 3.0.0 Patched (2013-04-08 r62531)
* 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 '1.0.1'
* 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 ... [29s/30s] 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 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 ... [137s/139s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
makeVariogram     22.688  0.659  23.781
estLocCor         21.930  0.541  22.757
betaRegression    17.538  1.739  19.939
compareTwoSamples  8.356  4.980  11.372
summarizeRegions   7.075  1.241   9.662
predictMeth        4.295  1.909   5.192
plotBindingSites   5.977  0.111   6.254
clusterSitesToGR   3.701  1.283   5.785
* 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-class0.2100.0180.233
BSrel-class0.1490.0240.180
DMRs0.0670.0080.075
annotateGRanges0.8080.0660.884
betaRegression17.538 1.73919.939
betaResults0.0190.0040.026
betaResultsNull0.0140.0030.017
binomLikelihoodSmooth0.0310.0060.040
clusterSites1.5060.6233.100
clusterSitesToGR3.7011.2835.785
compareTwoSamples 8.356 4.98011.372
covBoxplots0.6440.0910.744
covStatistics0.0860.0120.099
estLocCor21.930 0.54122.757
filterByCov0.2210.0150.236
filterBySharedRegions0.2250.0250.252
findDMRs1.5350.0151.554
limitCov1.4900.5743.312
logisticRegression2.5090.0952.622
makeVariogram22.688 0.65923.781
plotBindingSites5.9770.1116.254
plotMeth0.3660.0120.385
plotMethMap0.4880.0270.524
plotSmoothMeth0.2240.0130.249
predictMeth4.2951.9095.192
predictedMeth0.0270.0070.035
promoters0.1090.0140.124
rawToRel0.130.030.16
readBismark1.2010.0361.264
rrbs0.0700.0060.087
smoothVariogram0.0530.0110.070
summarizeRegions7.0751.2419.662
testClusters0.1550.0140.174
trimClusters0.9250.0380.990
vario0.0060.0030.009
writeBED1.0610.0311.105