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BioC 2.13: CHECK report for BiSeq on perceval

This page was generated on 2014-04-05 09:53:06 -0700 (Sat, 05 Apr 2014).

Package 95/750HostnameOS / ArchBUILDCHECKBUILD BIN
BiSeq 1.2.5
Katja Hebestreit
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/BiSeq
Last Changed Rev: 87090 / Revision: 88450
Last Changed Date: 2014-03-04 17:12:18 -0800 (Tue, 04 Mar 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: BiSeq
Version: 1.2.5
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BiSeq_1.2.5.tar.gz
StartedAt: 2014-04-04 23:53:13 -0700 (Fri, 04 Apr 2014)
EndedAt: 2014-04-05 00:01:18 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 484.6 seconds
RetCode: 0
Status:  OK 
CheckDir: BiSeq.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/BiSeq.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.2.5’
* 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 ... [34s/34s] 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 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 ... 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘BiSeq.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [153s/152s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
globalTest        29.244  0.083  29.383
estLocCor         21.286  0.206  21.520
makeVariogram     18.133  0.277  18.474
betaRegression    13.638  1.780  15.707
compareTwoSamples  7.859  7.089  13.975
summarizeRegions   6.210  1.213   8.517
* 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 4 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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-class0.7430.0170.760
BSrel-class0.1560.0170.172
DMRs0.0790.0020.081
annotateGRanges0.3920.0440.436
betaRegression13.638 1.78015.707
betaResults0.0190.0050.025
betaResultsNull0.0180.0040.022
binomLikelihoodSmooth0.0310.0050.036
clusterSites1.3480.6682.063
clusterSitesToGR1.0160.6021.647
compareTwoSamples 7.859 7.08913.975
covBoxplots0.1700.0170.188
covStatistics0.7290.0970.828
estLocCor21.286 0.20621.520
filterByCov0.2350.0140.250
filterBySharedRegions0.8310.0390.870
findDMRs0.9770.0161.005
globalTest29.244 0.08329.383
limitCov1.3240.6302.273
logisticRegression2.3880.1072.561
makeVariogram18.133 0.27718.474
plotBindingSites4.5590.0864.648
plotMeth0.4370.0120.451
plotMethMap0.9920.0271.020
plotSmoothMeth0.2890.0100.299
predictMeth2.1711.8553.717
predictedMeth0.0270.0050.031
promoters0.1090.0160.125
rawToRel0.7500.1310.881
readBismark0.1210.0060.127
rrbs0.0530.0070.060
smoothVariogram0.0380.0080.046
summarizeRegions6.2101.2138.517
testClusters0.1740.0150.190
trimClusters0.8540.0150.869
vario0.0050.0020.007
writeBED0.8630.0140.878