BioC 3.2: CHECK report for BiSeq on linux1.bioconductor.org
This page was generated on 2015-10-27 17:25:54 -0400 (Tue, 27 Oct 2015).
BiSeq 1.10.0 Katja Hebestreit
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/BiSeq | Last Changed Rev: 109589 / Revision: 109947 | Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015) |
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK |  |
perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK |  |
oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK |  |
Summary
Package: BiSeq |
Version: 1.10.0 |
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings BiSeq_1.10.0.tar.gz |
StartedAt: 2015-10-27 01:30:51 -0400 (Tue, 27 Oct 2015) |
EndedAt: 2015-10-27 01:34:27 -0400 (Tue, 27 Oct 2015) |
EllapsedTime: 215.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BiSeq.Rcheck |
Warnings: 0 |
Command output
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### Running command:
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### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings BiSeq_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.2-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 ‘1.10.0’
* 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 ... [14s/14s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [56s/56s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
globalTest 16.542 0.008 16.550
betaRegression 8.615 0.308 8.930
makeVariogram 5.461 0.024 5.493
* 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-3.2-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:
name | user | system | elapsed
|
BSraw-class | 0.116 | 0.000 | 0.117 |
|
BSrel-class | 0.359 | 0.003 | 0.363 |
|
DMRs | 0.036 | 0.000 | 0.036 |
|
annotateGRanges | 0.128 | 0.004 | 0.133 |
|
betaRegression | 8.615 | 0.308 | 8.930 |
|
betaResults | 0.003 | 0.004 | 0.007 |
|
betaResultsNull | 0.004 | 0.000 | 0.003 |
|
binomLikelihoodSmooth | 0.012 | 0.000 | 0.012 |
|
clusterSites | 0.237 | 0.072 | 0.366 |
|
clusterSitesToGR | 0.345 | 0.138 | 0.432 |
|
compareTwoSamples | 2.078 | 1.030 | 2.698 |
|
covBoxplots | 0.513 | 0.028 | 0.540 |
|
covStatistics | 0.072 | 0.000 | 0.072 |
|
estLocCor | 4.278 | 0.000 | 4.278 |
|
filterByCov | 0.093 | 0.000 | 0.092 |
|
filterBySharedRegions | 0.099 | 0.004 | 0.104 |
|
findDMRs | 0.402 | 0.000 | 0.402 |
|
globalTest | 16.542 | 0.008 | 16.550 |
|
limitCov | 0.570 | 0.129 | 0.776 |
|
logisticRegression | 1.003 | 0.004 | 1.007 |
|
makeVariogram | 5.461 | 0.024 | 5.493 |
|
plotBindingSites | 1.825 | 0.000 | 1.827 |
|
plotMeth | 0.167 | 0.000 | 0.167 |
|
plotMethMap | 0.171 | 0.004 | 0.175 |
|
plotSmoothMeth | 0.083 | 0.000 | 0.083 |
|
predictMeth | 0.819 | 0.343 | 1.013 |
|
predictedMeth | 0.020 | 0.004 | 0.023 |
|
promoters | 0.082 | 0.004 | 0.086 |
|
rawToRel | 0.077 | 0.004 | 0.081 |
|
readBismark | 0.060 | 0.004 | 0.064 |
|
rrbs | 0.073 | 0.000 | 0.073 |
|
smoothVariogram | 0.035 | 0.000 | 0.035 |
|
summarizeRegions | 1.788 | 0.175 | 2.077 |
|
testClusters | 0.117 | 0.000 | 0.117 |
|
trimClusters | 0.463 | 0.000 | 0.462 |
|
vario | 0.000 | 0.000 | 0.002 |
|
writeBED | 0.457 | 0.000 | 0.458 |
|