BioC 3.2: CHECK report for BiSeq on windows1.bioconductor.org
This page was generated on 2015-10-27 17:30:30 -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
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Version: 1.10.0
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Command: rm -rf BiSeq.buildbin-libdir BiSeq.Rcheck && mkdir BiSeq.buildbin-libdir BiSeq.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiSeq.buildbin-libdir BiSeq_1.10.0.tar.gz >BiSeq.Rcheck\00install.out 2>&1 && cp BiSeq.Rcheck\00install.out BiSeq-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=BiSeq.buildbin-libdir --install="check:BiSeq-install.out" --force-multiarch --no-vignettes --timings BiSeq_1.10.0.tar.gz
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StartedAt: 2015-10-27 00:09:31 -0400 (Tue, 27 Oct 2015)
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EndedAt: 2015-10-27 00:14:55 -0400 (Tue, 27 Oct 2015)
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EllapsedTime: 324.3 seconds
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RetCode: 0
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Status: OK
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CheckDir: BiSeq.Rcheck
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Warnings: 0
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Command output
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### Running command:
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### rm -rf BiSeq.buildbin-libdir BiSeq.Rcheck && mkdir BiSeq.buildbin-libdir BiSeq.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiSeq.buildbin-libdir BiSeq_1.10.0.tar.gz >BiSeq.Rcheck\00install.out 2>&1 && cp BiSeq.Rcheck\00install.out BiSeq-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=BiSeq.buildbin-libdir --install="check:BiSeq-install.out" --force-multiarch --no-vignettes --timings BiSeq_1.10.0.tar.gz
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* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/BiSeq.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'BiSeq' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... [51s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
globalTest 17.25 0.02 17.29
betaRegression 6.76 0.03 6.80
** running examples for arch 'x64' ... [68s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
globalTest 20.59 0.02 20.60
makeVariogram 9.25 0.03 9.28
estLocCor 8.72 0.05 8.77
betaRegression 7.65 0.07 7.72
* 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
'C:/biocbld/bbs-3.2-bioc/meat/BiSeq.Rcheck/00check.log'
for details.
BiSeq.Rcheck/00install.out:
install for i386
* 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
install for x64
* installing *source* package 'BiSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BiSeq' as BiSeq_1.10.0.zip
* DONE (BiSeq)
BiSeq.Rcheck/examples_i386/BiSeq-Ex.timings:
name | user | system | elapsed
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BSraw-class | 0.14 | 0.00 | 0.14 |
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BSrel-class | 0.28 | 0.00 | 0.28 |
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DMRs | 0.03 | 0.00 | 0.03 |
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annotateGRanges | 0.15 | 0.00 | 0.14 |
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betaRegression | 6.76 | 0.03 | 6.80 |
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betaResults | 0.02 | 0.00 | 0.01 |
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betaResultsNull | 0 | 0 | 0 |
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binomLikelihoodSmooth | 0 | 0 | 0 |
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clusterSites | 0.23 | 0.03 | 0.26 |
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clusterSitesToGR | 0.27 | 0.01 | 0.28 |
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compareTwoSamples | 1.47 | 0.02 | 1.49 |
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covBoxplots | 0.12 | 0.00 | 0.12 |
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covStatistics | 0.05 | 0.02 | 0.06 |
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estLocCor | 4.78 | 0.06 | 4.85 |
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filterByCov | 0.09 | 0.01 | 0.11 |
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filterBySharedRegions | 0.10 | 0.00 | 0.09 |
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findDMRs | 0.39 | 0.00 | 0.39 |
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globalTest | 17.25 | 0.02 | 17.29 |
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limitCov | 0.28 | 0.00 | 0.28 |
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logisticRegression | 1.14 | 0.02 | 1.16 |
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makeVariogram | 4.36 | 0.02 | 4.37 |
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plotBindingSites | 2.01 | 0.00 | 2.02 |
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plotMeth | 0.18 | 0.01 | 0.19 |
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plotMethMap | 0.2 | 0.0 | 0.2 |
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plotSmoothMeth | 0.08 | 0.00 | 0.08 |
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predictMeth | 0.5 | 0.0 | 0.5 |
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predictedMeth | 0.01 | 0.00 | 0.01 |
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promoters | 0.06 | 0.00 | 0.06 |
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rawToRel | 0.05 | 0.00 | 0.05 |
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readBismark | 0.03 | 0.00 | 0.03 |
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rrbs | 0.05 | 0.00 | 0.05 |
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smoothVariogram | 0.03 | 0.00 | 0.03 |
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summarizeRegions | 1.41 | 0.00 | 1.41 |
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testClusters | 0.05 | 0.02 | 0.06 |
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trimClusters | 0.34 | 0.00 | 0.34 |
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vario | 0 | 0 | 0 |
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writeBED | 0.17 | 0.01 | 0.19 |
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BiSeq.Rcheck/examples_x64/BiSeq-Ex.timings:
name | user | system | elapsed
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BSraw-class | 0.19 | 0.00 | 0.19 |
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BSrel-class | 0.47 | 0.05 | 0.51 |
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DMRs | 0.06 | 0.00 | 0.07 |
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annotateGRanges | 0.22 | 0.01 | 0.23 |
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betaRegression | 7.65 | 0.07 | 7.72 |
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betaResults | 0 | 0 | 0 |
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betaResultsNull | 0.02 | 0.00 | 0.02 |
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binomLikelihoodSmooth | 0 | 0 | 0 |
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clusterSites | 0.30 | 0.00 | 0.29 |
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clusterSitesToGR | 0.31 | 0.01 | 0.33 |
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compareTwoSamples | 1.86 | 0.00 | 1.86 |
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covBoxplots | 0.15 | 0.00 | 0.16 |
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covStatistics | 0.05 | 0.00 | 0.04 |
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estLocCor | 8.72 | 0.05 | 8.77 |
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filterByCov | 0.09 | 0.00 | 0.09 |
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filterBySharedRegions | 0.10 | 0.01 | 0.11 |
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findDMRs | 0.45 | 0.00 | 0.46 |
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globalTest | 20.59 | 0.02 | 20.60 |
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limitCov | 0.63 | 0.02 | 0.65 |
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logisticRegression | 1.37 | 0.00 | 1.37 |
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makeVariogram | 9.25 | 0.03 | 9.28 |
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plotBindingSites | 2.85 | 0.00 | 2.85 |
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plotMeth | 0.18 | 0.00 | 0.18 |
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plotMethMap | 0.21 | 0.00 | 0.21 |
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plotSmoothMeth | 0.09 | 0.01 | 0.11 |
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predictMeth | 0.64 | 0.00 | 0.64 |
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predictedMeth | 0.02 | 0.00 | 0.01 |
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promoters | 0.04 | 0.00 | 0.05 |
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rawToRel | 0.07 | 0.00 | 0.06 |
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readBismark | 0.04 | 0.00 | 0.05 |
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rrbs | 0.04 | 0.00 | 0.03 |
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smoothVariogram | 0.02 | 0.00 | 0.02 |
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summarizeRegions | 1.57 | 0.05 | 1.63 |
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testClusters | 0.08 | 0.00 | 0.07 |
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trimClusters | 0.39 | 0.00 | 0.39 |
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vario | 0 | 0 | 0 |
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writeBED | 0.18 | 0.02 | 0.19 |
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