BioC 3.1: CHECK report for regioneR on moscato2
This page was generated on 2015-10-09 09:32:13 -0700 (Fri, 09 Oct 2015).
regioneR 1.0.3
Bernat Gel
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/regioneR | | Last Changed Rev: 104740 / Revision: 109384 | | Last Changed Date: 2015-06-09 09:20:08 -0700 (Tue, 09 Jun 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
Summary
| Package: regioneR
|
| Version: 1.0.3
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| Command: rm -rf regioneR.buildbin-libdir regioneR.Rcheck && mkdir regioneR.buildbin-libdir regioneR.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=regioneR.buildbin-libdir regioneR_1.0.3.tar.gz >regioneR.Rcheck\00install.out 2>&1 && cp regioneR.Rcheck\00install.out regioneR-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=regioneR.buildbin-libdir --install="check:regioneR-install.out" --force-multiarch --no-vignettes --timings regioneR_1.0.3.tar.gz
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| StartedAt: 2015-10-09 05:27:30 -0700 (Fri, 09 Oct 2015)
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| EndedAt: 2015-10-09 05:56:50 -0700 (Fri, 09 Oct 2015)
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| EllapsedTime: 1759.7 seconds
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| RetCode: 0
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| Status: OK
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| CheckDir: regioneR.Rcheck
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| Warnings: 0
|
Command output
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###
### Running command:
###
### rm -rf regioneR.buildbin-libdir regioneR.Rcheck && mkdir regioneR.buildbin-libdir regioneR.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=regioneR.buildbin-libdir regioneR_1.0.3.tar.gz >regioneR.Rcheck\00install.out 2>&1 && cp regioneR.Rcheck\00install.out regioneR-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=regioneR.buildbin-libdir --install="check:regioneR-install.out" --force-multiarch --no-vignettes --timings regioneR_1.0.3.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/regioneR.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'regioneR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'regioneR' 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 whether package 'regioneR' 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:
'memoise' 'GenomicRanges' 'BSgenome' 'rtracklayer' 'parallel'
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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking 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 ... NOTE
createRandomRegions: no visible global function definition for
'seqlevels'
filterChromosomes: no visible global function definition for
'keepSeqlevels'
randomizeRegions: no visible global function definition for
'seqlevels<-'
randomizeRegions: no visible global function definition for 'seqlevels'
resampleRegions: no visible global function definition for 'seqlevels'
toGRanges: no visible global function definition for 'IRanges'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... NOTE
The following directory looks like a leftover from 'knitr':
'figure'
Please remove from your package.
* checking examples ...
** running examples for arch 'i386' ... [13m] OK
Examples with CPU or elapsed time > 5s
user system elapsed
filterChromosomes 120.61 3.79 124.48
circularRandomizeRegions 117.42 2.79 169.17
getMask 114.49 3.15 117.64
randomizeRegions 113.40 3.49 116.91
createRandomRegions 112.14 3.45 115.79
maskFromBSGenome 111.53 2.96 114.50
** running examples for arch 'x64' ... [13m] OK
Examples with CPU or elapsed time > 5s
user system elapsed
createRandomRegions 126.67 4.04 130.71
randomizeRegions 124.24 3.66 127.90
maskFromBSGenome 120.12 4.10 124.30
filterChromosomes 119.57 3.94 123.52
getMask 120.02 2.54 122.55
circularRandomizeRegions 117.16 3.12 120.28
* 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: 3 NOTEs
See
'E:/biocbld/bbs-3.1-bioc/meat/regioneR.Rcheck/00check.log'
for details.
regioneR.Rcheck/00install.out:
install for i386
* installing *source* package 'regioneR' ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
install for x64
* installing *source* package 'regioneR' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'regioneR' as regioneR_1.0.3.zip
* DONE (regioneR)
regioneR.Rcheck/examples_i386/regioneR-Ex.timings:
| name | user | system | elapsed
|
| characterToBSGenome | 0.79 | 0.22 | 1.09 |
|
| circularRandomizeRegions | 117.42 | 2.79 | 169.17 |
|
| commonRegions | 0.21 | 0.00 | 0.26 |
|
| createRandomRegions | 112.14 | 3.45 | 115.79 |
|
| emptyCacheRegioneR | 0 | 0 | 0 |
|
| extendRegions | 0.10 | 0.00 | 0.09 |
|
| filterChromosomes | 120.61 | 3.79 | 124.48 |
|
| getChromosomesByOrganism | 0.01 | 0.00 | 0.02 |
|
| getGenome | 0.07 | 0.00 | 0.06 |
|
| getGenomeAndMask | 0.74 | 0.25 | 1.00 |
|
| getMask | 114.49 | 3.15 | 117.64 |
|
| joinRegions | 0.13 | 0.00 | 0.13 |
|
| listChrTypes | 0.01 | 0.00 | 0.01 |
|
| localZScore | 0.82 | 0.00 | 0.81 |
|
| maskFromBSGenome | 111.53 | 2.96 | 114.50 |
|
| meanDistance | 0.12 | 0.00 | 0.13 |
|
| meanInRegions | 0.13 | 0.00 | 0.12 |
|
| mergeRegions | 0.11 | 0.00 | 0.11 |
|
| numOverlaps | 0.09 | 0.00 | 0.10 |
|
| overlapGraphicalSummary | 0.14 | 0.00 | 0.14 |
|
| overlapPermTest | 0.39 | 0.00 | 0.40 |
|
| overlapRegions | 0.06 | 0.00 | 0.06 |
|
| permTest | 1.06 | 0.00 | 1.06 |
|
| plot.localZScoreResults | 0.78 | 0.00 | 0.78 |
|
| plot.permTestResults | 1.50 | 0.02 | 1.52 |
|
| plotRegions | 0.05 | 0.00 | 0.04 |
|
| print.permTestResults | 1.12 | 0.00 | 1.13 |
|
| randomizeRegions | 113.40 | 3.49 | 116.91 |
|
| recomputePermTest | 1.56 | 0.00 | 1.56 |
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| resampleRegions | 0.04 | 0.00 | 0.04 |
|
| splitRegions | 0.1 | 0.0 | 0.1 |
|
| subtractRegions | 0.14 | 0.00 | 0.14 |
|
| toDataframe | 0.01 | 0.00 | 0.01 |
|
| toGRanges | 0.02 | 0.00 | 0.02 |
|
| uniqueRegions | 0.26 | 0.00 | 0.26 |
|
regioneR.Rcheck/examples_x64/regioneR-Ex.timings:
| name | user | system | elapsed
|
| characterToBSGenome | 0.53 | 0.23 | 0.76 |
|
| circularRandomizeRegions | 117.16 | 3.12 | 120.28 |
|
| commonRegions | 0.38 | 0.00 | 0.37 |
|
| createRandomRegions | 126.67 | 4.04 | 130.71 |
|
| emptyCacheRegioneR | 0 | 0 | 0 |
|
| extendRegions | 0.13 | 0.00 | 0.13 |
|
| filterChromosomes | 119.57 | 3.94 | 123.52 |
|
| getChromosomesByOrganism | 0 | 0 | 0 |
|
| getGenome | 0.06 | 0.00 | 0.06 |
|
| getGenomeAndMask | 0.06 | 0.00 | 0.07 |
|
| getMask | 120.02 | 2.54 | 122.55 |
|
| joinRegions | 0.21 | 0.00 | 0.22 |
|
| listChrTypes | 0.02 | 0.00 | 0.02 |
|
| localZScore | 1.15 | 0.00 | 1.17 |
|
| maskFromBSGenome | 120.12 | 4.10 | 124.30 |
|
| meanDistance | 0.15 | 0.00 | 0.14 |
|
| meanInRegions | 0.18 | 0.00 | 0.18 |
|
| mergeRegions | 0.14 | 0.00 | 0.15 |
|
| numOverlaps | 0.14 | 0.00 | 0.14 |
|
| overlapGraphicalSummary | 0.19 | 0.00 | 0.18 |
|
| overlapPermTest | 0.45 | 0.02 | 0.47 |
|
| overlapRegions | 0.07 | 0.00 | 0.06 |
|
| permTest | 1.32 | 0.00 | 1.33 |
|
| plot.localZScoreResults | 0.94 | 0.00 | 0.94 |
|
| plot.permTestResults | 1.93 | 0.00 | 1.93 |
|
| plotRegions | 0.08 | 0.00 | 0.07 |
|
| print.permTestResults | 1.23 | 0.00 | 1.24 |
|
| randomizeRegions | 124.24 | 3.66 | 127.90 |
|
| recomputePermTest | 1.87 | 0.00 | 1.87 |
|
| resampleRegions | 0.06 | 0.00 | 0.07 |
|
| splitRegions | 0.09 | 0.00 | 0.09 |
|
| subtractRegions | 0.18 | 0.00 | 0.18 |
|
| toDataframe | 0.01 | 0.00 | 0.01 |
|
| toGRanges | 0.03 | 0.00 | 0.03 |
|
| uniqueRegions | 0.36 | 0.00 | 0.36 |
|