BioC 3.3: CHECK report for regioneR on linux2.bioconductor.org
This page was generated on 2015-10-27 12:12:54 -0400 (Tue, 27 Oct 2015).
regioneR 1.3.0
Bernat Gel
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/regioneR | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
Summary
| Package: regioneR |
| Version: 1.3.0 |
| Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings regioneR_1.3.0.tar.gz |
| StartedAt: 2015-10-27 07:20:07 -0400 (Tue, 27 Oct 2015) |
| EndedAt: 2015-10-27 07:25:41 -0400 (Tue, 27 Oct 2015) |
| EllapsedTime: 334.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: regioneR.Rcheck |
| Warnings: 0 |
Command output
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings regioneR_1.3.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/regioneR.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘regioneR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘regioneR’ version ‘1.3.0’
* 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 ‘regioneR’ can be installed ... [13s/13s] 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
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
copySeqLevels: no visible global function definition for ‘seqlevels<-’
copySeqLevels: no visible global function definition for ‘seqlevels’
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 ‘IRanges’
resampleRegions: no visible global function definition for ‘seqlevels’
toGRanges: no visible global function definition for ‘IRanges’
Undefined global functions or variables:
IRanges keepSeqlevels seqlevels seqlevels<-
* 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’ ... OK
* checking examples ... [146s/148s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
createRandomRegions 21.188 1.832 23.063
circularRandomizeRegions 19.689 1.645 21.483
filterChromosomes 18.732 1.471 20.264
randomizeRegions 18.327 1.662 20.034
getMask 17.816 1.566 19.439
maskFromBSGenome 16.705 1.633 18.414
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [57s/57s]
[57s/57s] OK
* 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-3.3-bioc/meat/regioneR.Rcheck/00check.log’
for details.
regioneR.Rcheck/00install.out:
* installing *source* package ‘regioneR’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (regioneR)
regioneR.Rcheck/regioneR-Ex.timings:
| name | user | system | elapsed
|
| characterToBSGenome | 0.515 | 0.020 | 0.536 |
|
| circularRandomizeRegions | 19.689 | 1.645 | 21.483 |
|
| commonRegions | 0.161 | 0.003 | 0.164 |
|
| createFunctionsList | 0.678 | 0.083 | 0.762 |
|
| createRandomRegions | 21.188 | 1.832 | 23.063 |
|
| emptyCacheRegioneR | 0 | 0 | 0 |
|
| extendRegions | 0.089 | 0.000 | 0.089 |
|
| filterChromosomes | 18.732 | 1.471 | 20.264 |
|
| getChromosomesByOrganism | 0.001 | 0.000 | 0.001 |
|
| getGenome | 0.033 | 0.000 | 0.036 |
|
| getGenomeAndMask | 0.044 | 0.000 | 0.045 |
|
| getMask | 17.816 | 1.566 | 19.439 |
|
| joinRegions | 0.16 | 0.00 | 0.16 |
|
| listChrTypes | 0.019 | 0.000 | 0.018 |
|
| localZScore | 3.325 | 0.120 | 4.954 |
|
| maskFromBSGenome | 16.705 | 1.633 | 18.414 |
|
| meanDistance | 0.087 | 0.000 | 0.087 |
|
| meanInRegions | 0.093 | 0.000 | 0.092 |
|
| mergeRegions | 0.097 | 0.000 | 0.096 |
|
| numOverlaps | 0.163 | 0.000 | 0.164 |
|
| overlapGraphicalSummary | 0.180 | 0.000 | 0.181 |
|
| overlapPermTest | 0.606 | 0.000 | 0.606 |
|
| overlapRegions | 0.045 | 0.000 | 0.044 |
|
| permTest | 1.236 | 0.001 | 1.238 |
|
| plot.localZScoreResults | 0.895 | 0.000 | 0.895 |
|
| plot.localZScoreResultsList | 2.452 | 0.000 | 2.460 |
|
| plot.permTestResults | 2.029 | 0.007 | 2.036 |
|
| plot.permTestResultsList | 2.133 | 0.000 | 2.133 |
|
| plotRegions | 0.036 | 0.000 | 0.036 |
|
| print.permTestResults | 1.569 | 0.000 | 1.581 |
|
| randomizeRegions | 18.327 | 1.662 | 20.034 |
|
| recomputePermTest | 0.879 | 0.000 | 0.885 |
|
| resampleRegions | 0.063 | 0.000 | 0.063 |
|
| splitRegions | 0.106 | 0.000 | 0.106 |
|
| subtractRegions | 0.175 | 0.000 | 0.175 |
|
| toDataframe | 0.017 | 0.000 | 0.017 |
|
| toGRanges | 0.021 | 0.000 | 0.021 |
|
| uniqueRegions | 0.344 | 0.000 | 0.345 |
|