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BioC 3.5: CHECK report for derfinder on malbec2

This page was generated on 2017-08-16 13:16:05 -0400 (Wed, 16 Aug 2017).

Package 335/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
derfinder 1.10.5
Leonardo Collado-Torres
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/derfinder
Last Changed Rev: 131013 / Revision: 131943
Last Changed Date: 2017-07-06 12:11:37 -0400 (Thu, 06 Jul 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: derfinder
Version: 1.10.5
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings derfinder_1.10.5.tar.gz
StartedAt: 2017-08-15 22:29:11 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:37:02 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 471.8 seconds
RetCode: 0
Status:  OK 
CheckDir: derfinder.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings derfinder_1.10.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/derfinder.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘derfinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘derfinder’ version ‘1.10.5’
* 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 ‘derfinder’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
Unexported objects imported by ':::' calls:
  ‘GenomeInfoDb:::.guessSpeciesStyle’
  ‘GenomeInfoDb:::.supportedSeqnameMappings’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.smootherFstats’
* 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 ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
railMatrix 7.396  0.236   7.773
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/derfinder.Rcheck/00check.log’
for details.


derfinder.Rcheck/00install.out:

* installing *source* package ‘derfinder’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (derfinder)

derfinder.Rcheck/derfinder-Ex.timings:

nameusersystemelapsed
analyzeChr2.1240.0442.190
annotateRegions0.5760.0040.583
calculatePvalues0.9960.0001.001
calculateStats0.1560.0000.155
coerceGR0.0760.0000.077
collapseFullCoverage0.0080.0000.007
coverageToExon2.7801.6084.392
createBw0.1840.0000.184
createBwSample0.0440.0000.043
define_cluster0.0080.0000.004
derfinder-deprecated0.0000.0000.002
extendedMapSeqlevels0.0800.0000.076
filterData0.2120.0120.224
findRegions0.2120.0160.231
fullCoverage0.5080.0040.512
getRegionCoverage0.3040.0040.326
getTotalMapped0.1320.0000.134
loadCoverage0.1080.0000.108
makeGenomicState3.6320.0003.662
makeModels0.020.000.02
mergeResults0.3400.0000.344
preprocessCoverage0.1240.0000.127
railMatrix7.3960.2367.773
rawFiles0.0040.0000.003
regionMatrix0.3320.0000.332
sampleDepth0.0200.0000.018