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BioC 3.5: CHECK report for DChIPRep on malbec2

This page was generated on 2017-08-16 13:17:02 -0400 (Wed, 16 Aug 2017).

Package 319/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DChIPRep 1.6.1
Bernd Klaus
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/DChIPRep
Last Changed Rev: 130279 / Revision: 131943
Last Changed Date: 2017-06-13 05:53:19 -0400 (Tue, 13 Jun 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DChIPRep
Version: 1.6.1
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings DChIPRep_1.6.1.tar.gz
StartedAt: 2017-08-15 22:24:51 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:30:42 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 350.9 seconds
RetCode: 0
Status:  OK 
CheckDir: DChIPRep.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings DChIPRep_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/DChIPRep.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 ‘DChIPRep/DESCRIPTION’ ... OK
* this is package ‘DChIPRep’ version ‘1.6.1’
* 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 ‘DChIPRep’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 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 ... 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
plotProfiles 5.38  0.016   5.399
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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/DChIPRep.Rcheck/00check.log’
for details.


DChIPRep.Rcheck/00install.out:

* installing *source* package ‘DChIPRep’ ...
** R
** data
*** moving datasets to lazyload DB

Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'soGGi'
** exec
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'soGGi'
* DONE (DChIPRep)

DChIPRep.Rcheck/DChIPRep-Ex.timings:

nameusersystemelapsed
DChIPRepResults0.0640.0000.066
DESeq2Data0.0800.0040.082
FDRresults1.9680.0081.978
getMATfromDataFrame1.1480.0121.161
importData3.0360.0403.081
importDataFromMatrices0.3800.0000.377
importData_soGGi0.0000.0000.001
plotProfiles5.3800.0165.399
plotSignificance4.0080.0004.010
resultsDChIPRep1.1760.0041.182
robust_mean0.0320.0000.032
runTesting1.7920.0001.794
show1.1320.0001.130
summarizeCountsPerPosition0.5840.0000.584