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BioC 3.5: CHECK report for DChIPRep on veracruz2

This page was generated on 2017-10-18 14:33:43 -0400 (Wed, 18 Oct 2017).

Package 319/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DChIPRep 1.6.2
Bernd Klaus
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/DChIPRep
Branch: RELEASE_3_5
Last Commit: 09f7f9f
Last Changed Date: 2017-09-14 10:27:18 -0400 (Thu, 14 Sep 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: 1.6.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DChIPRep_1.6.2.tar.gz
StartedAt: 2017-10-18 02:30:38 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 02:37:51 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 432.5 seconds
RetCode: 0
Status:  OK 
CheckDir: DChIPRep.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DChIPRep_1.6.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/DChIPRep.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DChIPRep/DESCRIPTION’ ... OK
* this is package ‘DChIPRep’ version ‘1.6.2’
* 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     8.065  0.062   8.368
plotSignificance 5.742  0.037   5.958
* 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
  ‘/Users/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
DChIPRepResults0.0950.0040.100
DESeq2Data0.1430.0080.155
FDRresults3.9940.0874.175
getMATfromDataFrame1.4590.0291.516
importData3.5970.0413.760
importDataFromMatrices0.5080.0070.531
importData_soGGi0.0010.0000.001
plotProfiles8.0650.0628.368
plotSignificance5.7420.0375.958
resultsDChIPRep2.0400.0112.100
robust_mean0.0350.0010.036
runTesting2.6380.0152.708
show2.0710.0112.147
summarizeCountsPerPosition1.0260.0151.140