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BioC 3.3: CHECK report for consensusSeekeR on zin2

This page was generated on 2016-10-13 12:46:10 -0700 (Thu, 13 Oct 2016).

Package 237/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
consensusSeekeR 1.0.2
Astrid Louise Deschenes
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/consensusSeekeR
Last Changed Rev: 117513 / Revision: 122332
Last Changed Date: 2016-05-15 13:18:19 -0700 (Sun, 15 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: consensusSeekeR
Version: 1.0.2
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings consensusSeekeR_1.0.2.tar.gz
StartedAt: 2016-10-13 00:52:29 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 00:55:06 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 157.0 seconds
RetCode: 0
Status:  OK 
CheckDir: consensusSeekeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings consensusSeekeR_1.0.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/consensusSeekeR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘consensusSeekeR/DESCRIPTION’ ... OK
* this is package ‘consensusSeekeR’ version ‘1.0.2’
* 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 ‘consensusSeekeR’ 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 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: OK

consensusSeekeR.Rcheck/00install.out:

* installing *source* package ‘consensusSeekeR’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (consensusSeekeR)

consensusSeekeR.Rcheck/consensusSeekeR-Ex.timings:

nameusersystemelapsed
A549_CTCF_MYJ_NarrowPeaks_partial0.7170.0040.725
A549_CTCF_MYJ_Peaks_partial0.5940.0040.602
A549_CTCF_MYN_NarrowPeaks_partial0.3610.0120.380
A549_CTCF_MYN_Peaks_partial0.4570.0000.461
A549_FOSL2_01_NarrowPeaks_partial0.2640.0000.267
A549_FOSL2_01_Peaks_partial0.3710.0080.382
A549_FOXA1_01_NarrowPeaks_partial0.3880.0040.394
A549_FOXA1_01_Peaks_partial0.5270.0040.536
A549_NR3C1_CFQ_NarrowPeaks_partial0.3160.0040.321
A549_NR3C1_CFQ_Peaks_partial0.4400.0000.442
A549_NR3C1_CFR_NarrowPeaks_partial0.2970.0000.297
A549_NR3C1_CFR_Peaks_partial0.3140.0000.317
A549_NR3C1_CFS_NarrowPeaks_partial0.9750.0040.982
A549_NR3C1_CFS_Peaks_partial0.9880.0001.006
NOrMAL_nucleosome_positions0.6520.0000.653
NOrMAL_nucleosome_ranges0.6410.0080.650
NucPosSimulator_nucleosome_positions0.6530.0040.658
NucPosSimulator_nucleosome_ranges0.6270.0000.626
PING_nucleosome_positions0.4340.0040.437
PING_nucleosome_ranges0.3670.0080.388
findConsensusPeakRegions0.7740.0000.774
findConsensusPeakRegionsValidation0.0370.0000.036
readNarrowPeakFile0.0640.0000.066