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BioC 3.3: CHECK report for consensusSeekeR on moscato2

This page was generated on 2016-10-13 12:54:37 -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: rm -rf consensusSeekeR.buildbin-libdir consensusSeekeR.Rcheck && mkdir consensusSeekeR.buildbin-libdir consensusSeekeR.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=consensusSeekeR.buildbin-libdir consensusSeekeR_1.0.2.tar.gz >consensusSeekeR.Rcheck\00install.out 2>&1 && cp consensusSeekeR.Rcheck\00install.out consensusSeekeR-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=consensusSeekeR.buildbin-libdir --install="check:consensusSeekeR-install.out" --force-multiarch --no-vignettes --timings consensusSeekeR_1.0.2.tar.gz
StartedAt: 2016-10-13 02:31:37 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 02:37:31 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 354.4 seconds
RetCode: 0
Status:  OK  
CheckDir: consensusSeekeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf consensusSeekeR.buildbin-libdir consensusSeekeR.Rcheck && mkdir consensusSeekeR.buildbin-libdir consensusSeekeR.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=consensusSeekeR.buildbin-libdir consensusSeekeR_1.0.2.tar.gz >consensusSeekeR.Rcheck\00install.out 2>&1 && cp consensusSeekeR.Rcheck\00install.out consensusSeekeR-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=consensusSeekeR.buildbin-libdir --install="check:consensusSeekeR-install.out" --force-multiarch --no-vignettes --timings consensusSeekeR_1.0.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/consensusSeekeR.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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:


install for i386

* 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

install for x64

* installing *source* package 'consensusSeekeR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'consensusSeekeR' as consensusSeekeR_1.0.2.zip
* DONE (consensusSeekeR)

consensusSeekeR.Rcheck/examples_i386/consensusSeekeR-Ex.timings:

nameusersystemelapsed
A549_CTCF_MYJ_NarrowPeaks_partial1.030.001.03
A549_CTCF_MYJ_Peaks_partial0.530.030.56
A549_CTCF_MYN_NarrowPeaks_partial0.430.030.47
A549_CTCF_MYN_Peaks_partial0.770.030.80
A549_FOSL2_01_NarrowPeaks_partial0.420.010.44
A549_FOSL2_01_Peaks_partial0.580.000.58
A549_FOXA1_01_NarrowPeaks_partial0.590.020.61
A549_FOXA1_01_Peaks_partial0.920.030.95
A549_NR3C1_CFQ_NarrowPeaks_partial0.420.010.43
A549_NR3C1_CFQ_Peaks_partial0.730.030.77
A549_NR3C1_CFR_NarrowPeaks_partial0.410.020.42
A549_NR3C1_CFR_Peaks_partial0.550.030.58
A549_NR3C1_CFS_NarrowPeaks_partial1.550.021.56
A549_NR3C1_CFS_Peaks_partial1.420.031.45
NOrMAL_nucleosome_positions0.980.061.05
NOrMAL_nucleosome_ranges0.750.020.76
NucPosSimulator_nucleosome_positions0.960.000.97
NucPosSimulator_nucleosome_ranges0.780.030.81
PING_nucleosome_positions0.490.040.53
PING_nucleosome_ranges0.420.020.44
findConsensusPeakRegions1.250.021.26
findConsensusPeakRegionsValidation0.080.010.10
readNarrowPeakFile0.090.000.09

consensusSeekeR.Rcheck/examples_x64/consensusSeekeR-Ex.timings:

nameusersystemelapsed
A549_CTCF_MYJ_NarrowPeaks_partial1.060.021.07
A549_CTCF_MYJ_Peaks_partial0.860.000.86
A549_CTCF_MYN_NarrowPeaks_partial0.590.000.60
A549_CTCF_MYN_Peaks_partial0.630.000.62
A549_FOSL2_01_NarrowPeaks_partial0.330.000.33
A549_FOSL2_01_Peaks_partial0.560.020.57
A549_FOXA1_01_NarrowPeaks_partial0.470.010.49
A549_FOXA1_01_Peaks_partial0.840.030.87
A549_NR3C1_CFQ_NarrowPeaks_partial0.560.020.58
A549_NR3C1_CFQ_Peaks_partial0.870.010.89
A549_NR3C1_CFR_NarrowPeaks_partial0.550.020.56
A549_NR3C1_CFR_Peaks_partial0.390.020.40
A549_NR3C1_CFS_NarrowPeaks_partial1.790.001.80
A549_NR3C1_CFS_Peaks_partial1.440.011.45
NOrMAL_nucleosome_positions1.180.051.23
NOrMAL_nucleosome_ranges1.310.031.34
NucPosSimulator_nucleosome_positions1.280.001.28
NucPosSimulator_nucleosome_ranges0.910.000.91
PING_nucleosome_positions0.750.010.76
PING_nucleosome_ranges0.470.000.47
findConsensusPeakRegions1.020.001.01
findConsensusPeakRegionsValidation0.030.020.05
readNarrowPeakFile0.080.000.08