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BioC 3.4: CHECK report for consensusSeekeR on moscato1

This page was generated on 2016-09-21 03:47:46 -0700 (Wed, 21 Sep 2016).

Package 248/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
consensusSeekeR 1.1.3
Astrid Louise Deschenes
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/consensusSeekeR
Last Changed Rev: 119319 / Revision: 121152
Last Changed Date: 2016-07-12 12:35:53 -0700 (Tue, 12 Jul 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: consensusSeekeR
Version: 1.1.3
Command: rm -rf consensusSeekeR.buildbin-libdir consensusSeekeR.Rcheck && mkdir consensusSeekeR.buildbin-libdir consensusSeekeR.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=consensusSeekeR.buildbin-libdir consensusSeekeR_1.1.3.tar.gz >consensusSeekeR.Rcheck\00install.out 2>&1 && cp consensusSeekeR.Rcheck\00install.out consensusSeekeR-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=consensusSeekeR.buildbin-libdir --install="check:consensusSeekeR-install.out" --force-multiarch --no-vignettes --timings consensusSeekeR_1.1.3.tar.gz
StartedAt: 2016-09-20 06:21:07 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 06:26:19 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 312.6 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 && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=consensusSeekeR.buildbin-libdir consensusSeekeR_1.1.3.tar.gz >consensusSeekeR.Rcheck\00install.out 2>&1 && cp consensusSeekeR.Rcheck\00install.out consensusSeekeR-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=consensusSeekeR.buildbin-libdir --install="check:consensusSeekeR-install.out" --force-multiarch --no-vignettes --timings consensusSeekeR_1.1.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-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 '1.1.3'
* 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 ... NOTE
findConsensusPeakRegionsValidation: no visible global function
  definition for 'is'
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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: 1 NOTE
See
  'D:/biocbld/bbs-3.4-bioc/meat/consensusSeekeR.Rcheck/00check.log'
for details.


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_1.1.3.zip
* DONE (consensusSeekeR)

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

nameusersystemelapsed
A549_CTCF_MYJ_NarrowPeaks_partial0.700.000.71
A549_CTCF_MYJ_Peaks_partial0.360.000.35
A549_CTCF_MYN_NarrowPeaks_partial0.360.000.36
A549_CTCF_MYN_Peaks_partial0.450.010.47
A549_FOSL2_01_NarrowPeaks_partial0.280.000.28
A549_FOSL2_01_Peaks_partial0.350.020.37
A549_FOXA1_01_NarrowPeaks_partial0.390.000.39
A549_FOXA1_01_Peaks_partial0.520.010.53
A549_NR3C1_CFQ_NarrowPeaks_partial0.330.020.35
A549_NR3C1_CFQ_Peaks_partial0.450.010.46
A549_NR3C1_CFR_NarrowPeaks_partial0.30.00.3
A549_NR3C1_CFR_Peaks_partial0.310.000.31
A549_NR3C1_CFS_NarrowPeaks_partial0.960.041.00
A549_NR3C1_CFS_Peaks_partial0.890.030.92
NOrMAL_nucleosome_positions0.640.030.67
NOrMAL_nucleosome_ranges0.670.030.70
NucPosSimulator_nucleosome_positions0.630.020.64
NucPosSimulator_nucleosome_ranges0.610.030.64
PING_nucleosome_positions0.430.010.46
PING_nucleosome_ranges0.390.000.39
findConsensusPeakRegions0.780.020.79
findConsensusPeakRegionsValidation0.030.010.05
readNarrowPeakFile0.080.000.08

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

nameusersystemelapsed
A549_CTCF_MYJ_NarrowPeaks_partial0.810.020.82
A549_CTCF_MYJ_Peaks_partial0.410.020.42
A549_CTCF_MYN_NarrowPeaks_partial0.390.010.41
A549_CTCF_MYN_Peaks_partial0.530.020.54
A549_FOSL2_01_NarrowPeaks_partial0.300.010.32
A549_FOSL2_01_Peaks_partial0.420.020.43
A549_FOXA1_01_NarrowPeaks_partial0.460.000.47
A549_FOXA1_01_Peaks_partial0.630.010.64
A549_NR3C1_CFQ_NarrowPeaks_partial0.390.000.39
A549_NR3C1_CFQ_Peaks_partial0.510.020.53
A549_NR3C1_CFR_NarrowPeaks_partial0.330.050.38
A549_NR3C1_CFR_Peaks_partial0.380.010.39
A549_NR3C1_CFS_NarrowPeaks_partial1.180.021.20
A549_NR3C1_CFS_Peaks_partial1.230.011.25
NOrMAL_nucleosome_positions0.850.000.84
NOrMAL_nucleosome_ranges0.790.020.81
NucPosSimulator_nucleosome_positions0.770.010.78
NucPosSimulator_nucleosome_ranges0.800.020.81
PING_nucleosome_positions0.560.020.58
PING_nucleosome_ranges0.450.000.45
findConsensusPeakRegions0.980.011.00
findConsensusPeakRegionsValidation0.070.000.06
readNarrowPeakFile0.070.000.08