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BioC 3.4: CHECK report for DChIPRep on moscato1

This page was generated on 2016-09-21 03:47:42 -0700 (Wed, 21 Sep 2016).

Package 292/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DChIPRep 1.3.3
Bernd Klaus
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DChIPRep
Last Changed Rev: 117994 / Revision: 121152
Last Changed Date: 2016-05-31 04:28:08 -0700 (Tue, 31 May 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: DChIPRep
Version: 1.3.3
Command: rm -rf DChIPRep.buildbin-libdir DChIPRep.Rcheck && mkdir DChIPRep.buildbin-libdir DChIPRep.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DChIPRep.buildbin-libdir DChIPRep_1.3.3.tar.gz >DChIPRep.Rcheck\00install.out 2>&1 && cp DChIPRep.Rcheck\00install.out DChIPRep-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=DChIPRep.buildbin-libdir --install="check:DChIPRep-install.out" --force-multiarch --no-vignettes --timings DChIPRep_1.3.3.tar.gz
StartedAt: 2016-09-20 06:51:48 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 07:01:11 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 562.9 seconds
RetCode: 0
Status:  OK  
CheckDir: DChIPRep.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf DChIPRep.buildbin-libdir DChIPRep.Rcheck && mkdir DChIPRep.buildbin-libdir DChIPRep.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DChIPRep.buildbin-libdir DChIPRep_1.3.3.tar.gz >DChIPRep.Rcheck\00install.out 2>&1 && cp DChIPRep.Rcheck\00install.out DChIPRep-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=DChIPRep.buildbin-libdir --install="check:DChIPRep-install.out" --force-multiarch --no-vignettes --timings DChIPRep_1.3.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/DChIPRep.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 'DChIPRep/DESCRIPTION' ... OK
* this is package 'DChIPRep' version '1.3.3'
* 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 '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
* 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
Examples with CPU or elapsed time > 5s
           user system elapsed
importData 6.19   0.02     6.2
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
importData  5.9      0    5.89
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'D:/biocbld/bbs-3.4-bioc/meat/DChIPRep.Rcheck/00check.log'
for details.


DChIPRep.Rcheck/00install.out:


install for i386

* 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'

install for x64

* installing *source* package 'DChIPRep' ...
** testing if installed package can be loaded
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'soGGi'
* MD5 sums
packaged installation of 'DChIPRep' as DChIPRep_1.3.3.zip
* DONE (DChIPRep)

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

nameusersystemelapsed
DChIPRepResults0.060.000.06
DESeq2Data0.050.000.05
FDRresults2.760.002.76
getMATfromDataFrame2.530.002.53
importData6.190.026.20
importDataFromMatrices0.080.010.10
importData_soGGi000
plotProfiles4.020.034.15
plotSignificance4.270.004.28
resultsDChIPRep1.870.001.87
runTesting1.860.001.86
show1.870.031.90
summarizeCountsPerPosition2.610.002.60

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

nameusersystemelapsed
DChIPRepResults0.060.000.07
DESeq2Data0.080.000.08
FDRresults2.650.022.66
getMATfromDataFrame2.910.002.92
importData5.900.005.89
importDataFromMatrices0.100.020.11
importData_soGGi000
plotProfiles4.800.014.84
plotSignificance4.980.024.99
resultsDChIPRep1.960.011.98
runTesting2.500.022.53
show1.980.001.98
summarizeCountsPerPosition1.950.001.95