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BioC 3.2: CHECK report for MethTargetedNGS on windows1.bioconductor.org

This page was generated on 2015-10-27 17:32:12 -0400 (Tue, 27 Oct 2015).

Package 629/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MethTargetedNGS 1.2.0
Muhammad Ahmer Jamil
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/MethTargetedNGS
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  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: MethTargetedNGS
Version: 1.2.0
Command: rm -rf MethTargetedNGS.buildbin-libdir MethTargetedNGS.Rcheck && mkdir MethTargetedNGS.buildbin-libdir MethTargetedNGS.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MethTargetedNGS.buildbin-libdir MethTargetedNGS_1.2.0.tar.gz >MethTargetedNGS.Rcheck\00install.out 2>&1 && cp MethTargetedNGS.Rcheck\00install.out MethTargetedNGS-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=MethTargetedNGS.buildbin-libdir --install="check:MethTargetedNGS-install.out" --force-multiarch --no-vignettes --timings MethTargetedNGS_1.2.0.tar.gz
StartedAt: 2015-10-27 03:27:38 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 03:29:50 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 131.9 seconds
RetCode: 0
Status:  OK  
CheckDir: MethTargetedNGS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf MethTargetedNGS.buildbin-libdir MethTargetedNGS.Rcheck && mkdir MethTargetedNGS.buildbin-libdir MethTargetedNGS.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MethTargetedNGS.buildbin-libdir MethTargetedNGS_1.2.0.tar.gz >MethTargetedNGS.Rcheck\00install.out 2>&1 && cp MethTargetedNGS.Rcheck\00install.out MethTargetedNGS-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=MethTargetedNGS.buildbin-libdir --install="check:MethTargetedNGS-install.out" --force-multiarch --no-vignettes --timings MethTargetedNGS_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/MethTargetedNGS.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MethTargetedNGS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MethTargetedNGS' version '1.2.0'
* 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 'MethTargetedNGS' 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
methAlign: no visible global function definition for 'subject'
methAlign: no visible global function definition for 'pattern'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [23s] OK
** running examples for arch 'x64' ... [25s] 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
  'C:/biocbld/bbs-3.2-bioc/meat/MethTargetedNGS.Rcheck/00check.log'
for details.


MethTargetedNGS.Rcheck/00install.out:


install for i386

* installing *source* package 'MethTargetedNGS' ...
** R
** 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 'MethTargetedNGS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MethTargetedNGS' as MethTargetedNGS_1.2.0.zip
* DONE (MethTargetedNGS)

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

nameusersystemelapsed
bconv000
compare_samples4.090.024.11
fishertest_cpg3.990.024.00
hmmbuild000
methAlign2.050.002.05
methAvg1.900.001.91
methEntropy1.990.001.98
methHeatmap1.870.011.89
nhmmer000
odd_ratio3.880.003.88

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

nameusersystemelapsed
bconv000
compare_samples4.430.024.44
fishertest_cpg4.390.004.39
hmmbuild000
methAlign2.060.002.07
methAvg2.230.002.23
methEntropy2.240.002.23
methHeatmap2.220.002.22
nhmmer000
odd_ratio4.200.004.21