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BioC 3.4: CHECK report for DMRcate on moscato1

This page was generated on 2016-09-21 03:45:35 -0700 (Wed, 21 Sep 2016).

Package 326/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DMRcate 1.9.2
Tim Peters
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DMRcate
Last Changed Rev: 117512 / Revision: 121152
Last Changed Date: 2016-05-15 13:14:22 -0700 (Sun, 15 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: DMRcate
Version: 1.9.2
Command: rm -rf DMRcate.buildbin-libdir DMRcate.Rcheck && mkdir DMRcate.buildbin-libdir DMRcate.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DMRcate.buildbin-libdir DMRcate_1.9.2.tar.gz >DMRcate.Rcheck\00install.out 2>&1 && cp DMRcate.Rcheck\00install.out DMRcate-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=DMRcate.buildbin-libdir --install="check:DMRcate-install.out" --force-multiarch --no-vignettes --timings DMRcate_1.9.2.tar.gz
StartedAt: 2016-09-20 07:16:11 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 07:28:43 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 752.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: DMRcate.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf DMRcate.buildbin-libdir DMRcate.Rcheck && mkdir DMRcate.buildbin-libdir DMRcate.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DMRcate.buildbin-libdir DMRcate_1.9.2.tar.gz >DMRcate.Rcheck\00install.out 2>&1 && cp DMRcate.Rcheck\00install.out DMRcate-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=DMRcate.buildbin-libdir --install="check:DMRcate-install.out" --force-multiarch --no-vignettes --timings DMRcate_1.9.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/DMRcate.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 'DMRcate/DESCRIPTION' ... OK
* this is package 'DMRcate' version '1.9.2'
* 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 'DMRcate' 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 ... WARNING
Subdirectory 'data' contains no data sets.
* 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
* 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 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
DMR.plot: no visible global function definition for 'subjectHits'
DMR.plot: no visible binding for global variable 'tx.hg19'
DMR.plot: no visible binding for global variable 'tx.hg38'
DMR.plot: no visible binding for global variable 'tx.mm10'
KernelTest: no visible global function definition for 'pchisq'
SparseDeltas: no visible global function definition for 'approx'
dmrcate: no visible global function definition for 'p.adjust'
dmrcate : <anonymous>: no visible global function definition for
  'pnorm'
dmrcate : <anonymous>: no visible global function definition for
  'qnorm'
extractRanges: no visible binding for global variable 'tx.hg19'
extractRanges: no visible binding for global variable 'tx.hg38'
extractRanges: no visible binding for global variable 'tx.mm10'
rmSNPandCH: no visible global function definition for 'data'
rmSNPandCH: no visible binding for global variable 'dmrcatedata'
Undefined global functions or variables:
  approx data dmrcatedata p.adjust pchisq pnorm qnorm subjectHits
  tx.hg19 tx.hg38 tx.mm10
Consider adding
  importFrom("stats", "approx", "p.adjust", "pchisq", "pnorm", "qnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
* 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
DMRcate-package 46.33   0.91   76.22
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
DMRcate-package 51.39   1.27   75.31
* 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 WARNING, 1 NOTE
See
  'D:/biocbld/bbs-3.4-bioc/meat/DMRcate.Rcheck/00check.log'
for details.


DMRcate.Rcheck/00install.out:


install for i386

* installing *source* package 'DMRcate' ...
** 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 'DMRcate' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DMRcate' as DMRcate_1.9.2.zip
* DONE (DMRcate)

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

nameusersystemelapsed
DMR.plot000
DMRcate-package46.33 0.9176.22
cpg.annotate000
dmrcate000
extractRanges000
rmSNPandCH000

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

nameusersystemelapsed
DMR.plot000
DMRcate-package51.39 1.2775.31
cpg.annotate000
dmrcate000
extractRanges000
rmSNPandCH000