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BioC 3.4: CHECK report for methylMnM on zin1

This page was generated on 2016-09-21 03:38:37 -0700 (Wed, 21 Sep 2016).

Package 737/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methylMnM 1.11.0
Yan Zhou
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/methylMnM
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 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: methylMnM
Version: 1.11.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings methylMnM_1.11.0.tar.gz
StartedAt: 2016-09-20 09:16:08 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 09:16:40 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 31.5 seconds
RetCode: 0
Status:  OK 
CheckDir: methylMnM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings methylMnM_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/methylMnM.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘methylMnM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘methylMnM’ version ‘1.11.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘methylMnM’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 47.8Mb
  sub-directories of 1Mb or more:
    extdata  47.4Mb
* 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
* 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 ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  ‘edgeR’ ‘statmod’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘edgeR’ ‘statmod’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
CNVnormal: no visible global function definition for ‘read.table’
MnM.qvalue: no visible global function definition for ‘read.table’
MnM.qvalue: no visible global function definition for ‘write.table’
MnM.selectDMR: no visible global function definition for ‘quantile’
MnM.test: no visible global function definition for ‘read.table’
MnM.test: no visible global function definition for ‘calcNormFactors’
MnM.test: no visible global function definition for ‘sage.test’
MnM.test: no visible global function definition for ‘lm’
MnM.test: no visible global function definition for ‘write.table’
countMREbin: no visible global function definition for ‘read.table’
countMREbin: no visible global function definition for ‘count.fields’
countMREbin: no visible global function definition for ‘write.table’
countMREcpgbin: no visible global function definition for ‘read.table’
countMREcpgbin: no visible global function definition for
  ‘count.fields’
countMREcpgbin: no visible global function definition for ‘write.table’
countMeDIPbin: no visible global function definition for ‘read.table’
countMeDIPbin: no visible global function definition for ‘count.fields’
countMeDIPbin: no visible global function definition for ‘write.table’
countcpgbin: no visible global function definition for ‘read.table’
countcpgbin: no visible global function definition for ‘count.fields’
countcpgbin: no visible global function definition for ‘write.table’
normpdf: no visible global function definition for ‘pnorm’
removeblacklist: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  calcNormFactors count.fields lm pnorm quantile read.table sage.test
  write.table
Consider adding
  importFrom("stats", "lm", "pnorm", "quantile")
  importFrom("utils", "count.fields", "read.table", "write.table")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/methylMnM.Rcheck/00check.log’
for details.


methylMnM.Rcheck/00install.out:

* installing *source* package ‘methylMnM’ ...
** libs
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c CpGcount.c -o CpGcount.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c calculatecount.c -o calculatecount.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c calculatecount1.c -o calculatecount1.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c calculatecountneg.c -o calculatecountneg.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c pmultinom.c -o pmultinom.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c pvalueclassify.c -o pvalueclassify.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c register.c -o register.o
gcc -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o methylMnM.so CpGcount.o calculatecount.o calculatecount1.o calculatecountneg.o pmultinom.o pvalueclassify.o register.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/methylMnM.Rcheck/methylMnM/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (methylMnM)

methylMnM.Rcheck/methylMnM-Ex.timings:

nameusersystemelapsed
CNVnormal0.0120.0000.012
MnM.qvalue0.0080.0000.011
MnM.selectDMR0.0080.0040.009
MnM.test0.0240.0000.025
calcFactornew0.0040.0000.001
calculatecount0.0000.0000.001
calculatecount10.0040.0000.001
calculatecountneg0.0000.0000.001
countMREbin1.6720.0121.683
countMREcpgbin1.8000.0001.798
countMeDIPbin1.3640.0001.363
countcpgbin1.3920.0081.398
cpgcount0.0000.0000.001
normpdf0.0000.0000.001
normpdf1000
pmultinom1.660.001.66
qvalue.rank000
removeblacklist0.0080.0000.005