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BioC 3.5: CHECK report for methylMnM on oaxaca

This page was generated on 2017-03-04 16:46:16 -0500 (Sat, 04 Mar 2017).

Package 778/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methylMnM 1.13.0
Yan Zhou
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/methylMnM
Last Changed Rev: 122712 / Revision: 127142
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / 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 

Summary

Package: methylMnM
Version: 1.13.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings methylMnM_1.13.0.tar.gz
StartedAt: 2017-03-04 05:43:48 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 05:44:40 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 52.6 seconds
RetCode: 0
Status:  OK 
CheckDir: methylMnM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings methylMnM_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/methylMnM.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.13.0’
* 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 ... NOTE
File ‘methylMnM/libs/methylMnM.so’:
  Found ‘_printf’, possibly from ‘printf’ (C)
    Objects: ‘CpGcount.o’, ‘calculatecount.o’, ‘calculatecount1.o’,
      ‘calculatecountneg.o’, ‘pmultinom.o’, ‘pvalueclassify.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
countMREcpgbin 4.984  0.092    5.31
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/methylMnM.Rcheck/00check.log’
for details.


methylMnM.Rcheck/00install.out:

* installing *source* package ‘methylMnM’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c CpGcount.c -o CpGcount.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c calculatecount.c -o calculatecount.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c calculatecount1.c -o calculatecount1.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c calculatecountneg.c -o calculatecountneg.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c pmultinom.c -o pmultinom.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c pvalueclassify.c -o pvalueclassify.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c register.c -o register.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o methylMnM.so CpGcount.o calculatecount.o calculatecount1.o calculatecountneg.o pmultinom.o pvalueclassify.o register.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-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
CNVnormal0.0170.0010.018
MnM.qvalue0.0180.0010.021
MnM.selectDMR0.0160.0000.016
MnM.test0.0660.0020.069
calcFactornew0.0040.0000.003
calculatecount0.0010.0000.002
calculatecount10.0010.0000.002
calculatecountneg0.0010.0000.002
countMREbin4.8050.0914.900
countMREcpgbin4.9840.0925.310
countMeDIPbin3.5230.0773.602
countcpgbin3.6720.0733.746
cpgcount0.0010.0000.001
normpdf0.0010.0000.001
normpdf10.0010.0000.001
pmultinom0.8760.0000.877
qvalue.rank0.0010.0000.001
removeblacklist0.0070.0010.008