Package: methylMnM

Version: 1.16.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings methylMnM_1.16.0.tar.gz

StartedAt: 2018-04-12 01:02:21 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:02:55 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 34.3 seconds

RetCode: 0

Status:  OK

CheckDir: methylMnM.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings methylMnM_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/methylMnM.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.16.0’
* 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 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-3.6-bioc/meat/methylMnM.Rcheck/00check.log’
for details.

* installing *source* package ‘methylMnM’ ...
** libs
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c CpGcount.c -o CpGcount.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c calculatecount.c -o calculatecount.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c calculatecount1.c -o calculatecount1.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c calculatecountneg.c -o calculatecountneg.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c pmultinom.c -o pmultinom.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c pvalueclassify.c -o pvalueclassify.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c register.c -o register.o
g++ -shared -L/home/biocbuild/bbs-3.6-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-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-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)

name	user	system	elapsed
CNVnormal	0.012	0.000	0.012
MnM.qvalue	0.016	0.000	0.015
MnM.selectDMR	0.020	0.000	0.018
MnM.test	0.108	0.000	0.110
calcFactornew	0.000	0.000	0.002
calculatecount	0.004	0.000	0.001
calculatecount1	0	0	0
calculatecountneg	0.000	0.000	0.001
countMREbin	1.684	0.032	1.714
countMREcpgbin	1.556	0.012	1.568
countMeDIPbin	1.516	0.008	1.525
countcpgbin	1.392	0.004	1.400
cpgcount	0.000	0.000	0.001
normpdf	0.000	0.000	0.001
normpdf1	0	0	0
pmultinom	0.436	0.000	0.437
qvalue.rank	0	0	0
removeblacklist	0.004	0.000	0.006