Package: methylMnM

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:methylMnM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings methylMnM_1.22.0.tar.gz

StartedAt: 2019-10-16 04:32:52 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:33:52 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 60.1 seconds

RetCode: 0

Status:  OK

CheckDir: methylMnM.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:methylMnM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings methylMnM_1.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/methylMnM.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.22.0’
* 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 47.6Mb
  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 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
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/methylMnM/libs/methylMnM.so’:
  Found ‘_printf’, possibly from ‘printf’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/methylMnM.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL methylMnM
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘methylMnM’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c CpGcount.c -o CpGcount.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c calculatecount.c -o calculatecount.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c calculatecount1.c -o calculatecount1.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c calculatecountneg.c -o calculatecountneg.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c pmultinom.c -o pmultinom.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c pvalueclassify.c -o pvalueclassify.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -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 /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-methylMnM/00new/methylMnM/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (methylMnM)

name	user	system	elapsed
CNVnormal	0.020	0.004	0.025
MnM.qvalue	0.020	0.003	0.023
MnM.selectDMR	0.012	0.001	0.013
MnM.test	0.057	0.005	0.063
calcFactornew	0.003	0.001	0.003
calculatecount	0.001	0.001	0.002
calculatecount1	0.001	0.000	0.001
calculatecountneg	0.001	0.000	0.002
countMREbin	1.731	0.239	1.972
countMREcpgbin	1.725	0.156	1.884
countMeDIPbin	1.660	0.134	1.794
countcpgbin	1.608	0.167	1.775
cpgcount	0.001	0.001	0.001
normpdf	0.001	0.001	0.002
normpdf1	0.001	0.001	0.001
pmultinom	1.046	0.002	1.047
qvalue.rank	0.001	0.000	0.001
removeblacklist	0.009	0.001	0.011