BioC 3.5: CHECK report for methylPipe on tokay2

Package: methylPipe

Version: 1.10.0

Command: rm -rf methylPipe.buildbin-libdir methylPipe.Rcheck && mkdir methylPipe.buildbin-libdir methylPipe.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=methylPipe.buildbin-libdir methylPipe_1.10.0.tar.gz >methylPipe.Rcheck\00install.out 2>&1 && cp methylPipe.Rcheck\00install.out methylPipe-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=methylPipe.buildbin-libdir --install="check:methylPipe-install.out" --force-multiarch --no-vignettes --timings methylPipe_1.10.0.tar.gz

StartedAt: 2017-08-16 01:11:44 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:22:45 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 660.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: methylPipe.Rcheck

Warnings: 1

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### Running command:
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###   rm -rf methylPipe.buildbin-libdir methylPipe.Rcheck && mkdir methylPipe.buildbin-libdir methylPipe.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=methylPipe.buildbin-libdir methylPipe_1.10.0.tar.gz >methylPipe.Rcheck\00install.out 2>&1 && cp methylPipe.Rcheck\00install.out methylPipe-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=methylPipe.buildbin-libdir --install="check:methylPipe-install.out" --force-multiarch --no-vignettes --timings methylPipe_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/methylPipe.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'methylPipe/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'methylPipe' version '1.10.0'
* 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 whether package 'methylPipe' 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 ... OK
* 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
BSprepare : binomTestMulti: no visible global function definition for
  'binom.test'
BSprepare : binomTestMulti : pVfun: no visible global function
  definition for 'binom.test'
BSprepare : binomTestMulti: no visible global function definition for
  'p.adjust'
chiCombP: no visible global function definition for 'pchisq'
consolidateDMRs: no visible global function definition for 'p.adjust'
plotMeth: no visible global function definition for 'rainbow'
process.hmc: no visible global function definition for 'write.table'
findDMR,BSdataSet : DMRchr: no visible global function definition for
  'kruskal.test'
findDMR,BSdataSet : DMRchr: no visible global function definition for
  'wilcox.test'
findDMR,BSdataSet: no visible global function definition for
  'stopCluster'
findPMDs,BSdata : PMDchr: no visible global function definition for
  'segmentPMDs'
mCsmoothing,BSdata: no visible global function definition for
  'smooth.spline'
mCsmoothing,BSdata: no visible global function definition for 'box'
mCsmoothing,BSdata: no visible global function definition for 'axis'
mCsmoothing,BSdata: no visible global function definition for 'mtext'
methstats,BSdataSet: no visible global function definition for
  'stopCluster'
methstats,BSdataSet : panel.cor: no visible global function definition
  for 'par'
methstats,BSdataSet : panel.cor: no visible global function definition
  for 'cor.test'
methstats,BSdataSet : panel.cor: no visible global function definition
  for 'text'
methstats,BSdataSet : panel.smooth: no visible global function
  definition for 'points'
methstats,BSdataSet : panel.smooth: no visible global function
  definition for 'lines'
methstats,BSdataSet : panel.hist: no visible global function definition
  for 'par'
methstats,BSdataSet : panel.hist: no visible global function definition
  for 'hist'
methstats,BSdataSet : panel.hist: no visible global function definition
  for 'rect'
methstats,BSdataSet: no visible global function definition for 'pairs'
methstats,BSdataSet: no visible global function definition for 'dist'
methstats,BSdataSet: no visible global function definition for 'hclust'
methstats,BSdataSet: no visible global function definition for
  'dev.new'
methstats,BSdataSet: no visible global function definition for 'plot'
show,BSdata: no visible global function definition for 'organism'
show,BSdataSet: no visible global function definition for 'organism'
Undefined global functions or variables:
  axis binom.test box cor.test dev.new dist hclust hist kruskal.test
  lines mtext organism p.adjust pairs par pchisq plot points rainbow
  rect segmentPMDs smooth.spline stopCluster text wilcox.test
  write.table
Consider adding
  importFrom("grDevices", "dev.new", "rainbow")
  importFrom("graphics", "axis", "box", "hist", "lines", "mtext",
             "pairs", "par", "plot", "points", "rect", "text")
  importFrom("stats", "binom.test", "cor.test", "dist", "hclust",
             "kruskal.test", "p.adjust", "pchisq", "smooth.spline",
             "wilcox.test")
  importFrom("utils", "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'BSdataSet,ANY,ANY,ANY'
  generic '[' and siglist 'GElist,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.5-bioc/meat/methylPipe.buildbin-libdir/methylPipe/libs/i386/methylPipe.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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.
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 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
findDMR  0.77   4.47   27.94
findPMDs 0.22   0.22   20.61
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
findDMR  0.66   4.40   34.21
findPMDs 0.30   0.27   17.19
* 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, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/methylPipe.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'methylPipe' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_methylPipe.c -o R_init_methylPipe.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c binning.c -o binning.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o methylPipe.dll tmp.def R_init_methylPipe.o binning.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/methylPipe.buildbin-libdir/methylPipe/libs/i386
** R
** exec
** 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 'methylPipe' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_methylPipe.c -o R_init_methylPipe.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c binning.c -o binning.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o methylPipe.dll tmp.def R_init_methylPipe.o binning.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/methylPipe.buildbin-libdir/methylPipe/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'methylPipe' as methylPipe_1.10.0.zip
* DONE (methylPipe)

name	user	system	elapsed
BSdata-class	0.45	0.00	0.46
BSdataSet-class	0.26	0.00	0.27
BSprepare	0	0	0
GEcollection-class	2.39	0.07	2.46
GElist-class	0.09	0.00	0.09
chiCombP	0	0	0
consolidateDMRs	0.25	0.04	0.30
extractBinGRanges	0.02	0.00	0.01
findDMR	0.77	4.47	27.94
findPMDs	0.22	0.22	20.61
getCpos	0.26	0.05	0.31
getCposDensity	0.11	0.00	0.11
mCsmoothing	0.26	0.01	0.29
mapBSdata2GRanges	1.5	0.0	1.5

name	user	system	elapsed
BSdata-class	0.61	0.03	0.64
BSdataSet-class	0.46	0.00	0.46
BSprepare	0	0	0
GEcollection-class	3.37	0.03	3.40
GElist-class	0.11	0.00	0.11
chiCombP	0	0	0
consolidateDMRs	0.25	0.04	0.28
extractBinGRanges	0.03	0.00	0.03
findDMR	0.66	4.40	34.21
findPMDs	0.30	0.27	17.19
getCpos	0.40	0.01	0.42
getCposDensity	0.14	0.00	0.14
mCsmoothing	0.25	0.00	0.30
mapBSdata2GRanges	1.03	0.03	1.06