Package: methylPipe

Version: 1.18.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:methylPipe.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings methylPipe_1.18.0.tar.gz

StartedAt: 2019-10-16 04:32:55 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:43:11 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 616.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: methylPipe.Rcheck

Warnings: 2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:methylPipe.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings methylPipe_1.18.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/methylPipe.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 ‘methylPipe/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘methylPipe’ version ‘1.18.0’
* 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 ‘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
* 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 is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:
  Warning: working directory was changed to '/private/tmp/Rtmp5unUEg', resetting
Examples with CPU or elapsed time > 5s
            user system elapsed
plotMeth  33.288  2.222  47.826
findDMR    3.443  6.527  50.654
methstats  1.247  0.574  28.242
findPMDs   0.371  0.503  34.826
* 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: 2 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/methylPipe.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 methylPipe
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘methylPipe’ ...
** 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 R_init_methylPipe.c -o R_init_methylPipe.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 binning.c -o binning.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 methylPipe.so R_init_methylPipe.o binning.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-methylPipe/00new/methylPipe/libs
** R
** exec
** 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 (methylPipe)

name	user	system	elapsed
BSdata-class	0.261	0.007	0.270
BSdataSet-class	0.308	0.012	0.323
BSprepare	0	0	0
GEcollection-class	4.246	0.174	4.424
GElist-class	0.067	0.005	0.074
chiCombP	0.001	0.000	0.001
consolidateDMRs	0.370	0.002	0.372
extractBinGRanges	0.018	0.001	0.019
findDMR	3.443	6.527	50.654
findPMDs	0.371	0.503	34.826
getCpos	0.221	0.028	0.249
getCposDensity	0.164	0.012	0.176
mCsmoothing	0.472	0.047	0.520
mapBSdata2GRanges	1.317	0.038	1.428
methstats	1.247	0.574	28.242
plotMeth	33.288	2.222	47.826
pool.reads	0	0	0
process.hmc	0	0	0
profileDNAmetBin	1.789	0.249	2.038