BioC 3.2: CHECK report for methylPipe on oaxaca

Package: methylPipe

Version: 1.4.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings methylPipe_1.4.5.tar.gz

StartedAt: 2016-04-23 02:02:36 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 02:09:38 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 421.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: methylPipe.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings methylPipe_1.4.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/methylPipe.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.4.5’
* 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 ... [33s/33s] 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
findDMR,BSdataSet: no visible global function definition for
  ‘stopCluster’
findPMDs,BSdata : PMDchr: no visible global function definition for
  ‘segmentPMDs’
methstats,BSdataSet: no visible global function definition for
  ‘stopCluster’
show,BSdata: no visible global function definition for ‘organism’
show,BSdataSet: no visible global function definition for ‘organism’
* 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [46s/123s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
findDMR  0.625  1.593  25.796
findPMDs 0.190  0.130  18.410
* 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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/methylPipe.Rcheck/00check.log’
for details.

* installing *source* package ‘methylPipe’ ...
** 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 R_init_methylPipe.c -o R_init_methylPipe.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 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 /Users/biocbuild/bbs-3.2-bioc/meat/methylPipe.Rcheck/methylPipe/libs
** R
** exec
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (methylPipe)

name	user	system	elapsed
BSdata-class	0.277	0.015	0.292
BSdataSet-class	0.180	0.004	0.184
BSprepare	0	0	0
GEcollection-class	2.279	0.055	2.401
GElist-class	0.043	0.005	0.048
chiCombP	0.001	0.000	0.001
consolidateDMRs	0.135	0.000	0.136
extractBinGRanges	0.034	0.001	0.035
findDMR	0.625	1.593	25.796
findPMDs	0.19	0.13	18.41
getCpos	0.175	0.006	0.181
getCposDensity	0.167	0.004	0.171
mCsmoothing	0.401	0.010	0.414
mapBSdata2GRanges	1.876	0.025	1.902