BioC 3.1: CHECK report for methylPipe on morelia

Package: methylPipe

Version: 1.2.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings methylPipe_1.2.6.tar.gz

StartedAt: 2015-10-09 03:49:53 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 03:54:59 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 305.7 seconds

RetCode: 0

Status:  OK

CheckDir: methylPipe.Rcheck

Warnings: 0

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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_1.2.6.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/methylPipe.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.2.6’
* 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 ... [24s/24s] 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
plotMeth: no visible global function definition for ‘rowRanges’
profileDNAmetBinParallel: no visible global function definition for
  ‘rowRanges’
binscore<-,GEcollection: no visible global function definition for
  ‘assays<-’
findPMDs,BSdata : PMDchr: no visible global function definition for
  ‘segmentPMDs’
length,GEcollection: no visible global function definition for
  ‘rowRanges’
show,BSdata: no visible global function definition for ‘organism’
show,BSdataSet: no visible global function definition for ‘organism’
show,GEcollection: no visible global function definition for
  ‘rowRanges’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [34s/91s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
findDMR  0.509  1.609  19.782
findPMDs 0.138  0.130  14.601
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.1-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-3.1-bioc/meat/methylPipe.Rcheck/methylPipe/libs
** R
** exec
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (methylPipe)

name	user	system	elapsed
BSdata-class	0.162	0.014	0.176
BSdataSet-class	0.163	0.019	0.183
BSprepare	0	0	0
GEcollection-class	1.739	0.106	1.872
GElist-class	0.024	0.000	0.025
chiCombP	0.001	0.000	0.000
consolidateDMRs	0.088	0.000	0.089
extractBinGRanges	0.023	0.000	0.023
findDMR	0.509	1.609	19.782
findPMDs	0.138	0.130	14.601
getCpos	0.151	0.014	0.164
getCposDensity	0.130	0.003	0.135
mCsmoothing	0.355	0.015	0.370
mapBSdata2GRanges	1.626	0.149	1.777