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BioC 3.5: CHECK report for methylPipe on oaxaca

This page was generated on 2017-03-04 16:48:02 -0500 (Sat, 04 Mar 2017).

Package 779/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methylPipe 1.9.0
Kamal Kishore
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/methylPipe
Last Changed Rev: 122712 / Revision: 127142
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ WARNINGS ] OK 

Summary

Package: methylPipe
Version: 1.9.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings methylPipe_1.9.0.tar.gz
StartedAt: 2017-03-04 05:44:51 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 05:51:40 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 409.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: methylPipe.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings methylPipe_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/methylPipe.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.9.0’
* 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
findDMR  0.773  1.578  28.374
findPMDs 0.282  0.116  18.160
* 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-3.5-bioc/meat/methylPipe.Rcheck/00check.log’
for details.

methylPipe.Rcheck/00install.out:

* 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-3.5-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)

methylPipe.Rcheck/methylPipe-Ex.timings:

nameusersystemelapsed
BSdata-class0.4440.0060.450
BSdataSet-class0.2120.0020.214
BSprepare000
GEcollection-class2.0250.0412.103
GElist-class0.1270.0040.131
chiCombP0.0010.0000.001
consolidateDMRs0.2480.0260.274
extractBinGRanges0.0160.0030.019
findDMR 0.773 1.57828.374
findPMDs 0.282 0.11618.160
getCpos0.3710.0040.376
getCposDensity0.1110.0020.113
mCsmoothing0.2030.0050.208
mapBSdata2GRanges1.0970.0071.103