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BioC 3.1: CHECK report for methylPipe on morelia

This page was generated on 2015-10-09 09:42:08 -0700 (Fri, 09 Oct 2015).

Package 592/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methylPipe 1.2.6
Kamal Kishore
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/methylPipe
Last Changed Rev: 108919 / Revision: 109384
Last Changed Date: 2015-09-29 02:46:22 -0700 (Tue, 29 Sep 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

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


* 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.


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-3.1-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)

methylPipe.Rcheck/methylPipe-Ex.timings:

nameusersystemelapsed
BSdata-class0.1620.0140.176
BSdataSet-class0.1630.0190.183
BSprepare000
GEcollection-class1.7390.1061.872
GElist-class0.0240.0000.025
chiCombP0.0010.0000.000
consolidateDMRs0.0880.0000.089
extractBinGRanges0.0230.0000.023
findDMR 0.509 1.60919.782
findPMDs 0.138 0.13014.601
getCpos0.1510.0140.164
getCposDensity0.1300.0030.135
mCsmoothing0.3550.0150.370
mapBSdata2GRanges1.6260.1491.777