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BioC 3.4: CHECK report for BayesPeak on morelia

This page was generated on 2017-04-15 16:23:14 -0400 (Sat, 15 Apr 2017).

Package 88/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BayesPeak 1.26.0
Jonathan Cairns
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/BayesPeak
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BayesPeak
Version: 1.26.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BayesPeak_1.26.0.tar.gz
StartedAt: 2017-04-14 22:56:56 -0700 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 23:00:04 -0700 (Fri, 14 Apr 2017)
EllapsedTime: 188.7 seconds
RetCode: 0
Status:  OK 
CheckDir: BayesPeak.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BayesPeak_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/BayesPeak.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BayesPeak/DESCRIPTION’ ... OK
* this is package ‘BayesPeak’ version ‘1.26.0’
* 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 ‘BayesPeak’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data      1.0Mb
    extdata   5.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘IRanges’
A package should be listed in only one of these fields.
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘parallel’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
identify.overfitdiag: no visible global function definition for
  ‘identify’
plot.job: no visible global function definition for ‘plot’
plot.overfitdiag: no visible global function definition for ‘plot’
region.overfitdiag: no visible global function definition for ‘locator’
region.overfitdiag: no visible global function definition for ‘polygon’
Undefined global functions or variables:
  identify locator plot polygon
Consider adding
  importFrom("graphics", "identify", "locator", "plot", "polygon")
to your NAMESPACE file.
* 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 ... NOTE
S3 methods shown with full name in documentation object 'overfittingDiagnostics':
  ‘plot.overfitdiag’ ‘identify.overfitdiag’

S3 methods shown with full name in documentation object 'plot.PP':
  ‘plot.PP’

S3 methods shown with full name in documentation object 'plot.bed':
  ‘plot.bed’

S3 methods shown with full name in documentation object 'plot.job':
  ‘plot.job’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
File ‘BayesPeak/libs/BayesPeak.so’:
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
    Object: ‘bayespeak.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* 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
bayespeak       57.972  0.096  58.242
summarise.peaks 56.580  0.104  56.762
plot.job         6.171  0.072   6.287
* 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: 6 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/BayesPeak.Rcheck/00check.log’
for details.


BayesPeak.Rcheck/00install.out:

* installing *source* package ‘BayesPeak’ ...
** 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 bayespeak.c -o bayespeak.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 BayesPeak.so bayespeak.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.4-bioc/meat/BayesPeak.Rcheck/BayesPeak/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BayesPeak)

BayesPeak.Rcheck/BayesPeak-Ex.timings:

nameusersystemelapsed
bayespeak57.972 0.09658.242
overfitting0.1280.0120.149
plot.PP0.1160.0080.134
plot.bed1.3260.0201.346
plot.job6.1710.0726.287
read.bed1.2170.0121.230
summarise.peaks56.580 0.10456.762