Back to the "Multiple platform build/check report" A [B] C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.0: CHECK report for BayesPeak on oaxaca

This page was generated on 2015-04-10 10:04:07 -0700 (Fri, 10 Apr 2015).

Package 70/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BayesPeak 1.18.2
Jonathan Cairns
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/BayesPeak
Last Changed Rev: 98073 / Revision: 102249
Last Changed Date: 2015-01-06 10:34:11 -0800 (Tue, 06 Jan 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: BayesPeak
Version: 1.18.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BayesPeak_1.18.2.tar.gz
StartedAt: 2015-04-09 21:33:36 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 21:37:23 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 226.3 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 --no-multiarch BayesPeak_1.18.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/BayesPeak.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.18.2’
* 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 ... [8s/9s] 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 ... OK
* 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 ... [138s/139s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
bayespeak       62.206  0.103  62.572
summarise.peaks 61.763  0.124  62.296
plot.job         7.044  0.080   7.247
* 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

NOTE: There were 5 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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-3.0-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
bayespeak62.206 0.10362.572
overfitting0.1520.0070.160
plot.PP0.1230.0050.129
plot.bed1.4950.0211.533
plot.job7.0440.0807.247
read.bed1.4560.0201.486
summarise.peaks61.763 0.12462.296