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BioC 3.2: CHECK report for BayesPeak on linux1.bioconductor.org

This page was generated on 2015-10-27 17:24:37 -0400 (Tue, 27 Oct 2015).

Package 75/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BayesPeak 1.22.0
Jonathan Cairns
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/BayesPeak
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BayesPeak
Version: 1.22.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings BayesPeak_1.22.0.tar.gz
StartedAt: 2015-10-27 01:13:04 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 01:18:14 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 309.8 seconds
RetCode: 0
Status:  OK 
CheckDir: BayesPeak.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings BayesPeak_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/BayesPeak.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BayesPeak/DESCRIPTION’ ... OK
* this is package ‘BayesPeak’ version ‘1.22.0’
* 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 ... [6s/6s] 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 ‘stdout’, 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [260s/260s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
bayespeak       127.112  0.039 127.321
summarise.peaks 124.346  0.004 124.465
* 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: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/BayesPeak.Rcheck/00check.log’
for details.


BayesPeak.Rcheck/00install.out:

* installing *source* package ‘BayesPeak’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c bayespeak.c -o bayespeak.o
bayespeak.c: In function ‘bayespeak’:
bayespeak.c:176:27: warning: variable ‘M’ set but not used [-Wunused-but-set-variable]
   double  M1, M2, M3, M4, M, a, b;
                           ^
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o BayesPeak.so bayespeak.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-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
bayespeak127.112 0.039127.321
overfitting0.1580.0080.165
plot.PP0.1410.0000.140
plot.bed0.9240.0080.932
plot.job4.5240.0204.548
read.bed0.5770.0000.577
summarise.peaks124.346 0.004124.465