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CHECK report for BayesPeak on malbec2

This page was generated on 2018-10-17 08:23:04 -0400 (Wed, 17 Oct 2018).

Package 99/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BayesPeak 1.32.0
Jonathan Cairns
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/BayesPeak
Branch: RELEASE_3_7
Last Commit: 3923deb
Last Changed Date: 2018-04-30 10:35:13 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BayesPeak
Version: 1.32.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:BayesPeak.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings BayesPeak_1.32.0.tar.gz
StartedAt: 2018-10-15 22:38:45 -0400 (Mon, 15 Oct 2018)
EndedAt: 2018-10-15 22:45:44 -0400 (Mon, 15 Oct 2018)
EllapsedTime: 419.2 seconds
RetCode: 0
Status:  OK 
CheckDir: BayesPeak.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:BayesPeak.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings BayesPeak_1.32.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/BayesPeak.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.32.0’
* 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  6.3Mb
  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 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
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.7-bioc/R/library/BayesPeak/libs/BayesPeak.so’:
  Found ‘stdout’, possibly from ‘stdout’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
bayespeak       280.336  0.048 280.600
summarise.peaks  93.716  0.008  93.782
* 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
  ‘/home/biocbuild/bbs-3.7-bioc/meat/BayesPeak.Rcheck/00check.log’
for details.



Installation output

BayesPeak.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL BayesPeak
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘BayesPeak’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.7-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 -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o BayesPeak.so bayespeak.o -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/library/BayesPeak/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BayesPeak)

Tests output


Example timings

BayesPeak.Rcheck/BayesPeak-Ex.timings

nameusersystemelapsed
bayespeak280.336 0.048280.600
overfitting0.1320.0040.137
plot.PP0.1040.0000.103
plot.bed0.7200.0080.727
plot.job3.5320.0243.560
read.bed0.6680.0000.670
summarise.peaks93.716 0.00893.782