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BioC 3.1: CHECK report for ChIPseqR on zin2

This page was generated on 2015-10-09 09:23:53 -0700 (Fri, 09 Oct 2015).

Package 161/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPseqR 1.22.1
Peter Humburg
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/ChIPseqR
Last Changed Rev: 105972 / Revision: 109384
Last Changed Date: 2015-07-10 03:01:43 -0700 (Fri, 10 Jul 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: ChIPseqR
Version: 1.22.1
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings ChIPseqR_1.22.1.tar.gz
StartedAt: 2015-10-08 23:26:53 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 23:34:02 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 429.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: ChIPseqR.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings ChIPseqR_1.22.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/ChIPseqR.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 ‘ChIPseqR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPseqR’ version ‘1.22.1’
* 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 ‘ChIPseqR’ can be installed ... [13s/18s] WARNING
Found the following significant warnings:
  Warning: replacing previous import by ‘graphics::image’ when loading ‘ChIPseqR’
  Warning: replacing previous import by ‘utils::head’ when loading ‘ChIPseqR’
  Warning: replacing previous import by ‘utils::tail’ when loading ‘ChIPseqR’
See ‘/home/biocbuild/bbs-3.1-bioc/meat/ChIPseqR.Rcheck/00install.out’ for details.
* 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 loading without being on the library search path ... 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 ... 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 ... 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 ... [231s/269s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
alignFeature       83.987  0.032  99.153
BindScore          34.451  5.173  45.611
callBindingSites   38.786  0.670  44.721
RLEBindScore-class 31.979  0.104  36.036
simpleNucCall      29.715  0.035  36.420
* 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 WARNING
See
  ‘/home/biocbuild/bbs-3.1-bioc/meat/ChIPseqR.Rcheck/00check.log’
for details.


ChIPseqR.Rcheck/00install.out:

* installing *source* package ‘ChIPseqR’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c startScore.c -o startScore.o
startScore.c: In function ‘_ratioStat_pois’:
startScore.c:66:15: warning: unused variable ‘tmp_stat’ [-Wunused-variable]
  double stat, tmp_stat;
               ^
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.1-bioc/R/lib -L/usr/local/lib -o ChIPseqR.so startScore.o -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-bioc/meat/ChIPseqR.Rcheck/ChIPseqR/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Warning: replacing previous import by ‘graphics::image’ when loading ‘ChIPseqR’
Warning: replacing previous import by ‘utils::head’ when loading ‘ChIPseqR’
Warning: replacing previous import by ‘utils::tail’ when loading ‘ChIPseqR’
** 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’
Warning: replacing previous import by ‘graphics::image’ when loading ‘ChIPseqR’
Warning: replacing previous import by ‘utils::head’ when loading ‘ChIPseqR’
Warning: replacing previous import by ‘utils::tail’ when loading ‘ChIPseqR’
* DONE (ChIPseqR)

ChIPseqR.Rcheck/ChIPseqR-Ex.timings:

nameusersystemelapsed
BindScore34.451 5.17345.611
ChIPseqR-package0.0010.0000.000
RLEBindScore-class31.979 0.10436.036
RLEReadCounts-class0.0170.0040.021
ReadCounts0.0310.0000.031
alignFeature83.987 0.03299.153
callBindingSites38.786 0.67044.721
pos2gff0.0040.0000.005
simpleNucCall29.715 0.03536.420
strandPileup0.0080.0000.015
windowCounts0.0530.0000.052