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BioC 3.6: CHECK report for ChIPseqR on malbec1

This page was generated on 2017-08-16 13:18:44 -0400 (Wed, 16 Aug 2017).

Package 214/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPseqR 1.31.0
Peter Humburg
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChIPseqR
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: ChIPseqR
Version: 1.31.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings ChIPseqR_1.31.0.tar.gz
StartedAt: 2017-08-15 21:57:31 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:01:17 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 226.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: ChIPseqR.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings ChIPseqR_1.31.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/ChIPseqR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.31.0’
* 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 ‘ChIPseqR’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘BiocGenerics::image’ by ‘graphics::image’ when loading ‘ChIPseqR’
  Warning: replacing previous import ‘S4Vectors::head’ by ‘utils::head’ when loading ‘ChIPseqR’
  Warning: replacing previous import ‘S4Vectors::tail’ by ‘utils::tail’ when loading ‘ChIPseqR’
See ‘/home/biocbuild/bbs-3.6-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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
BindScore          13.460  0.096  13.574
RLEBindScore-class 10.300  0.080  10.383
callBindingSites    9.192  0.064   9.260
simpleNucCall       9.116  0.024   9.145
alignFeature        6.064  1.352   7.426
* 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-3.6-bioc/meat/ChIPseqR.Rcheck/00check.log’
for details.


ChIPseqR.Rcheck/00install.out:

* installing *source* package ‘ChIPseqR’ ...
** libs
gcc -I/home/biocbuild/bbs-3.6-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 -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o ChIPseqR.so startScore.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/ChIPseqR.Rcheck/ChIPseqR/libs
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘BiocGenerics::image’ by ‘graphics::image’ when loading ‘ChIPseqR’
Warning: replacing previous import ‘S4Vectors::head’ by ‘utils::head’ when loading ‘ChIPseqR’
Warning: replacing previous import ‘S4Vectors::tail’ by ‘utils::tail’ when loading ‘ChIPseqR’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘BiocGenerics::image’ by ‘graphics::image’ when loading ‘ChIPseqR’
Warning: replacing previous import ‘S4Vectors::head’ by ‘utils::head’ when loading ‘ChIPseqR’
Warning: replacing previous import ‘S4Vectors::tail’ by ‘utils::tail’ when loading ‘ChIPseqR’
* DONE (ChIPseqR)

ChIPseqR.Rcheck/ChIPseqR-Ex.timings:

nameusersystemelapsed
BindScore13.460 0.09613.574
ChIPseqR-package0.0000.0000.001
RLEBindScore-class10.300 0.08010.383
RLEReadCounts-class0.0160.0000.015
ReadCounts0.0400.0000.041
alignFeature6.0641.3527.426
callBindingSites9.1920.0649.260
pos2gff0.0040.0000.004
simpleNucCall9.1160.0249.145
strandPileup0.0080.0000.007
windowCounts0.0880.0000.087