Package: ChIPseqR

Version: 1.32.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings ChIPseqR_1.32.0.tar.gz

StartedAt: 2018-04-11 22:11:46 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 22:15:39 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 233.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: ChIPseqR.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings ChIPseqR_1.32.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/ChIPseqR.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.32.0’
* 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 ‘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
alignFeature       16.716  0.444  17.173
BindScore          13.904  0.104  14.016
RLEBindScore-class 11.404  0.008  11.417
callBindingSites    9.968  0.008   9.983
simpleNucCall       9.956  0.008   9.971
* 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.

* 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;
               ^
g++ -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)

name	user	system	elapsed
BindScore	13.904	0.104	14.016
ChIPseqR-package	0	0	0
RLEBindScore-class	11.404	0.008	11.417
RLEReadCounts-class	0.016	0.000	0.016
ReadCounts	0.036	0.004	0.041
alignFeature	16.716	0.444	17.173
callBindingSites	9.968	0.008	9.983
pos2gff	0.004	0.000	0.004
simpleNucCall	9.956	0.008	9.971
strandPileup	0.008	0.000	0.007
windowCounts	0.088	0.000	0.089