Package: ChIPseqR

Version: 1.40.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:ChIPseqR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings ChIPseqR_1.40.0.tar.gz

StartedAt: 2020-04-15 00:42:37 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 00:46:43 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 246.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: ChIPseqR.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:ChIPseqR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings ChIPseqR_1.40.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/ChIPseqR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.40.0’
* 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-3.10-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 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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
alignFeature       10.684  0.624  11.352
BindScore           6.884  0.088   6.985
callBindingSites    5.100  0.004   5.120
RLEBindScore-class  5.028  0.012   5.045
* 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, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/ChIPseqR.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL ChIPseqR
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘ChIPseqR’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/lib -L/usr/local/lib -o ChIPseqR.so startScore.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-ChIPseqR/00new/ChIPseqR/libs
** R
** inst
** byte-compile and prepare 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’
No methods found in package ‘IRanges’ for request: ‘score’ when loading ‘ChIPseqR’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
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’
No methods found in package ‘IRanges’ for request: ‘score’ when loading ‘ChIPseqR’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
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’
No methods found in package ‘IRanges’ for request: ‘score’ when loading ‘ChIPseqR’
** testing if installed package keeps a record of temporary installation path
* DONE (ChIPseqR)

name	user	system	elapsed
BindScore	6.884	0.088	6.985
ChIPseqR-package	0	0	0
RLEBindScore-class	5.028	0.012	5.045
RLEReadCounts-class	0.024	0.000	0.024
ReadCounts	0.028	0.000	0.027
alignFeature	10.684	0.624	11.352
callBindingSites	5.100	0.004	5.120
pos2gff	0.008	0.000	0.008
simpleNucCall	4.900	0.048	4.951
strandPileup	0.012	0.000	0.013
windowCounts	0.228	0.004	0.233