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CHECK report for ChIPseqR on malbec1

This page was generated on 2021-05-06 12:27:08 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the ChIPseqR package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 290/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPseqR 1.44.0  (landing page)
Peter Humburg
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/ChIPseqR
Branch: RELEASE_3_12
Last Commit: 719fbb0
Last Changed Date: 2020-10-27 10:36:51 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: ChIPseqR
Version: 1.44.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:ChIPseqR.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings ChIPseqR_1.44.0.tar.gz
StartedAt: 2021-05-05 23:59:01 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-06 00:03:11 -0400 (Thu, 06 May 2021)
EllapsedTime: 249.9 seconds
RetCode: 0
Status:   OK  
CheckDir: ChIPseqR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:ChIPseqR.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings ChIPseqR_1.44.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/ChIPseqR.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.44.0’
* 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 ... OK
* 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 ... NOTE
.fixCounts: no visible global function definition for ‘runLength’
.fixCounts: no visible global function definition for ‘runValue’
getBindLen: no visible global function definition for ‘window’
pickPeak: no visible global function definition for ‘start’
pickPeak: no visible global function definition for ‘runLength’
pickPeak : <anonymous>: no visible global function definition for
  ‘window’
[[,BindScore-ANY-numeric: no visible global function definition for
  ‘window’
decompress,Rle: no visible global function definition for ‘runValue’
decompress,RleList : <anonymous>: no visible global function definition
  for ‘runValue’
initialize,RLEBindScore : <anonymous>: no visible global function
  definition for ‘Rle’
initialize,RLEBindScore : <anonymous>: no visible global function
  definition for ‘runValue’
initialize,RLEBindScore : <anonymous>: no visible global function
  definition for ‘runValue<-’
plot,RLEReadCounts-missing : <anonymous>: no visible global function
  definition for ‘window’
Undefined global functions or variables:
  Rle runLength runValue runValue<- start window
Consider adding
  importFrom("stats", "start", "window")
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 ... 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 (user + system) or elapsed time > 5s
                     user system elapsed
alignFeature       10.880  0.240  11.136
BindScore           6.952  0.056   7.062
RLEBindScore-class  5.160  0.036   5.206
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/ChIPseqR.Rcheck/00check.log’
for details.



Installation output

ChIPseqR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL ChIPseqR
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘ChIPseqR’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.12-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-3.12-bioc/R/lib -L/usr/local/lib -o ChIPseqR.so startScore.o -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-ChIPseqR/00new/ChIPseqR/libs
** R
** 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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ChIPseqR)

Tests output


Example timings

ChIPseqR.Rcheck/ChIPseqR-Ex.timings

nameusersystemelapsed
BindScore6.9520.0567.062
ChIPseqR-package000
RLEBindScore-class5.1600.0365.206
RLEReadCounts-class0.0280.0000.028
ReadCounts0.0280.0000.027
alignFeature10.880 0.24011.136
callBindingSites3.9160.0243.950
pos2gff0.0040.0000.005
simpleNucCall4.1600.0324.196
strandPileup0.0080.0000.009
windowCounts0.1640.0000.161