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This page was generated on 2021-09-22 15:04:48 -0400 (Wed, 22 Sep 2021).

CHECK results for ChIPseqR on nebbiolo1

To the developers/maintainers of the ChIPseqR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChIPseqR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 298/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPseqR 1.46.0  (landing page)
Peter Humburg
Snapshot Date: 2021-09-21 04:50:12 -0400 (Tue, 21 Sep 2021)
git_url: https://git.bioconductor.org/packages/ChIPseqR
git_branch: RELEASE_3_13
git_last_commit: d242683
git_last_commit_date: 2021-05-19 11:44:14 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ChIPseqR
Version: 1.46.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:ChIPseqR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings ChIPseqR_1.46.0.tar.gz
StartedAt: 2021-09-21 09:16:12 -0400 (Tue, 21 Sep 2021)
EndedAt: 2021-09-21 09:20:00 -0400 (Tue, 21 Sep 2021)
EllapsedTime: 227.5 seconds
RetCode: 0
Status:   OK  
CheckDir: ChIPseqR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:ChIPseqR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings ChIPseqR_1.46.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/ChIPseqR.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.46.0’
* 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 9.711  0.588  10.298
BindScore    5.475  0.067   5.543
* 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-3.13-bioc/meat/ChIPseqR.Rcheck/00check.log’
for details.



Installation output

ChIPseqR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL ChIPseqR
###
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘ChIPseqR’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.13-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]
   66 |  double stat, tmp_stat;
      |               ^~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o ChIPseqR.so startScore.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-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
BindScore5.4750.0675.543
ChIPseqR-package0.0010.0000.000
RLEBindScore-class4.0740.0404.114
RLEReadCounts-class0.0260.0000.026
ReadCounts0.0250.0000.025
alignFeature 9.711 0.58810.298
callBindingSites3.0610.0163.077
pos2gff0.0050.0000.005
simpleNucCall4.2990.0284.327
strandPileup0.0110.0000.011
windowCounts0.1870.0030.191