Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-10-16 11:35:15 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 333/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPsim 1.54.0  (landing page)
Peter Humburg
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/ChIPsim
git_branch: RELEASE_3_17
git_last_commit: 26c7230
git_last_commit_date: 2023-04-25 09:49:17 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for ChIPsim on nebbiolo1


To the developers/maintainers of the ChIPsim package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChIPsim.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: ChIPsim
Version: 1.54.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ChIPsim.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings ChIPsim_1.54.0.tar.gz
StartedAt: 2023-10-15 20:03:27 -0400 (Sun, 15 Oct 2023)
EndedAt: 2023-10-15 20:07:54 -0400 (Sun, 15 Oct 2023)
EllapsedTime: 266.9 seconds
RetCode: 0
Status:   OK  
CheckDir: ChIPsim.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ChIPsim.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings ChIPsim_1.54.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ChIPsim.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘ChIPsim/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPsim’ version ‘1.54.0’
* 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 ‘ChIPsim’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biostrings’
A package should be listed in only one of these fields.
* 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 ... NOTE
print.SimulatedFeature: no visible global function definition for ‘str’
Undefined global functions or variables:
  str
Consider adding
  importFrom("utils", "str")
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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘ChIPsimIntro.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/ChIPsim.Rcheck/00check.log’
for details.



Installation output

ChIPsim.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL ChIPsim
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘ChIPsim’ ...
** using staged installation
** R
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ChIPsim)

Tests output


Example timings

ChIPsim.Rcheck/ChIPsim-Ex.timings

nameusersystemelapsed
ChIPsim-package000
bindDens2readDens1.3560.0321.387
decodeQuality0.0010.0000.001
defaultControl0.0010.0000.002
defaultErrorProb0.0000.0000.001
defaultFunctions0.0020.0000.002
defaultGenerator0.0460.0000.046
extractQuality0.0000.0000.001
feat2dens1.3110.0071.319
featureDensity0.0000.0000.001
makeFeatures0.0490.0000.049
placeFeatures0.0530.0080.061
pos2fastq0.0590.0000.059
readError0.0010.0000.001
reconcileFeatures0.0590.0000.060
sampleReads0.6490.0150.666
simChIP000
simpleNames0.0000.0000.001
stableFeature000
writeFASTQ0.0010.0000.001