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This page was generated on 2021-10-14 12:06:19 -0400 (Thu, 14 Oct 2021).

CHECK results for REDseq on merida1

To the developers/maintainers of the REDseq package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/REDseq.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 1549/2056HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
REDseq 1.39.0  (landing page)
Lihua Julie Zhu
Snapshot Date: 2021-10-13 14:50:09 -0400 (Wed, 13 Oct 2021)
git_url: https://git.bioconductor.org/packages/REDseq
git_branch: master
git_last_commit: 515e072
git_last_commit_date: 2021-05-19 11:48:43 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: REDseq
Version: 1.39.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:REDseq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings REDseq_1.39.0.tar.gz
StartedAt: 2021-10-14 07:22:37 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 07:28:42 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 364.9 seconds
RetCode: 0
Status:   OK  
CheckDir: REDseq.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:REDseq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings REDseq_1.39.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/REDseq.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘REDseq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘REDseq’ version ‘1.39.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'BiocGenerics', 'BSgenome.Celegans.UCSC.ce2', 'multtest',
  'Biostrings', 'BSgenome', 'ChIPpeakAnno'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘REDseq’ 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
buildREmap: no visible global function definition for 'start<-'
Undefined global functions or variables:
  start<-
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
buildREmap 5.419  0.166   5.729
* 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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/REDseq.Rcheck/00check.log’
for details.



Installation output

REDseq.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL REDseq
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘REDseq’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'IRanges' for requests: '%in%', 'rep.int' when loading 'REDseq'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package 'IRanges' for requests: '%in%', 'rep.int' when loading 'REDseq'
** testing if installed package can be loaded from final location
No methods found in package 'IRanges' for requests: '%in%', 'rep.int' when loading 'REDseq'
** testing if installed package keeps a record of temporary installation path
* DONE (REDseq)

Tests output


Example timings

REDseq.Rcheck/REDseq-Ex.timings

nameusersystemelapsed
REDseq-package0.0050.0010.005
assignSeq2REsite0.4720.0190.490
binom.test.REDseq0.0100.0010.011
buildREmap5.4190.1665.729
compareREDseq0.0240.0010.025
distanceHistSeq2RE0.0310.0040.036
example.REDseq0.0010.0020.003
example.assignedREDseq0.0010.0020.003
example.map0.0010.0020.003
plotCutDistribution0.0140.0050.019
searchPattern3.0600.0673.131
summarizeByRE0.0060.0040.010
summarizeBySeq0.0040.0030.007
writeHits0.0100.0010.011