Back to Multiple platform build/check report for BioC 3.17
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This page was generated on 2023-01-27 11:06:26 -0500 (Fri, 27 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4465
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4246
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4269
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

CHECK results for REDseq on nebbiolo1


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? 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 1626/2162HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
REDseq 1.45.0  (landing page)
Lihua Julie Zhu
Snapshot Date: 2023-01-26 14:00:20 -0500 (Thu, 26 Jan 2023)
git_url: https://git.bioconductor.org/packages/REDseq
git_branch: master
git_last_commit: 8569e52
git_last_commit_date: 2022-11-01 11:05:56 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 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 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: REDseq
Version: 1.45.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:REDseq.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings REDseq_1.45.0.tar.gz
StartedAt: 2023-01-26 23:08:44 -0500 (Thu, 26 Jan 2023)
EndedAt: 2023-01-26 23:13:56 -0500 (Thu, 26 Jan 2023)
EllapsedTime: 311.6 seconds
RetCode: 0
Status:   OK  
CheckDir: REDseq.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:REDseq.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings REDseq_1.45.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/REDseq.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘REDseq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘REDseq’ version ‘1.45.0’
* 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 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 ...
  ‘REDseq.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/REDseq.Rcheck/00check.log’
for details.



Installation output

REDseq.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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-package0.0020.0000.002
assignSeq2REsite0.2860.0200.306
binom.test.REDseq0.0090.0000.009
buildREmap4.2080.2684.485
compareREDseq0.0100.0040.014
distanceHistSeq2RE0.0170.0040.021
example.REDseq0.0000.0010.002
example.assignedREDseq0.0000.0010.002
example.map0.0000.0010.001
plotCutDistribution0.0070.0020.008
searchPattern1.9650.0962.060
summarizeByRE0.0050.0000.004
summarizeBySeq0.0040.0000.005
writeHits0.0050.0000.005