Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

This page was generated on 2024-03-04 11:37:08 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
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 1692/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
REDseq 1.49.0  (landing page)
Lihua Julie Zhu
Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/REDseq
git_branch: devel
git_last_commit: 8a499f7
git_last_commit_date: 2023-10-24 09:46:52 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 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 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for REDseq on nebbiolo1


To the developers/maintainers of the REDseq package:
- 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 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: REDseq
Version: 1.49.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:REDseq.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings REDseq_1.49.0.tar.gz
StartedAt: 2024-03-02 01:26:34 -0500 (Sat, 02 Mar 2024)
EndedAt: 2024-03-02 01:32:09 -0500 (Sat, 02 Mar 2024)
EllapsedTime: 334.5 seconds
RetCode: 0
Status:   OK  
CheckDir: REDseq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:REDseq.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings REDseq_1.49.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/REDseq.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘REDseq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘REDseq’ version ‘1.49.0’
* 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 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
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 ... NOTE
Auto-generated content requiring editing in Rd file 'REDseq-package.Rd':
  \details: ‘...o use the package, including the most important functions ~~’
* 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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/REDseq.Rcheck/00check.log’
for details.



Installation output

REDseq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL REDseq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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
assignSeq2REsite0.2590.0170.275
binom.test.REDseq0.010.000.01
buildREmap2.8810.1633.046
compareREDseq0.0150.0000.015
distanceHistSeq2RE0.0230.0000.023
example.REDseq0.0000.0020.002
example.assignedREDseq0.0000.0010.002
example.map0.0010.0000.001
plotCutDistribution0.0050.0040.010
searchPattern2.0900.2562.346
summarizeByRE0.0050.0010.005
summarizeBySeq0.0020.0020.005
writeHits0.0040.0020.006