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 11:35:20 -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 612/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ecolitk 1.72.0  (landing page)
Laurent Gautier
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/ecolitk
git_branch: RELEASE_3_17
git_last_commit: 8215898
git_last_commit_date: 2023-04-25 09:39:36 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for ecolitk on nebbiolo1


To the developers/maintainers of the ecolitk package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ecolitk.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: ecolitk
Version: 1.72.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ecolitk.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings ecolitk_1.72.0.tar.gz
StartedAt: 2023-10-15 21:01:46 -0400 (Sun, 15 Oct 2023)
EndedAt: 2023-10-15 21:02:35 -0400 (Sun, 15 Oct 2023)
EllapsedTime: 49.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ecolitk.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ecolitk.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings ecolitk_1.72.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ecolitk.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 ‘ecolitk/DESCRIPTION’ ... OK
* this is package ‘ecolitk’ version ‘1.72.0’
* 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 ‘ecolitk’ can be installed ... WARNING
Found the following significant warnings:
  Note: possible error in 'strsplit(line, "\t", ': unused argument (extended = TRUE) 
See ‘/home/biocbuild/bbs-3.17-bioc/meat/ecolitk.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* 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 ... NOTE
'library' or 'require' call to ‘graph’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.buildGENEPRODFUN: possible error in strsplit(line, "\t", extended =
  TRUE): unused argument (extended = TRUE)
* checking Rd files ... NOTE
prepare_Rd: multiFun.Rd:16-18: Dropping empty section \details
prepare_Rd: polar2xy.Rd:28-33: Dropping empty section \value
prepare_Rd: polygonChrom.Rd:59: Dropping empty section \seealso
prepare_Rd: wstringapply.Rd:24-25: Dropping empty section \examples
* 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 ...
  ‘ecolitk.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/ecolitk.Rcheck/00check.log’
for details.



Installation output

ecolitk.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘ecolitk’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
Note: possible error in 'strsplit(line, "\t", ': unused argument (extended = TRUE) 
** 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 (ecolitk)

Tests output


Example timings

ecolitk.Rcheck/ecolitk-Ex.timings

nameusersystemelapsed
ecoli.data0.1020.0120.115
ecoligenome.operon0.1040.0040.108
linkedmultiget0.0510.0000.051
multiFun000
pointsCircle0.0590.0080.067
polar2xy0.0190.0000.019
polygonChrom0.0520.0000.053