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This page was generated on 2024-06-21 13:21 -0400 (Fri, 21 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4690
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4404
kjohnson3macOS 13.6.5 Venturaarm644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4353
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 1091/2242HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LOBSTAHS 1.31.0  (landing page)
Henry Holm
Snapshot Date: 2024-06-20 14:00 -0400 (Thu, 20 Jun 2024)
git_url: https://git.bioconductor.org/packages/LOBSTAHS
git_branch: devel
git_last_commit: 305ce8d
git_last_commit_date: 2024-04-30 10:52:17 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    WARNINGS    OK  NO, package depends on 'xcms' which is only available as a source package that needs compilation


CHECK results for LOBSTAHS on nebbiolo2

To the developers/maintainers of the LOBSTAHS package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/LOBSTAHS.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: LOBSTAHS
Version: 1.31.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:LOBSTAHS.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings LOBSTAHS_1.31.0.tar.gz
StartedAt: 2024-06-21 00:30:25 -0400 (Fri, 21 Jun 2024)
EndedAt: 2024-06-21 00:36:09 -0400 (Fri, 21 Jun 2024)
EllapsedTime: 343.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: LOBSTAHS.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:LOBSTAHS.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings LOBSTAHS_1.31.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/LOBSTAHS.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* 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 ‘LOBSTAHS/DESCRIPTION’ ... OK
* this is package ‘LOBSTAHS’ version ‘1.31.0’
* 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 ‘LOBSTAHS’ can be installed ... WARNING
Found the following significant warnings:
  Warning: multiple methods tables found for ‘polarity<-’
See ‘/home/biocbuild/bbs-3.20-bioc/meat/LOBSTAHS.Rcheck/00install.out’ for details.
* 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 code 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 ... NOTE
Warning: multiple methods tables found for ‘polarity<-’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
loadLOBdbase 5.484  0.184   5.668
* 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: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/LOBSTAHS.Rcheck/00check.log’
for details.


Installation output

LOBSTAHS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL LOBSTAHS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘LOBSTAHS’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘polarity<-’ in package ‘LOBSTAHS’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: multiple methods tables found for ‘polarity<-’
** testing if installed package can be loaded from final location
Warning: multiple methods tables found for ‘polarity<-’
** testing if installed package keeps a record of temporary installation path
* DONE (LOBSTAHS)

Tests output


Example timings

LOBSTAHS.Rcheck/LOBSTAHS-Ex.timings

nameusersystemelapsed
LOBSet-class0.0010.0010.001
LOBSet0.0010.0000.002
LOBdbase-class0.0010.0000.001
LOBdbase0.0010.0000.001
doLOBscreen2.6370.1312.771
exportDBtoCSV1.4500.0561.506
extractLOBdbasedata0.3950.0360.431
generateLOBdbase000
getLOBpeaklist0.0290.0120.042
loadLOBdbase5.4840.1845.668