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This page was generated on 2021-08-03 12:05:46 -0400 (Tue, 03 Aug 2021).

CHECK results for LOBSTAHS on nebbiolo2

To the developers/maintainers of the LOBSTAHS package:
- Please 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 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 979/2015HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LOBSTAHS 1.19.0  (landing page)
James Collins
Snapshot Date: 2021-08-02 14:50:09 -0400 (Mon, 02 Aug 2021)
URL: https://git.bioconductor.org/packages/LOBSTAHS
Branch: master
Last Commit: 3deb41f
Last Changed Date: 2021-05-19 12:21:39 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  NO, package depends on 'xcms' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: LOBSTAHS
Version: 1.19.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:LOBSTAHS.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings LOBSTAHS_1.19.0.tar.gz
StartedAt: 2021-08-02 20:08:24 -0400 (Mon, 02 Aug 2021)
EndedAt: 2021-08-02 20:12:06 -0400 (Mon, 02 Aug 2021)
EllapsedTime: 221.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: LOBSTAHS.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:LOBSTAHS.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings LOBSTAHS_1.19.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/LOBSTAHS.Rcheck’
* using R version 4.1.0 beta (2021-05-03 r80259)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LOBSTAHS/DESCRIPTION’ ... OK
* this is package ‘LOBSTAHS’ version ‘1.19.0’
* 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 ‘bin’
  Warning: multiple methods tables found for ‘polarity<-’
See ‘/home/biocbuild/bbs-3.14-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 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 ... 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 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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                         old_size new_size compress
  default.LOBdbase.RData    2.0Mb    622Kb       xz
* 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 5.629  0.396   6.025
* 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 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/LOBSTAHS.Rcheck/00check.log’
for details.



Installation output

LOBSTAHS.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL LOBSTAHS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘LOBSTAHS’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning message:
multiple methods tables found for ‘bin’ 
Creating a new generic function for ‘polarity<-’ in package ‘LOBSTAHS’
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘LOBSTAHS.Rmd’ using ‘UTF-8’ 
** testing if installed package can be loaded from temporary location
Warning: multiple methods tables found for ‘bin’
Warning: multiple methods tables found for ‘polarity<-’
** testing if installed package can be loaded from final location
Warning: multiple methods tables found for ‘bin’
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-class0.0010.0000.001
LOBSet0.0010.0000.001
LOBdbase-class0.0010.0000.001
LOBdbase0.0020.0000.002
doLOBscreen2.5700.0722.644
exportDBtoCSV1.3890.0321.420
extractLOBdbasedata0.3510.0030.355
generateLOBdbase000
getLOBpeaklist0.0410.0000.041
loadLOBdbase5.6290.3966.025