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CHECK report for LOBSTAHS on malbec1

This page was generated on 2020-04-15 12:11:35 -0400 (Wed, 15 Apr 2020).

Package 914/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LOBSTAHS 1.12.0
James Collins
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/LOBSTAHS
Branch: RELEASE_3_10
Last Commit: e6adc05
Last Changed Date: 2019-10-29 13:09:52 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: LOBSTAHS
Version: 1.12.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:LOBSTAHS.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings LOBSTAHS_1.12.0.tar.gz
StartedAt: 2020-04-15 03:58:15 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 04:02:14 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 239.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: LOBSTAHS.Rcheck
Warnings: 2

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:LOBSTAHS.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings LOBSTAHS_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/LOBSTAHS.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.12.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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-3.10-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    619Kb       xz
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
loadLOBdbase 13.12  0.056  13.483
* 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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/LOBSTAHS.Rcheck/00check.log’
for details.



Installation output

LOBSTAHS.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL LOBSTAHS
###
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘LOBSTAHS’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning message:
replacing previous import ‘xcms::plot’ by ‘graphics::plot’ when loading ‘CAMERA’ 
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: replacing previous import ‘xcms::plot’ by ‘graphics::plot’ when loading ‘CAMERA’
Warning: multiple methods tables found for ‘polarity<-’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘xcms::plot’ by ‘graphics::plot’ when loading ‘CAMERA’
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-class0.0000.0000.002
LOBSet0.0000.0000.003
LOBdbase-class0.0040.0000.001
LOBdbase0.0000.0000.003
doLOBscreen3.1600.0883.514
exportDBtoCSV2.5760.0122.660
extractLOBdbasedata0.5960.0040.643
generateLOBdbase000
getLOBpeaklist0.0400.0000.044
loadLOBdbase13.120 0.05613.483