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

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### Running command:
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###   /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.

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### Running command:
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###   /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)

name	user	system	elapsed
LOBSet-class	0.000	0.000	0.002
LOBSet	0.000	0.000	0.003
LOBdbase-class	0.004	0.000	0.001
LOBdbase	0.000	0.000	0.003
doLOBscreen	3.160	0.088	3.514
exportDBtoCSV	2.576	0.012	2.660
extractLOBdbasedata	0.596	0.004	0.643
generateLOBdbase	0	0	0
getLOBpeaklist	0.040	0.000	0.044
loadLOBdbase	13.120	0.056	13.483