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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:PtH2O2lipids.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings PtH2O2lipids_1.31.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-data-experiment/meat/PtH2O2lipids.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘PtH2O2lipids/DESCRIPTION’ ... OK
* this is package ‘PtH2O2lipids’ version ‘1.31.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘PtH2O2lipids’ can be installed ... WARNING
Found the following significant warnings:
  Warning: multiple methods tables found for ‘polarity<-’
  Warning: replacing previous import ‘xcms::polarity<-’ by ‘LOBSTAHS::polarity<-’ when loading ‘PtH2O2lipids’
See ‘/home/biocbuild/bbs-3.21-data-experiment/meat/PtH2O2lipids.Rcheck/00install.out’ for details.
* checking installed package size ... INFO
  installed size is 15.6Mb
  sub-directories of 1Mb or more:
    data  15.5Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 ... OK
* 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 ... WARNING
Missing link or links in Rd file 'PtH2O2lipids.Rd':
  ‘LOBSet-class-class’

See section 'Cross-references' in the 'Writing R Extensions' manual.

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  PtH2O2lipids.Rd: doLOBscreen, LOBSet, xsAnnotate, LOBSet-class,
    LOBSet-class-class, getLOBpeaklist, xcmsSet-class, xsAnnotate-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 examples ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-data-experiment/meat/PtH2O2lipids.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL PtH2O2lipids
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘PtH2O2lipids’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning message:
multiple methods tables found for ‘polarity<-’ 
Warning: replacing previous import ‘xcms::polarity<-’ by ‘LOBSTAHS::polarity<-’ when loading ‘PtH2O2lipids’
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Warning: multiple methods tables found for ‘polarity<-’
Warning: replacing previous import ‘xcms::polarity<-’ by ‘LOBSTAHS::polarity<-’ when loading ‘PtH2O2lipids’
** testing if installed package can be loaded from final location
Warning: multiple methods tables found for ‘polarity<-’
Warning: replacing previous import ‘xcms::polarity<-’ by ‘LOBSTAHS::polarity<-’ when loading ‘PtH2O2lipids’
** testing if installed package keeps a record of temporary installation path
* DONE (PtH2O2lipids)