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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:LOBSTAHS.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings LOBSTAHS_1.35.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/LOBSTAHS.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘LOBSTAHS/DESCRIPTION’ ... OK
* this is package ‘LOBSTAHS’ version ‘1.35.0’
* 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 ... OK
* 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 ... 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  LOBSet-class.Rd: xsAnnotate-class
  LOBSet.Rd: xsAnnotate-class
  doLOBscreen.Rd: xsAnnotate-class, xcmsSet-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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘LOBSTAHS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: loadLOBdbase
> ### Title: Import and reconstruct LOBdbase from a text file
> ### Aliases: loadLOBdbase
> ### Keywords: methods
> 
> ### ** Examples
> 
> ## save the default negative mode database as a .csv file
> 
> data(default.LOBdbase)
> 
> neg.DB = default.LOBdbase$negative
> 
> fname = paste0("LOBSTAHS_lipid-oxy_DB_",
+                strtrim(as.character(polarity(neg.DB)),3),".csv")
> 
> exportmat = data.frame(frag_ID(neg.DB),
+                          mz(neg.DB),
+                          exact_parent_neutral_mass(neg.DB),
+                          as.character(lipid_class(neg.DB)),
+                          as.character(species(neg.DB)),
+                          as.character(adduct(neg.DB)),
+                          as.character(adduct_rank(neg.DB)),
+                          FA_total_no_C(neg.DB),
+                          FA_total_no_DB(neg.DB),
+                          degree_oxidation(neg.DB),
+                          parent_elem_formula(neg.DB),
+                          parent_compound_name(neg.DB),
+                          stringsAsFactors = FALSE)
> 
> colnames(exportmat) = c("frag_ID","mz","exact_parent_neutral_mass",
+                         "lipid_class","species","adduct","adduct_rank",
+                         "FA_total_no_C","FA_total_no_DB","degree_oxidation",
+                         "parent_elem_formula","parent_compound_name")
> 
> write.csv(exportmat, fname)
> 
> ## reimport it
> 
> neg.DB.reimported = loadLOBdbase("LOBSTAHS_lipid-oxy_DB_neg.csv",
+                                  polarity = "negative",
+                                  num_compounds = NULL)
Error in grepl(as.character(pattern), x, ignore.case, FALSE, perl, fixed,  : 
  NA in coercion to boolean
Calls: loadLOBdbase ... rowSums -> is.data.frame -> sapply -> lapply -> FUN
Execution halted
* 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 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/LOBSTAHS.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL LOBSTAHS
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘LOBSTAHS’ ...
** this is package ‘LOBSTAHS’ version ‘1.35.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (LOBSTAHS)