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### Running command:
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###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:customProDB.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings customProDB_1.41.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/customProDB.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘customProDB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘customProDB’ version ‘1.41.0’
* 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 ‘customProDB’ 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 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 ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘biomaRt:::martBM’ ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Bed2Range: no visible binding for global variable ‘V5’
OutputNovelJun: no visible binding for global variable ‘jun_type’
OutputVarproseq: no visible binding for global variable ‘genename’
OutputVarproseq: no visible binding for global variable ‘txname’
OutputVarproseq: no visible binding for global variable ‘proname’
OutputVarproseq: no visible binding for global variable ‘aaref’
OutputVarproseq: no visible binding for global variable ‘aapos’
OutputVarproseq: no visible binding for global variable ‘aavar’
OutputVarproseq: no visible binding for global variable ‘rsid’
OutputVarproseq_single: no visible binding for global variable
  ‘genename’
OutputVarproseq_single: no visible binding for global variable ‘txname’
OutputVarproseq_single: no visible binding for global variable
  ‘proname’
OutputVarproseq_single: no visible binding for global variable ‘aaref’
OutputVarproseq_single: no visible binding for global variable ‘aapos’
OutputVarproseq_single: no visible binding for global variable ‘aavar’
OutputVarproseq_single: no visible binding for global variable ‘rsid’
Outputaberrant: no visible binding for global variable ‘pro_name’
Positionincoding: no visible binding for global variable ‘cds_start’
Positionincoding: no visible binding for global variable ‘cds_end’
PrepareAnnotationEnsembl: no visible binding for global variable
  ‘ensembl_gene_id’
PrepareAnnotationEnsembl: no visible binding for global variable
  ‘pro_name’
PrepareAnnotationEnsembl: no visible binding for global variable
  ‘chrom’
PrepareAnnotationEnsembl: no visible binding for global variable ‘name’
PrepareAnnotationEnsembl: no visible binding for global variable
  ‘alleleCount’
PrepareAnnotationEnsembl: no visible binding for global variable
  ‘alleles’
PrepareAnnotationRefseq: no visible binding for global variable ‘name’
PrepareAnnotationRefseq: no visible binding for global variable
  ‘mrnaAcc’
PrepareAnnotationRefseq: no visible binding for global variable
  ‘protAcc’
PrepareAnnotationRefseq: no visible binding for global variable
  ‘transcript’
PrepareAnnotationRefseq: no visible binding for global variable ‘chrom’
PrepareAnnotationRefseq: no visible binding for global variable
  ‘alleleCount’
PrepareAnnotationRefseq: no visible binding for global variable
  ‘alleles’
PrepareAnnotationRefseq: no visible binding for global variable
  ‘COSMIC’
Varlocation: no visible binding for global variable ‘pro_name’
Undefined global functions or variables:
  COSMIC V5 aapos aaref aavar alleleCount alleles cds_end cds_start
  chrom ensembl_gene_id genename jun_type mrnaAcc name pro_name proname
  protAcc rsid transcript txname
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
PrepareAnnotationEnsembl 5.483  0.874 283.106
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘customProDB.Rnw’ using ‘UTF-8’... failed
 ERROR
Errors in running code in vignettes:
when running code in ‘customProDB.Rnw’
  ...
> annotation_path <- tempdir()

> PrepareAnnotationRefseq(genome = "hg19", CDSfasta, 
+     pepfasta, annotation_path, dbsnp = NULL, transcript_ids = transcript_ids, 
+     splice_ma .... [TRUNCATED] 
Build TranscriptDB object (txdb.sqlite) ... 

  When sourcing ‘customProDB.R’:
Error: UCSC table "refGene" does not exist for genome "hg19", sorry
Execution halted

* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
--- re-building ‘customProDB.Rnw’ using Sweave
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:utils’:

    findMatches

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb

Error: processing vignette 'customProDB.Rnw' failed with diagnostics:
 chunk 1 (label = dbSNPversion) 
Error in .local(.Object, ...) : Failed to obtain 'hguid' cookie

--- failed re-building ‘customProDB.Rnw’

SUMMARY: processing the following file failed:
  ‘customProDB.Rnw’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/customProDB.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL customProDB
###
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* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘customProDB’ ...
** using staged installation
** R
** 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 (customProDB)