* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/utr.annotation.Rcheck’
* using R Under development (unstable) (2024-02-12 r85893)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 13.2.1 20231011 (Red Hat 13.2.1-4)
    GNU Fortran (GCC) 13.2.1 20231011 (Red Hat 13.2.1-4)
* running under: Fedora Linux 38 (Workstation Edition)
* using session charset: UTF-8
* checking for file ‘utr.annotation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘utr.annotation’ version ‘1.0.4’
* package encoding: UTF-8
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘utr.annotation’ can be installed ... [41s/41s] 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 ... [13s/13s] OK
* checking whether the package can be loaded with stated dependencies ... [13s/13s] OK
* checking whether the package can be unloaded cleanly ... [13s/13s] OK
* checking whether the namespace can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the namespace can be unloaded cleanly ... [13s/13s] OK
* checking loading without being on the library search path ... [13s/13s] OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  'parallel' 'xml2'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [56s/56s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
Documented arguments not in \usage in Rd file 'countDNAPatternInAlt.Rd':
  ‘trascriptsTable’

Documented arguments not in \usage in Rd file 'countDNAPatternInAltOneVariant.Rd':
  ‘trascriptsTable’

Documented arguments not in \usage in Rd file 'getAltSequence.Rd':
  ‘trascriptsTable’

Documented arguments not in \usage in Rd file 'getCodonInAlt.Rd':
  ‘trascriptsTable’ ‘codonPositionsColumnn’

Documented arguments not in \usage in Rd file 'getCodonInAltOneVariant.Rd':
  ‘trascriptsTable’ ‘codonPositionsColumnn’

Documented arguments not in \usage in Rd file 'getTSSKozakOneVariant.Rd':
  ‘variantsTable’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [12s/12s] OK
* checking examples with --run-donttest ... [97s/102s] ERROR
Running examples in ‘utr.annotation-Ex.R’ failed
The error most likely occurred in:

> ### Name: initUTRAnnotation
> ### Title: Query transcripts regions and sequences from Ensembl database
> ### Aliases: initUTRAnnotation
> 
> ### ** Examples
> 
> ## No test: 
> test_variant_file <- system.file("extdata", "variants_sample.csv", package = "utr.annotation")
> initUTRAnnotation(variantFile = test_variant_file,
+                   species = "human",
+                   ensemblVersion = 93,
+                   dataDir = "test_db")
Fetching data ... Warning in readGFFAsGRanges(resource, version = version, colnames = colnames,  :
  cannot set the seqlengths or circularity flags on the GRanges object to
  return because the sequence names in the GTF or GFF file are in
  disagreement with the sequence names implied by the genome assembly
  (GRCh38) specified via the 'genome' argument
OK
  -------------
Proceeding to create the database.
Processing genes ... 
Warning in ensDbFromGRanges(gff, outfile = outfile, path = path, organism = orgFromAH,  :
   I'm missing column(s): 'entrezid'. The corresponding database column(s) will be empty!
 Attribute availability:
  o gene_id ... OK
  o gene_name ... OK
  o entrezid ... Nope
  o gene_biotype ... OK
OK
Processing transcripts ... 
 Attribute availability:
  o transcript_id ... OK
  o gene_id ... OK
  o transcript_biotype ... OK
  o transcript_name ... OK
OK
Processing exons ... OK
Processing chromosomes ... Fetch seqlengths from ensembl ... OK
Processing metadata ... OK
Generating index ... OK
  -------------
Verifying validity of the information in the database:
Checking transcripts ... OK
Checking exons ... OK
Warning: executing %dopar% sequentially: no parallel backend registered
Warning: call dbDisconnect() when finished working with a connection
Error: Specified Ensembl version is not available.
Use listEnsemblArchives() to view available versions.
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [11s/11s]
 [12s/12s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [23s/23s] OK
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
  ‘test_db’
* checking for detritus in the temp directory ... OK
* checking for new files in some other directories ... OK
* DONE

Status: 1 ERROR, 3 NOTEs
See
  ‘/data/blackswan/ripley/R/packages/tests-devel/utr.annotation.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 7:36.28, 415.67 + 33.90