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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomeInfoDb.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings GenomeInfoDb_1.35.9.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/GenomeInfoDb.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'GenomeInfoDb/DESCRIPTION' ... OK
* this is package 'GenomeInfoDb' version '1.35.9'
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'GenomeInfoDb' 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 dependencies in R code ... NOTE
Unexported object imported by a ':::' call: 'utils:::.roman2numeric'
  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 ... OK
* checking Rd files ... WARNING
checkRd: (5) GenomeDescription-class.Rd:53-58: \item in \describe must have non-empty label
checkRd: (5) GenomeDescription-class.Rd:59-63: \item in \describe must have non-empty label
checkRd: (5) GenomeDescription-class.Rd:64-70: \item in \describe must have non-empty label
checkRd: (5) GenomeDescription-class.Rd:71-75: \item in \describe must have non-empty label
checkRd: (5) GenomeDescription-class.Rd:76-79: \item in \describe must have non-empty label
checkRd: (5) GenomeDescription-class.Rd:80-88: \item in \describe must have non-empty label
checkRd: (5) Seqinfo-class.Rd:83-93: \item in \describe must have non-empty label
checkRd: (5) Seqinfo-class.Rd:101-104: \item in \describe must have non-empty label
checkRd: (5) Seqinfo-class.Rd:105-115: \item in \describe must have non-empty label
checkRd: (5) Seqinfo-class.Rd:116-119: \item in \describe must have non-empty label
checkRd: (5) Seqinfo-class.Rd:120-123: \item in \describe must have non-empty label
checkRd: (5) Seqinfo-class.Rd:124-149: \item in \describe must have non-empty label
checkRd: (5) Seqinfo-class.Rd:150-153: \item in \describe must have non-empty label
checkRd: (5) Seqinfo-class.Rd:154-157: \item in \describe must have non-empty label
checkRd: (5) Seqinfo-class.Rd:158-162: \item in \describe must have non-empty label
checkRd: (5) Seqinfo-class.Rd:170-178: \item in \describe must have non-empty label
checkRd: (5) Seqinfo-class.Rd:186-189: \item in \describe must have non-empty label
checkRd: (5) Seqinfo-class.Rd:226-249: \item in \describe must have non-empty label
checkRd: (5) Seqinfo-class.Rd:250-256: \item in \describe must have non-empty label
checkRd: (5) Seqinfo-class.Rd:257-262: \item in \describe must have non-empty label
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
loadTaxonomyDb          6.81   0.16    7.09
GenomeDescription-class 5.50   0.23    5.75
getChromInfoFromEnsembl 0.39   0.13   28.18
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'run_unitTests.R'
 ERROR
Running the tests in 'tests/run_unitTests.R' failed.
Last 13 lines of output:
  1 Test Suite : 
  GenomeInfoDb RUnit Tests - 21 test functions, 1 error, 0 failures
  ERROR in test_seqlevelsStyle_Seqinfo: Error in .format_NCBI_chrom_info(assembly_report, circ_seqs = circ_seqs) : 
    is_primary_key(sequence_name) is not TRUE
  
  Test files with failing tests
  
     test_seqlevelsStyle.R 
       test_seqlevelsStyle_Seqinfo 
  
  
  Error in BiocGenerics:::testPackage("GenomeInfoDb") : 
    unit tests failed for package GenomeInfoDb
  Calls: <Anonymous> -> <Anonymous>
  Execution halted
* 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: 1 ERROR, 1 WARNING, 1 NOTE
See
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/GenomeInfoDb.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL GenomeInfoDb
###
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'GenomeInfoDb' ...
** 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 (GenomeInfoDb)

R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require("GenomeInfoDb") || stop("unable to load GenomeInfoDb package")
Loading required package: GenomeInfoDb
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
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

[1] TRUE
> GenomeInfoDb:::.test()
Timing stopped at: 15.03 1.49 20.05
Error in .format_NCBI_chrom_info(assembly_report, circ_seqs = circ_seqs) : 
  is_primary_key(sequence_name) is not TRUE
In addition: Warning messages:
1: In (function (seqlevels, genome, new_style)  :
  cannot switch some of apiMel2's seqlevels from UCSC to NCBI style
2: In (function (seqlevels, genome, new_style)  :
  cannot switch some of Amel_2.0's seqlevels from NCBI to UCSC style
3: In (function (seqlevels, genome, new_style)  :
  cannot switch some of bosTau7's seqlevels from UCSC to NCBI style
4: In (function (seqlevels, genome, new_style)  :
  cannot switch some of Btau_4.6.1's seqlevels from NCBI to UCSC style
5: In getChromInfoFromNCBI(genome, as.Seqinfo = TRUE) :
  Assembly Bos_taurus_UMD_3.1.1 is mapped to more than one assembly
  (GCF_000003055.5, GCA_000003055.5). The first one was selected.
6: In (function (seqlevels, genome, new_style)  :
  cannot switch some of ARS-UCD1.2's seqlevels from NCBI to UCSC style


RUNIT TEST PROTOCOL -- Thu Dec 29 00:06:04 2022 
*********************************************** 
Number of test functions: 21 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
GenomeInfoDb RUnit Tests - 21 test functions, 1 error, 0 failures
ERROR in test_seqlevelsStyle_Seqinfo: Error in .format_NCBI_chrom_info(assembly_report, circ_seqs = circ_seqs) : 
  is_primary_key(sequence_name) is not TRUE

Test files with failing tests

   test_seqlevelsStyle.R 
     test_seqlevelsStyle_Seqinfo 


Error in BiocGenerics:::testPackage("GenomeInfoDb") : 
  unit tests failed for package GenomeInfoDb
Calls: <Anonymous> -> <Anonymous>
Execution halted