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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GenomeInfoDb.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings GenomeInfoDb_1.35.15.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/GenomeInfoDb.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘GenomeInfoDb/DESCRIPTION’ ... OK
* this is package ‘GenomeInfoDb’ version ‘1.35.15’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘GenomeInfoDb’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
* 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    NEW FEATURES
  Cannot process chunk/lines:
    SIGNIFICANT USER-VISIBLE CHANGES
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘GenomeInfoDb-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: seqlevelsStyle
> ### Title: Conveniently rename the seqlevels of an object according to a
> ###   given style
> ### Aliases: seqlevelsStyle seqlevelsStyle<- seqlevelsStyle,ANY-method
> ###   seqlevelsStyle<-,ANY-method seqlevelsStyle,Seqinfo-method
> ###   seqlevelsStyle<-,Seqinfo-method seqlevelsStyle,character-method
> ###   seqlevelsStyle<-,character-method genomeStyles extractSeqlevels
> ###   extractSeqlevelsByGroup mapSeqlevels seqlevelsInGroup
> 
> ### ** Examples
> 
> ## ---------------------------------------------------------------------
> ## seqlevelsStyle() getter and setter
> ## ---------------------------------------------------------------------
> 
> ## On a character vector:
> x <- paste0("chr", 1:5)
> seqlevelsStyle(x)
[1] "UCSC"
> seqlevelsStyle(x) <- "NCBI"
> x
[1] "1" "2" "3" "4" "5"
> 
> ## On a GRanges object:
> library(GenomicRanges)
> gr <- GRanges(rep(c("chr2", "chr3", "chrM"), 2), IRanges(1:6, 10))
> 
> seqlevelsStyle(gr)
[1] "UCSC"
> seqlevelsStyle(gr) <- "NCBI"
> gr
GRanges object with 6 ranges and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]        2      1-10      *
  [2]        3      2-10      *
  [3]       MT      3-10      *
  [4]        2      4-10      *
  [5]        3      5-10      *
  [6]       MT      6-10      *
  -------
  seqinfo: 3 sequences from an unspecified genome; no seqlengths
> 
> seqlevelsStyle(gr)
[1] "NCBI"    "Ensembl"
> seqlevelsStyle(gr) <- "dbSNP"
> gr
GRanges object with 6 ranges and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]      ch2      1-10      *
  [2]      ch3      2-10      *
  [3]     chMT      3-10      *
  [4]      ch2      4-10      *
  [5]      ch3      5-10      *
  [6]     chMT      6-10      *
  -------
  seqinfo: 3 sequences from an unspecified genome; no seqlengths
> 
> seqlevelsStyle(gr)
[1] "dbSNP"
> seqlevelsStyle(gr) <- "UCSC"
> gr
GRanges object with 6 ranges and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr2      1-10      *
  [2]     chr3      2-10      *
  [3]     chrM      3-10      *
  [4]     chr2      4-10      *
  [5]     chr3      5-10      *
  [6]     chrM      6-10      *
  -------
  seqinfo: 3 sequences from an unspecified genome; no seqlengths
> 
> ## In general the seqlevelsStyle() setter doesn't know how to rename
> ## scaffolds. However, if the genome is specified, it's very likely
> ## that seqlevelsStyle() will be able to take advantage of that:
> gr <- GRanges(rep(c("2", "Y", "Hs6_111610_36"), 2), IRanges(1:6, 10))
> genome(gr) <- "NCBI36"
> seqlevelsStyle(gr) <- "UCSC"
> gr
GRanges object with 6 ranges and 0 metadata columns:
           seqnames    ranges strand
              <Rle> <IRanges>  <Rle>
  [1]          chr2      1-10      *
  [2]          chrY      2-10      *
  [3] chr6_cox_hap1      3-10      *
  [4]          chr2      4-10      *
  [5]          chrY      5-10      *
  [6] chr6_cox_hap1      6-10      *
  -------
  seqinfo: 3 sequences from hg18 genome; no seqlengths
> 
> ## On a Seqinfo object:
> si <- si0 <- Seqinfo(genome="apiMel2")
> si
Seqinfo object with 17 sequences from apiMel2 genome:
  seqnames seqlengths isCircular  genome
  Group1     25433307      FALSE apiMel2
  Group2     14233499      FALSE apiMel2
  Group3     11790680      FALSE apiMel2
  Group4     10665743      FALSE apiMel2
  Group5     13312070      FALSE apiMel2
  ...             ...        ...     ...
  Group13     8846036      FALSE apiMel2
  Group14     8017760      FALSE apiMel2
  Group15     7326077      FALSE apiMel2
  Group16     5608962      FALSE apiMel2
  GroupUn   321143811      FALSE apiMel2
> seqlevelsStyle(si) <- "NCBI"
Warning in (function (seqlevels, genome, new_style)  :
  cannot switch some apiMel2's seqlevels from UCSC to NCBI style
> si
Seqinfo object with 17 sequences from 2 genomes (Amel_2.0, apiMel2):
  seqnames seqlengths isCircular   genome
  LG1        25433307      FALSE Amel_2.0
  LG2        14233499      FALSE Amel_2.0
  LG3        11790680      FALSE Amel_2.0
  LG4        10665743      FALSE Amel_2.0
  LG5        13312070      FALSE Amel_2.0
  ...             ...        ...      ...
  LG13        8846036      FALSE Amel_2.0
  LG14        8017760      FALSE Amel_2.0
  LG15        7326077      FALSE Amel_2.0
  LG16        5608962      FALSE Amel_2.0
  GroupUn   321143811      FALSE  apiMel2
> seqlevelsStyle(si) <- "RefSeq"
Warning in (function (seqlevels, genome, new_style)  :
  cannot switch apiMel2's seqlevels from UCSC to RefSeq style
> si
Seqinfo object with 17 sequences from 2 genomes (Amel_2.0, apiMel2):
  seqnames    seqlengths isCircular   genome
  NC_007070.1   25433307      FALSE Amel_2.0
  NC_007071.1   14233499      FALSE Amel_2.0
  NC_007072.1   11790680      FALSE Amel_2.0
  NC_007073.1   10665743      FALSE Amel_2.0
  NC_007074.1   13312070      FALSE Amel_2.0
  ...                ...        ...      ...
  NC_007082.1    8846036      FALSE Amel_2.0
  NC_007083.1    8017760      FALSE Amel_2.0
  NC_007084.1    7326077      FALSE Amel_2.0
  NC_007085.1    5608962      FALSE Amel_2.0
  GroupUn      321143811      FALSE  apiMel2
> seqlevelsStyle(si) <- "UCSC"
> stopifnot(identical(si0, si))
> 
> si <- si0 <- Seqinfo(genome="WBcel235")
> si
Seqinfo object with 7 sequences (1 circular) from WBcel235 genome:
  seqnames seqlengths isCircular   genome
  I          15072434      FALSE WBcel235
  II         15279421      FALSE WBcel235
  III        13783801      FALSE WBcel235
  IV         17493829      FALSE WBcel235
  V          20924180      FALSE WBcel235
  X          17718942      FALSE WBcel235
  MT            13794       TRUE WBcel235
> seqlevelsStyle(si) <- "UCSC"
> si
Seqinfo object with 7 sequences (1 circular) from ce11 genome:
  seqnames seqlengths isCircular genome
  chrI       15072434      FALSE   ce11
  chrII      15279421      FALSE   ce11
  chrIII     13783801      FALSE   ce11
  chrIV      17493829      FALSE   ce11
  chrV       20924180      FALSE   ce11
  chrX       17718942      FALSE   ce11
  chrM          13794       TRUE   ce11
> seqlevelsStyle(si) <- "RefSeq"
> si
Seqinfo object with 7 sequences (1 circular) from WBcel235 genome:
  seqnames     seqlengths isCircular   genome
  NC_003279.8    15072434      FALSE WBcel235
  NC_003280.10   15279421      FALSE WBcel235
  NC_003281.10   13783801      FALSE WBcel235
  NC_003282.8    17493829      FALSE WBcel235
  NC_003283.11   20924180      FALSE WBcel235
  NC_003284.9    17718942      FALSE WBcel235
  NC_001328.1       13794       TRUE WBcel235
> seqlevelsStyle(si) <- "NCBI"
> stopifnot(identical(si0, si))
> 
> si <- Seqinfo(genome="macFas5")
> si
Seqinfo object with 7601 sequences (1 circular) from macFas5 genome:
  seqnames       seqlengths isCircular  genome
  chr1            227556264      FALSE macFas5
  chr2            192460366      FALSE macFas5
  chr3            192294377      FALSE macFas5
  chr4            170955103      FALSE macFas5
  chr5            189454096      FALSE macFas5
  ...                   ...        ...     ...
  chrUn_KE147191       5581      FALSE macFas5
  chrUn_KE147192      21004      FALSE macFas5
  chrUn_KE147193       5184      FALSE macFas5
  chrUn_KE147194       8082      FALSE macFas5
  chrUn_KE147195       7181      FALSE macFas5
> seqlevelsStyle(si) <- "NCBI"
Error in download.file(url, destfile, quiet = TRUE) : 
  download from 'https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/364/345/GCA_000364345.1_Macaca_fascicularis_5.0/GCA_000364345.1_Macaca_fascicularis_5.0_assembly_report.txt' failed
Calls: seqlevelsStyle<- ... .fetch_assembly_report_from_url -> fetch_table_from_url
Execution halted
* 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 download.file(url, destfile, quiet = TRUE) : 
    download from 'https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/195/GCF_000002195.1_Amel_2.0/GCF_000002195.1_Amel_2.0_assembly_report.txt' failed
  
  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 ...
  ‘Accept-organism-for-GenomeInfoDb.Rmd’ using ‘UTF-8’... OK
  ‘GenomeInfoDb.Rnw’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/GenomeInfoDb.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL GenomeInfoDb
###
##############################################################################
##############################################################################


* installing to library ‘/home/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) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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
[1] TRUE
> GenomeInfoDb:::.test()
Timing stopped at: 0.938 0.217 224
Error in download.file(url, destfile, quiet = TRUE) : 
  download from 'https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/195/GCF_000002195.1_Amel_2.0/GCF_000002195.1_Amel_2.0_assembly_report.txt' failed


RUNIT TEST PROTOCOL -- Tue Feb  7 02:37:27 2023 
*********************************************** 
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 download.file(url, destfile, quiet = TRUE) : 
  download from 'https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/195/GCF_000002195.1_Amel_2.0/GCF_000002195.1_Amel_2.0_assembly_report.txt' failed

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