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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:GenomicFeatures.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings GenomicFeatures_1.61.6.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/GenomicFeatures.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘GenomicFeatures/DESCRIPTION’ ... OK
* this is package ‘GenomicFeatures’ version ‘1.61.6’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Depends: includes the non-default packages:
  'BiocGenerics', 'S4Vectors', 'IRanges', 'Seqinfo', 'GenomicRanges',
  'AnnotationDbi'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘GenomicFeatures’ 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘AnnotationDbi:::.getMetaValue’ ‘AnnotationDbi:::.valid.colnames’
  ‘AnnotationDbi:::.valid.metadata.table’
  ‘AnnotationDbi:::.valid.table.colnames’ ‘AnnotationDbi:::dbEasyQuery’
  ‘AnnotationDbi:::dbQuery’ ‘AnnotationDbi:::smartKeys’
  ‘BiocGenerics:::testPackage’
  ‘GenomicRanges:::unsafe.transcriptLocs2refLocs’
  ‘GenomicRanges:::unsafe.transcriptWidths’
  ‘IRanges:::regroupBySupergroup’ ‘S4Vectors:::V_recycle’
  ‘S4Vectors:::decodeRle’ ‘S4Vectors:::extract_data_frame_rows’
  ‘Seqinfo:::getSeqlevelsReplacementMode’ ‘Seqinfo:::normarg_new2old’
  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 ... 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 ... ERROR
Running examples in ‘GenomicFeatures-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getPromoterSeq
> ### Title: Get gene promoter or terminator sequences
> ### Aliases: getPromoterSeq getTerminatorSeq getPromoterSeq,GRanges-method
> ###   getTerminatorSeq,GRanges-method getPromoterSeq,GRangesList-method
> ###   getTerminatorSeq,GRangesList-method
> ### Keywords: methods manip
> 
> ### ** Examples
> 
> library(TxDb.Hsapiens.UCSC.hg19.knownGene)
> library(BSgenome.Hsapiens.UCSC.hg19)
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector

Attaching package: ‘Biostrings’

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

    strsplit

Loading required package: BiocIO
Loading required package: rtracklayer
> 
> 
> ## A GRangesList object describing all the known Human transcripts grouped
> ## by gene:
> txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
> tx_by_gene <- transcriptsBy(txdb, by="gene")
> 
> e2f3 <- "1871"  # entrez geneID for a cell cycle control transcription
>                 # factor, chr6 on the plus strand
> 
> ## A GRanges object describing the three transcripts for gene 1871:
> e2f3_tx <- tx_by_gene[[e2f3]]
> 
> ## Promoter sequences for gene 1871:
> e2f3_promoter_seqs <- getPromoterSeq(e2f3_tx, Hsapiens,
+                                      upstream=40, downstream=15)
Error in mergeNamedAtomicVectors(isCircular(x), isCircular(y), what = c("sequence",  : 
  sequence chrMT has incompatible circularity flags:
  - in 'x': TRUE
  - in 'y': FALSE
Calls: getPromoterSeq ... .merge_two_Seqinfo_objects -> mergeNamedAtomicVectors
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
exonicParts                98.594  2.164 100.782
coverageByTranscript       72.633  3.645  76.287
coordinate-mapping-methods 54.316  6.444  60.906
extractTranscriptSeqs      12.236  0.191  12.447
* 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:
  
  
  Error in BiocGenerics:::testPackage("GenomicFeatures") : 
    unit tests failed for package GenomicFeatures
  Calls: <Anonymous> -> <Anonymous>
  In addition: Warning messages:
  1: In .makeTxDb_normarg_chrominfo(chrominfo) :
    genome version information is not available for this TxDb object
  2: In (function (seqlevels, genome, new_style)  :
    cannot switch some hg19's seqlevels from UCSC to NCBI style
  3: In .makeTxDb_normarg_chrominfo(chrominfo) :
    genome version information is not available for this TxDb object
  4: In (function (seqlevels, genome, new_style)  :
    cannot switch some hg19's seqlevels from UCSC to NCBI style
  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: 2 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/GenomicFeatures.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL GenomicFeatures
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘GenomicFeatures’ ...
** this is package ‘GenomicFeatures’ version ‘1.61.6’
** 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 (GenomicFeatures)

R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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("GenomicFeatures") || stop("unable to load GenomicFeatures package")
Loading required package: GenomicFeatures
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

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: Seqinfo
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

[1] TRUE
> GenomicFeatures:::.test()
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: BiocIO
Loading required package: rtracklayer
Timing stopped at: 2.193 0.086 2.279
Error in mergeNamedAtomicVectors(isCircular(x), isCircular(y), what = c("sequence",  : 
  sequence chrMT has incompatible circularity flags:
  - in 'x': TRUE
  - in 'y': FALSE
In addition: Warning messages:
1: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 7 out-of-bound ranges located on sequence chrMT. Note
  that ranges located on a sequence whose length is unknown (NA) or on a
  circular sequence are not considered out-of-bound (use seqlengths() and
  isCircular() to get the lengths and circularity flags of the underlying
  sequences). You can use trim() to trim these ranges. See
  ?`trim,GenomicRanges-method` for more information.
2: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 5 out-of-bound ranges located on sequence chrMT. Note
  that ranges located on a sequence whose length is unknown (NA) or on a
  circular sequence are not considered out-of-bound (use seqlengths() and
  isCircular() to get the lengths and circularity flags of the underlying
  sequences). You can use trim() to trim these ranges. See
  ?`trim,GenomicRanges-method` for more information.
3: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 3 out-of-bound ranges located on sequences a, b, and
  c. Note that ranges located on a sequence whose length is unknown (NA) or on
  a circular sequence are not considered out-of-bound (use seqlengths() and
  isCircular() to get the lengths and circularity flags of the underlying
  sequences). You can use trim() to trim these ranges. See
  ?`trim,GenomicRanges-method` for more information.
4: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 1 out-of-bound range located on sequence c. Note that
  ranges located on a sequence whose length is unknown (NA) or on a circular
  sequence are not considered out-of-bound (use seqlengths() and isCircular()
  to get the lengths and circularity flags of the underlying sequences). You
  can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for
  more information.
5: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 1 out-of-bound range located on sequence c. Note that
  ranges located on a sequence whose length is unknown (NA) or on a circular
  sequence are not considered out-of-bound (use seqlengths() and isCircular()
  to get the lengths and circularity flags of the underlying sequences). You
  can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for
  more information.
6: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 4 out-of-bound ranges located on sequences 1, 2, 3,
  and 4. Note that ranges located on a sequence whose length is unknown (NA) or
  on a circular sequence are not considered out-of-bound (use seqlengths() and
  isCircular() to get the lengths and circularity flags of the underlying
  sequences). You can use trim() to trim these ranges. See
  ?`trim,GenomicRanges-method` for more information.
Timing stopped at: 1.257 0.031 1.288
Error in mergeNamedAtomicVectors(isCircular(x), isCircular(y), what = c("sequence",  : 
  sequence chrMT has incompatible circularity flags:
  - in 'x': TRUE
  - in 'y': FALSE

Attaching package: 'txdbmaker'

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

    UCSCFeatureDbTableSchema, browseUCSCtrack, getChromInfoFromBiomart,
    makeFDbPackageFromUCSC, makeFeatureDbFromUCSC, makePackageName,
    makeTxDb, makeTxDbFromBiomart, makeTxDbFromEnsembl,
    makeTxDbFromGFF, makeTxDbFromGRanges, makeTxDbFromUCSC,
    makeTxDbPackage, makeTxDbPackageFromBiomart,
    makeTxDbPackageFromUCSC, supportedMiRBaseBuildValues,
    supportedUCSCFeatureDbTables, supportedUCSCFeatureDbTracks,
    supportedUCSCtables

Timing stopped at: 0.007 0 0.007
Error in checkIdentical(res, exp) : FALSE 
 
In addition: Warning messages:
1: In .get_cds_IDX(mcols0$type, mcols0$phase) :
  The "phase" metadata column contains non-NA values for features of type
  stop_codon. This information was ignored.
2: In .makeTxDb_normarg_chrominfo(chrominfo) :
  genome version information is not available for this TxDb object
Timing stopped at: 0.807 0.206 1.014
Error in checkTrue("uc001aaa.3" %in% k1) : Test not TRUE

Timing stopped at: 0.013 0 0.013
Error in checkTrue(length(res) == 21, length(unique(unlist(res2)))) : 
  Test not TRUE
22
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK


RUNIT TEST PROTOCOL -- Thu Oct  9 00:45:51 2025 
*********************************************** 
Number of test functions: 67 
Number of errors: 2 
Number of failures: 3 

 
1 Test Suite : 
GenomicFeatures RUnit Tests - 67 test functions, 2 errors, 3 failures
ERROR in test_GRangesBSgenomeHumanGetPromoterSeq: Error in mergeNamedAtomicVectors(isCircular(x), isCircular(y), what = c("sequence",  : 
  sequence chrMT has incompatible circularity flags:
  - in 'x': TRUE
  - in 'y': FALSE
ERROR in test_GRangesListBSgenomeHumanGetPromoterSeq: Error in mergeNamedAtomicVectors(isCircular(x), isCircular(y), what = c("sequence",  : 
  sequence chrMT has incompatible circularity flags:
  - in 'x': TRUE
  - in 'y': FALSE
FAILURE in test_getTableColMapping: Error in checkIdentical(res, exp) : FALSE 
 
FAILURE in test_keys_advancedArgs: Error in checkTrue("uc001aaa.3" %in% k1) : Test not TRUE

FAILURE in test_makeColAbbreviations: Error in checkTrue(length(res) == 21, length(unique(unlist(res2)))) : 
  Test not TRUE
22

Test files with failing tests

   test_getPromoterSeq-methods.R 
     test_GRangesBSgenomeHumanGetPromoterSeq 
     test_GRangesListBSgenomeHumanGetPromoterSeq 

   test_select-methods.R 
     test_getTableColMapping 
     test_keys_advancedArgs 
     test_makeColAbbreviations 


Error in BiocGenerics:::testPackage("GenomicFeatures") : 
  unit tests failed for package GenomicFeatures
Calls: <Anonymous> -> <Anonymous>
In addition: Warning messages:
1: In .makeTxDb_normarg_chrominfo(chrominfo) :
  genome version information is not available for this TxDb object
2: In (function (seqlevels, genome, new_style)  :
  cannot switch some hg19's seqlevels from UCSC to NCBI style
3: In .makeTxDb_normarg_chrominfo(chrominfo) :
  genome version information is not available for this TxDb object
4: In (function (seqlevels, genome, new_style)  :
  cannot switch some hg19's seqlevels from UCSC to NCBI style
Execution halted