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### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomicFeatures.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings GenomicFeatures_1.59.1.tar.gz
###
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/GenomicFeatures.Rcheck'
* using R Under development (unstable) (2025-01-21 r87610 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'GenomicFeatures/DESCRIPTION' ... OK
* this is package 'GenomicFeatures' version '1.59.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Depends: includes the non-default packages:
  'BiocGenerics', 'S4Vectors', 'IRanges', 'GenomeInfoDb',
  '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 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 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'
  'GenomeInfoDb:::getSeqlevelsReplacementMode'
  'GenomeInfoDb:::normarg_new2old'
  'GenomicRanges:::unsafe.transcriptLocs2refLocs'
  'GenomicRanges:::unsafe.transcriptWidths'
  'IRanges:::regroupBySupergroup' 'S4Vectors:::V_recycle'
  'S4Vectors:::decodeRle' 'S4Vectors:::extract_data_frame_rows'
  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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  FeatureDb-class.Rd: saveDb, loadDb
  extractUpstreamSeqs.Rd: mcols
  getPromoterSeq-methods.Rd: GRanges, GRangesList
  nearest-methods.Rd: GenomicRanges
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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
coordinate-mapping-methods 107.24   3.69  120.11
coverageByTranscript        87.96   5.75   93.69
exonicParts                 45.03   3.13   49.33
extractTranscriptSeqs       16.27   0.74   17.04
transcriptLocs2refLocs       9.49   1.68   11.31
getPromoterSeq-methods       3.87   1.39    9.39
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'run_unitTests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/GenomicFeatures.Rcheck/00check.log'
for details.

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### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL GenomicFeatures
###
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* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'GenomicFeatures' ...
** this is package 'GenomicFeatures' version '1.59.1'
** 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 Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
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

Attaching package: 'rtracklayer'

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

    FileForFormat

'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: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: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: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
Error in x$.self$finalize() : attempt to apply non-function
In addition: Warning messages:
1: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 1 out-of-bound range located on sequence
  chrUn_gl000237. 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 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.
3: 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.
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 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.
6: In call_fun_in_txdbmaker("makeTxDbFromGRanges", ...) :
  makeTxDbFromGRanges() has moved from GenomicFeatures to the txdbmaker
  package, and is formally deprecated in GenomicFeatures >= 1.59.1. Please call
  txdbmaker::makeTxDbFromGRanges() to get rid of this warning.
7: 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.
8: In .makeTxDb_normarg_chrominfo(chrominfo) :
  genome version information is not available for this TxDb object
9: In call_fun_in_txdbmaker("makeTxDbFromGFF", ...) :
  makeTxDbFromGFF() has moved from GenomicFeatures to the txdbmaker package,
  and is formally deprecated in GenomicFeatures >= 1.59.1. Please call
  txdbmaker::makeTxDbFromGFF() to get rid of this warning.
10: In .makeTxDb_normarg_chrominfo(chrominfo) :
  genome version information is not available for this TxDb object
Error in x$.self$finalize() : attempt to apply non-function
In addition: Warning message:
call dbDisconnect() when finished working with a connection 
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 -- Sat Jan 25 02:05:45 2025 
*********************************************** 
Number of test functions: 67 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GenomicFeatures RUnit Tests - 67 test functions, 0 errors, 0 failures
Number of test functions: 67 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In (function (seqlevels, genome, new_style)  :
  cannot switch some hg19's seqlevels from UCSC to NCBI style
2: In call_fun_in_txdbmaker("makeTxDbFromGFF", ...) :
  makeTxDbFromGFF() has moved from GenomicFeatures to the txdbmaker package,
  and is formally deprecated in GenomicFeatures >= 1.59.1. Please call
  txdbmaker::makeTxDbFromGFF() to get rid of this warning.
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
> 
> proc.time()
   user  system elapsed 
  81.06    2.59   84.46