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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenomicFeatures.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenomicFeatures_1.54.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/GenomicFeatures.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicFeatures/DESCRIPTION’ ... OK
* this is package ‘GenomicFeatures’ version ‘1.54.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
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 for sufficient/correct file permissions ... OK
* checking whether package ‘GenomicFeatures’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R         2.0Mb
    extdata   3.0Mb
* 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
':::' call which should be '::': ‘rtracklayer:::tableNames’
  See the note in ?`:::` about the use of this operator.
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:::check_tax_id’
  ‘GenomeInfoDb:::getSeqlevelsReplacementMode’
  ‘GenomeInfoDb:::lookup_organism_by_tax_id’
  ‘GenomeInfoDb:::lookup_tax_id_by_organism’
  ‘GenomeInfoDb:::make_circ_flags_from_circ_seqs’
  ‘GenomeInfoDb:::normarg_new2old’
  ‘GenomicRanges:::unsafe.transcriptLocs2refLocs’
  ‘GenomicRanges:::unsafe.transcriptWidths’
  ‘IRanges:::regroupBySupergroup’ ‘S4Vectors:::V_recycle’
  ‘S4Vectors:::anyMissingOrOutside’ ‘S4Vectors:::decodeRle’
  ‘S4Vectors:::extract_data_frame_rows’ ‘S4Vectors:::quick_togroup’
  ‘biomaRt:::martBM’ ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’
  ‘rtracklayer:::resourceDescription’
  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: makeTxDbFromUCSC
> ### Title: Make a TxDb object from annotations available at the UCSC Genome
> ###   Browser
> ### Aliases: supportedUCSCtables browseUCSCtrack makeTxDbFromUCSC
> 
> ### ** Examples
> 
> ## ---------------------------------------------------------------------
> ## A. BASIC USAGE
> ## ---------------------------------------------------------------------
> 
> ## Use ucscGenomes() from the rtracklayer package to display the list of
> ## genomes available at UCSC:
> library(rtracklayer)
> ucscGenomes()[ , "db"]
  [1] "ailMel1"     "allMis1"     "anoCar1"     "anoCar2"     "anoGam1"    
  [6] "anoGam3"     "apiMel1"     "apiMel2"     "aplCal1"     "aptMan1"    
 [11] "aquChr2"     "balAcu1"     "bisBis1"     "bosTau2"     "bosTau3"    
 [16] "bosTau4"     "bosTau6"     "bosTau7"     "bosTau8"     "bosTau9"    
 [21] "braFlo1"     "caeJap1"     "caePb1"      "caePb2"      "caeRem2"    
 [26] "caeRem3"     "calJac1"     "calJac3"     "calJac4"     "calMil1"    
 [31] "canFam1"     "canFam2"     "canFam3"     "canFam4"     "canFam5"    
 [36] "canFam6"     "cavPor3"     "cb1"         "cb3"         "ce10"       
 [41] "ce11"        "ce2"         "ce4"         "ce6"         "cerSim1"    
 [46] "chlSab2"     "choHof1"     "chrPic1"     "ci1"         "ci2"        
 [51] "ci3"         "criGri1"     "criGriChoV1" "criGriChoV2" "danRer10"   
 [56] "danRer11"    "danRer3"     "danRer4"     "danRer5"     "danRer6"    
 [61] "danRer7"     "dasNov3"     "dipOrd1"     "dm1"         "dm2"        
 [66] "dm3"         "dm6"         "dp2"         "dp3"         "droAna1"    
 [71] "droAna2"     "droEre1"     "droGri1"     "droMoj1"     "droMoj2"    
 [76] "droPer1"     "droSec1"     "droSim1"     "droVir1"     "droVir2"    
 [81] "droYak1"     "droYak2"     "eboVir3"     "echTel1"     "echTel2"    
 [86] "enhLutNer1"  "equCab1"     "equCab2"     "equCab3"     "eriEur1"    
 [91] "eriEur2"     "felCat3"     "felCat4"     "felCat5"     "felCat8"    
 [96] "felCat9"     "fr1"         "fr2"         "fr3"         "gadMor1"    
[101] "galGal2"     "galGal3"     "galGal4"     "galGal5"     "galGal6"    
[106] "galVar1"     "gasAcu1"     "geoFor1"     "gorGor3"     "gorGor4"    
[111] "gorGor5"     "gorGor6"     "hetGla1"     "hetGla2"     "hg16"       
[116] "hg17"        "hg18"        "hg19"        "hg38"        "hs1"        
[121] "latCha1"     "loxAfr3"     "macEug2"     "macFas5"     "manPen1"    
[126] "melGal1"     "melGal5"     "melUnd1"     "micMur1"     "micMur2"    
[131] "mm10"        "mm39"        "mm7"         "mm8"         "mm9"        
[136] "monDom1"     "monDom4"     "monDom5"     "mpxvRivers"  "musFur1"    
[141] "nanPar1"     "nasLar1"     "neoSch1"     "nomLeu1"     "nomLeu2"    
[146] "nomLeu3"     "ochPri2"     "ochPri3"     "oreNil2"     "ornAna1"    
[151] "ornAna2"     "oryCun2"     "oryLat2"     "otoGar3"     "oviAri1"    
[156] "oviAri3"     "oviAri4"     "panPan1"     "panPan2"     "panPan3"    
[161] "panTro1"     "panTro2"     "panTro3"     "panTro4"     "panTro5"    
[166] "panTro6"     "papAnu2"     "papAnu4"     "papHam1"     "petMar1"    
[171] "petMar2"     "petMar3"     "ponAbe2"     "ponAbe3"     "priPac1"    
[176] "proCap1"     "pteVam1"     "rheMac10"    "rheMac2"     "rheMac3"    
[181] "rheMac8"     "rhiRox1"     "rn3"         "rn4"         "rn5"        
[186] "rn6"         "rn7"         "sacCer1"     "sacCer2"     "sacCer3"    
[191] "saiBol1"     "sarHar1"     "sorAra1"     "sorAra2"     "speTri2"    
[196] "strPur1"     "strPur2"     "susScr11"    "susScr2"     "susScr3"    
[201] "taeGut1"     "taeGut2"     "tarSyr1"     "tarSyr2"     "tetNig1"    
[206] "tetNig2"     "thaSir1"     "triMan1"     "tupBel1"     "turTru2"    
[211] "vicPac1"     "vicPac2"     "wuhCor1"     "xenLae2"     "xenTro1"    
[216] "xenTro10"    "xenTro2"     "xenTro3"     "xenTro7"     "xenTro9"    
> 
> ## Display the list of tables known to work with makeTxDbFromUCSC():
> supportedUCSCtables("hg38")
Error in names(trackIds) <- sub("^ ", "", nms) : 
  attempt to set an attribute on NULL
Calls: supportedUCSCtables ... trackNames -> .local -> ucscTracks -> ucscTracks -> .local
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’
 OK
* 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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/GenomicFeatures.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GenomicFeatures
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘GenomicFeatures’ ...
** 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 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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("GenomicFeatures") || stop("unable to load GenomicFeatures package")
Loading required package: GenomicFeatures
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 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: 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

Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... 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
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
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
'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
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... 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 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.
2: 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.
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 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.
5: In .get_cds_IDX(mcols0$type, mcols0$phase) :
  The "phase" metadata column contains non-NA values for features of type
  exon. This information was ignored.
6: 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.
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 (function (seqlevels, genome, new_style)  :
  cannot switch some hg19's seqlevels from UCSC to NCBI style
OK


RUNIT TEST PROTOCOL -- Tue Feb 27 20:58:08 2024 
*********************************************** 
Number of test functions: 75 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GenomicFeatures RUnit Tests - 75 test functions, 0 errors, 0 failures
Number of test functions: 75 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: call dbDisconnect() when finished working with a connection 
2: In (function (seqlevels, genome, new_style)  :
  cannot switch some hg19's seqlevels from UCSC to NCBI style
> 
> proc.time()
   user  system elapsed 
158.079   3.979 198.009