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###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD check --install=check:ensembldb.install-out.txt --library=/home/rapidbuild/bbs-3.23-bioc-rapid/R/site-library --timings ensembldb_2.35.0.tar.gz
###
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/ensembldb.Rcheck’
* using R Under development (unstable) (2025-10-28 r88973)
* 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 ‘ensembldb/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ensembldb’ version ‘2.35.0’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Johannes Rainer <johannes.rainer@eurac.edu>’

Unknown, possibly misspelled, fields in DESCRIPTION:
  ‘git_url’ ‘git_branch’ ‘git_last_commit’ ‘git_last_commit_date’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

The Title field should be in title case. Current version is:
  ‘Utilities to create and use Ensembl-based annotation databases’
In title case that is:
  ‘Utilities to Create and Use Ensembl-Based Annotation Databases’

The Description field should not start with the package name,
  'This package' or similar.
* 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 ‘ensembldb’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Author field differs from that derived from Authors@R
  Author:    ‘Johannes Rainer <johannes.rainer@eurac.edu> with contributions from Tim Triche, Sebastian Gibb, Laurent Gatto Christian Weichenberger and Boyu Yu.’
  Authors@R: ‘Johannes Rainer [aut, cre] (ORCID: <https://orcid.org/0000-0002-6977-7147>), Tim Triche [ctb], Christian Weichenberger [ctb] (ORCID: <https://orcid.org/0000-0002-2176-0274>), Sebastian Gibb [ctb] (ORCID: <https://orcid.org/0000-0001-7406-4443>), Laurent Gatto [ctb] (ORCID: <https://orcid.org/0000-0002-1520-2268>), Boyu Yu [ctb]’

* 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 whether startup messages can be suppressed ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* 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:
  EnsDb-exonsBy.Rd: supportedFilters, GRangesFilter
  EnsDb-sequences.Rd: TwoBitFile-class
  Filter-classes.Rd: AnnotationFilter, supportedFilters, GeneIdFilter
  ProteinFunctionality.Rd: supportedFilters
  proteinToTranscript.Rd: fiveUTRsByTranscript
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 ... ERROR
Running examples in ‘ensembldb-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: genomeToTranscript
> ### Title: Map genomic coordinates to transcript coordinates
> ### Aliases: genomeToTranscript
> 
> ### ** Examples
> 
> 
> library(EnsDb.Hsapiens.v86)
> 
> ## Subsetting the EnsDb object to chromosome X only to speed up execution
> ## time of examples
> edbx <- filter(EnsDb.Hsapiens.v86, filter = ~ seq_name == "X")
> 
> ## Define a genomic region and calculate within-transcript coordinates
> gnm <- GRanges("X:107716399-107716401")
> 
> res <- genomeToTranscript(gnm, edbx)
> ## Result is an IRanges object with the start and end coordinates within
> ## each transcript that has an exon at the genomic range.
> res
IRangesList object of length 1:
[[1]]
IRanges object with 2 ranges and 7 metadata columns:
                      start       end     width |           tx_id
                  <integer> <integer> <integer> |     <character>
  ENST00000372390       145       147         3 | ENST00000372390
  ENST00000486554         1         3         3 | ENST00000486554
                          exon_id exon_rank seq_start   seq_end    seq_name
                      <character> <integer> <integer> <integer> <character>
  ENST00000372390 ENSE00001457675         1 107716399 107716401           X
  ENST00000486554 ENSE00001927337         1 107716399 107716401           X
                   seq_strand
                  <character>
  ENST00000372390           *
  ENST00000486554           *

> 
> ## An IRanges with negative coordinates is returned if at the provided
> ## position no exon is present. Below we use the same coordinates but
> ## specify that the coordinates are on the forward (+) strand
> gnm <- GRanges("X:107716399-107716401:+")
> genomeToTranscript(gnm, edbx)
Warning: 1 genomic region(s) could not be mapped to a transcript; hint: see ?seqlevelsStyle if you used UCSC chromosome names
IRangesList object of length 1:
[[1]]
IRanges object with 1 range and 7 metadata columns:
          start       end     width |       tx_id     exon_id exon_rank
      <integer> <integer> <integer> | <character> <character> <integer>
  [1]        -1        -1         1 |        <NA>        <NA>      <NA>
      seq_start   seq_end    seq_name  seq_strand
      <integer> <integer> <character> <character>
  [1] 107716399 107716401           X           +

> 
> ## Next we provide multiple genomic positions.
> gnm <- GRanges("X", IRanges(start = c(644635, 107716399, 107716399),
+     end = c(644639, 107716401, 107716401)), strand = c("*", "*", "+"))
> 
> ## The result of the mapping is an IRangesList each element providing the
> ## within-transcript coordinates for each input region
> genomeToTranscript(gnm, edbx)
Warning: 1 genomic region(s) could not be mapped to a transcript; hint: see ?seqlevelsStyle if you used UCSC chromosome names
IRangesList object of length 3:
[[1]]
IRanges object with 2 ranges and 7 metadata columns:
                      start       end     width |           tx_id
                  <integer> <integer> <integer> |     <character>
  ENST00000381578      1569      1573         5 | ENST00000381578
  ENST00000554971       969       973         5 | ENST00000554971
                          exon_id exon_rank seq_start   seq_end    seq_name
                      <character> <integer> <integer> <integer> <character>
  ENST00000381578 ENSE00001489174         6    644635    644639           X
  ENST00000554971 ENSE00002438186         5    644635    644639           X
                   seq_strand
                  <character>
  ENST00000381578           *
  ENST00000554971           *

[[2]]
IRanges object with 2 ranges and 7 metadata columns:
                      start       end     width |           tx_id
                  <integer> <integer> <integer> |     <character>
  ENST00000372390       145       147         3 | ENST00000372390
  ENST00000486554         1         3         3 | ENST00000486554
                          exon_id exon_rank seq_start   seq_end    seq_name
                      <character> <integer> <integer> <integer> <character>
  ENST00000372390 ENSE00001457675         1 107716399 107716401           X
  ENST00000486554 ENSE00001927337         1 107716399 107716401           X
                   seq_strand
                  <character>
  ENST00000372390           *
  ENST00000486554           *

[[3]]
IRanges object with 1 range and 7 metadata columns:
       start       end     width |       tx_id     exon_id exon_rank seq_start
   <integer> <integer> <integer> | <character> <character> <integer> <integer>
          -1        -1         1 |        <NA>        <NA>      <NA> 107716399
     seq_end    seq_name  seq_strand
   <integer> <character> <character>
   107716401           X           +

> 
> ## If you are tring to calculate within-transcript coordinates of a huge 
> ## list of genomic region, you shall use pre-loaded exons GRangesList to  
> ## replace the SQLite db edbx
>  
> ## Below is just a lazy demo of querying multiple genomic region 
> library(parallel)
> 
> gnm <- rep(GRanges("X:107715899-107715901"),10)
> 
> exons <- exonsBy(EnsDb.Hsapiens.v86)
> 
> ## You can pre-define the exons region to further accelerate the code.
> 
> exons <- exonsBy(
+     EnsDb.Hsapiens.v86, by = "tx",
+     filter = AnnotationFilterList(
+         SeqNameFilter(as.character(unique(seqnames(gnm)))),
+         GeneStartFilter(max(end(gnm)), condition = "<="),
+         GeneEndFilter(min(start(gnm)), condition = ">=")
+     )
+ )
> 
> ## only run in Linux ## 
> # res_temp <- mclapply(1:10, function(ind){
> #     genomeToTranscript(gnm[ind], exons)
> # }, mc.preschedule = TRUE, mc.cores = detectCores() - 1)
> 
> # res <- do.call(c,res_temp)
> 
> cl <- makeCluster(detectCores() - 1)
> clusterExport(cl,c('genomeToTranscript','gnm','exons'))
Killed
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
cdsToTranscript     13.373  3.790  17.667
EnsDb-AnnotationDbi  2.138  0.316   5.519
Filter-classes       1.379  1.002   8.759
EnsDb-exonsBy        1.263  0.411   5.147
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: 1 ERROR, 3 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/ensembldb.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD INSTALL ensembldb
###
##############################################################################
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* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library’
* installing *source* package ‘ensembldb’ ...
** this is package ‘ensembldb’ version ‘2.35.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function from function ‘.cds_for_id2’ in package ‘ensembldb’
** 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 (ensembldb)

R Under development (unstable) (2025-10-28 r88973) -- "Unsuffered Consequences"
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.

> library(testthat)
> library(ensembldb)
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: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

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: GenomicFeatures
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")'.

Loading required package: AnnotationFilter

Attaching package: 'AnnotationFilter'

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

    not


Attaching package: 'ensembldb'

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

    filter

> library(EnsDb.Hsapiens.v86)
> edb <- EnsDb.Hsapiens.v86
> 
> test_check("ensembldb")
Creating package in /tmp/RtmpIcrFTP/EnsDb.Hsapiens.v75 

Comparing chromosome data:
 Sequence names: (180) common, (0) only in x, (0) only in y.
 Sequence lengths: (180) identical, (0) different.
Done. Result: OK

Comparing gene data:
 gene IDs: (4045) common, (0) only in x, (0) only in y.
 Sequence names: (4045) identical, (0) different.
 Gene start coordinates: (4045) identical, (0) different.
 Gene end coordinates: (4045) identical, (0) different.
 Gene strand: (4045) identical, (0) different.
 Gene names: (132) identical, (3913) different.
 Entrezgene IDs: (4045) identical, (0) different.
 Gene biotypes: (4045) identical, (0) different.
Done. Result: WARN

Comparing transcript data:
 transcript IDs: (4045) common, (0) only in x, (0) only in y.
 Transcript start coordinates: (4045) identical, (0) different.
 Transcript end coordinates: (4045) identical, (0) different.
 Transcript biotypes: (4045) identical, (0) different.
 Common transcripts with defined CDS: (3996) common, (0) only in x, (0) only in y.
 CDS start coordinates: (3996) identical, (0) different.
 CDS end coordinates: (3996) identical, (0) different.
 Associated gene IDs: (4045) identical, (0) different.
Done. Result: OK

Comparing exon data:
 exon IDs: (4045) common, (0) only in x, (0) only in y.
 Exon start coordinates: (4045) identical, (0) different.
 Exon end coordinates: (4045) identical, (0) different.
 Exon index in transcript models: (4045) identical, (0) different.
Done. Result: OK

Comparing metadata:
 Ensembl versions match.
 Genome builds match.
 All differences: <name>: <value x> != <value y>
  -  Creation time : Wed Dec  3 14:28:13 2025  !=  Wed Dec  3 14:28:05 2025 
  -  source_file : Devosia_geojensis.ASM96941v1.32.gtf.gz  !=  Devosia_geojensis.ASM96941v1.32.gff3.gz 
Done. Result: NOTE

Comparing chromosome data:
 Sequence names: (180) common, (0) only in x, (0) only in y.
 Sequence lengths: (180) identical, (0) different.
Done. Result: OK

Comparing gene data:
 gene IDs: (4045) common, (0) only in x, (0) only in y.
 Sequence names: (4045) identical, (0) different.
 Gene start coordinates: (4045) identical, (0) different.
 Gene end coordinates: (4045) identical, (0) different.
 Gene strand: (4045) identical, (0) different.
 Gene names: (132) identical, (3913) different.
 Entrezgene IDs: (4045) identical, (0) different.
 Gene biotypes: (4045) identical, (0) different.
Done. Result: WARN

Comparing transcript data:
 transcript IDs: (4045) common, (0) only in x, (0) only in y.
 Transcript start coordinates: (4045) identical, (0) different.
 Transcript end coordinates: (4045) identical, (0) different.
 Transcript biotypes: (4045) identical, (0) different.
 Common transcripts with defined CDS: (3996) common, (0) only in x, (0) only in y.
 CDS start coordinates: (3996) identical, (0) different.
 CDS end coordinates: (3996) identical, (0) different.
 Associated gene IDs: (4045) identical, (0) different.
Done. Result: OK

Comparing exon data:
 exon IDs: (4045) common, (0) only in x, (0) only in y.
 Exon start coordinates: (4045) identical, (0) different.
 Exon end coordinates: (4045) identical, (0) different.
 Exon index in transcript models: (4045) identical, (0) different.
Done. Result: OK

Comparing protein data:
 protein IDs: (103725) common, (0) only in x, (0) only in y.
 Transcript IDs: (103725) identical, (0) different.
 Protein sequence: (103725) identical, (0) different.
Done. Result: OK
[ FAIL 0 | WARN 75 | SKIP 3 | PASS 1632 ]

══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• empty test (3): 'test_Methods.R:129:1', 'test_Methods.R:273:1',
  'test_seqLevelStyle.R:40:1'

[ FAIL 0 | WARN 75 | SKIP 3 | PASS 1632 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
225.785  47.171 330.154