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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:Bioc.gff.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings Bioc.gff_0.99.16.tar.gz
###
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##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/Bioc.gff.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 ‘Bioc.gff/DESCRIPTION’ ... OK
* this is package ‘Bioc.gff’ version ‘0.99.16’
* 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 ‘Bioc.gff’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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
':::' call which should be '::': ‘XVector:::open_input_files’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘BiocIO:::.parseURI’ ‘XVector:::rewind_filexp’
  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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘Bioc.gff/libs/Bioc.gff.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
        user system elapsed
asGFF 17.433  0.513  19.706
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘tinytest.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘Bioc.gff.Rmd’ using rmarkdown

Quitting from Bioc.gff.Rmd:194-209 [make-txdb-from-gff]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `loadTaxonomyDb()`:
! Could not load package GenomeInfoDbData. Is it installed?

  Note that loadTaxonomyDb() requires the GenomeInfoDbData package. Please
  install it with:

    BiocManager::install("GenomeInfoDbData")
---
Backtrace:
    ▆
 1. └─txdbmaker::makeTxDbFromGFF(...)
 2.   └─txdbmaker:::.prepareGFFMetadata(...)
 3.     └─GenomeInfoDb:::check_tax_id(taxonomyId)
 4.       └─GenomeInfoDb::loadTaxonomyDb()
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Bioc.gff.Rmd' failed with diagnostics:
Could not load package GenomeInfoDbData. Is it installed?

  Note that loadTaxonomyDb() requires the GenomeInfoDbData package. Please
  install it with:

    BiocManager::install("GenomeInfoDbData")
--- failed re-building ‘Bioc.gff.Rmd’

SUMMARY: processing the following file failed:
  ‘Bioc.gff.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/Bioc.gff.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL Bioc.gff
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘Bioc.gff’ ...
** this is package ‘Bioc.gff’ version ‘0.99.16’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c R_init_Bioc_gff.c -o R_init_Bioc_gff.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c readGFF.c -o readGFF.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c utils.c -o utils.o
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o Bioc.gff.so R_init_Bioc_gff.o S4Vectors_stubs.o XVector_stubs.o readGFF.o utils.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-Bioc.gff/00new/Bioc.gff/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Bioc.gff)

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.

> if (requireNamespace("tinytest", quietly = TRUE))
+     tinytest::test_package("Bioc.gff")
Loading required package: stats4
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

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

test_GFF-coercion.R...........    0 tests    
test_GFF-coercion.R...........    0 tests    
test_GFF-coercion.R...........    0 tests    
test_GFF-coercion.R...........    0 tests    
test_GFF-coercion.R...........    1 tests OK 
test_GFF-coercion.R...........    2 tests OK 
test_GFF-coercion.R...........    3 tests OK 
test_GFF-coercion.R...........    4 tests OK 
test_GFF-coercion.R...........    4 tests OK 
test_GFF-coercion.R...........    4 tests OK 
test_GFF-coercion.R...........    5 tests OK 
test_GFF-coercion.R...........    5 tests OK 
test_GFF-coercion.R...........    6 tests OK 
test_GFF-coercion.R...........    6 tests OK 
test_GFF-coercion.R...........    7 tests OK 0.9s

test_index.R..................    0 tests    
test_index.R..................    0 tests    Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit


test_index.R..................    0 tests    
test_index.R..................    0 tests    
test_index.R..................    0 tests    
test_index.R..................    0 tests    
test_index.R..................    0 tests    
test_index.R..................    0 tests    
test_index.R..................    0 tests    
test_index.R..................    0 tests    
test_index.R..................    0 tests    
test_index.R..................    0 tests    
test_index.R..................    0 tests    
test_index.R..................    0 tests    
test_index.R..................    0 tests    
test_index.R..................    0 tests    
test_index.R..................    0 tests    
test_index.R..................    0 tests    
test_index.R..................    0 tests    
test_index.R..................    1 tests OK 
test_index.R..................    2 tests OK 
test_index.R..................    2 tests OK 
test_index.R..................    3 tests OK 
test_index.R..................    4 tests OK 
test_index.R..................    4 tests OK 
test_index.R..................    4 tests OK 0.3s

test_metadataFromNCBI.R.......    0 tests    
test_metadataFromNCBI.R.......    0 tests    
test_metadataFromNCBI.R.......    0 tests    
test_metadataFromNCBI.R.......    1 tests OK 
test_metadataFromNCBI.R.......    1 tests OK 
test_metadataFromNCBI.R.......    2 tests OK 1.1s

test_utilities.R..............    0 tests    
test_utilities.R..............    0 tests    
test_utilities.R..............    0 tests    
test_utilities.R..............    1 tests OK 
test_utilities.R..............    2 tests OK 
test_utilities.R..............    2 tests OK 
test_utilities.R..............    3 tests OK 
test_utilities.R..............    4 tests OK 
test_utilities.R..............    4 tests OK 
test_utilities.R..............    5 tests OK 
test_utilities.R..............    5 tests OK 
test_utilities.R..............    6 tests OK 60ms
All ok, 19 results (2.4s)
Warning message:
In .local(object, con, format, ...) :
  The phase information is missing for some CDS. The written file will contain
  some CDS with no phase information.
> 
> proc.time()
   user  system elapsed 
  6.111   0.449   7.445