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###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:AnnotationForge.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings AnnotationForge_1.49.1.tar.gz
###
##############################################################################
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/AnnotationForge.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* 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 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘AnnotationForge/DESCRIPTION’ ... OK
* this is package ‘AnnotationForge’ version ‘1.49.1’
* 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 ‘AnnotationForge’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    AnnDbPkg-templates   1.8Mb
    extdata              3.3Mb
* 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:
  ‘BiocGenerics:::testPackage’
  ‘GenomeInfoDb:::lookup_organism_by_tax_id’
  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:
  AnnDbPkg-maker.Rd: AnnDbPkg-checker
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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘AnnotationForge_unit_tests.R’
 ERROR
Running the tests in ‘tests/AnnotationForge_unit_tests.R’ failed.
Last 13 lines of output:
  1 Test Suite : 
  AnnotationForge RUnit Tests - 4 test functions, 1 error, 0 failures
  ERROR in test_makeOrgPackage: Error in .makeAnnDbPkg(x, dbfile, dest_dir = dest_dir, no.man = no.man,  : 
    cannot copy file '/tmp/RtmpCjKoy1/file1d0756311a7af3/org.Tguttata.eg.sqlite' to '/tmp/RtmpCjKoy1/file1d0756311a7af3/org.Tguttata.eg.db/inst/extdata/org.Tguttata.eg.sqlite'
  
  Test files with failing tests
  
     test_makeOrgPackage.R 
       test_makeOrgPackage 
  
  
  Error in BiocGenerics:::testPackage("AnnotationForge") : 
    unit tests failed for package AnnotationForge
  Calls: <Anonymous> -> <Anonymous>
  Execution halted
* 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 ‘makeProbePackage.Rmd’ using rmarkdown

See
  ‘/tmp/Rtmpv5im8U/hgu95av2probe.Rcheck/00check.log’
for details.

--- finished re-building ‘makeProbePackage.Rmd’

--- re-building ‘MakingNewAnnotationPackages.Rnw’ using knitr
trying URL 'http://rest.uniprot.org/uniprotkb/search?query=P13368%20OR%20Q6GZX4&format=xml'
Content type 'application/xml' length 50315 bytes (49 KB)
==================================================
downloaded 49 KB

--- finished re-building ‘MakingNewAnnotationPackages.Rnw’

--- re-building ‘MakingNewOrganismPackages.Rmd’ using knitr
--- finished re-building ‘MakingNewOrganismPackages.Rmd’

--- re-building ‘SQLForge.Rnw’ using knitr

Quitting from SQLForge.Rnw:176-193 [SQLForge]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! database or disk is full
---
Backtrace:
     x
  1. \-AnnotationForge::makeDBPackage(...)
  2.   \-AnnotationForge:::.makeHUMANCHIP_DB(...)
  3.     \-AnnotationForge:::popHUMANCHIPDB(...)
  4.       \-AnnotationForge:::appendGOALL(db, subStrs = subStrs, printSchema = printSchema)
  5.         +-DBI::dbExecute(db, sql)
  6.         \-DBI::dbExecute(db, sql)
  7.           +-DBI::dbSendStatement(conn, statement, ...)
  8.           \-DBI::dbSendStatement(conn, statement, ...)
  9.             +-DBI::dbSendQuery(conn, statement, ...)
 10.             \-RSQLite::dbSendQuery(conn, statement, ...)
 11.               \-RSQLite (local) .local(conn, statement, ...)
 12.                 +-methods::new(...)
 13.                 | +-methods::initialize(value, ...)
 14.                 | \-methods::initialize(value, ...)
 15.                 \-RSQLite:::result_create(conn@ptr, statement)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'SQLForge.Rnw' failed with diagnostics:
database or disk is full
--- failed re-building ‘SQLForge.Rnw’

SUMMARY: processing the following file failed:
  ‘SQLForge.Rnw’

Error: Vignette re-building failed.
Execution halted

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

Status: 2 ERRORs, 2 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/AnnotationForge.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL AnnotationForge
###
##############################################################################
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* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’
* installing *source* package ‘AnnotationForge’ ...
** this is package ‘AnnotationForge’ version ‘1.49.1’
** 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 (AnnotationForge)

R Under development (unstable) (2025-01-20 r87609) -- "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.

> require("AnnotationForge") || stop("unable to load AnnotationForge package")
Loading required package: AnnotationForge
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: 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: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
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

[1] TRUE
> AnnotationForge:::.test()

'select()' returned many:1 mapping between keys and columns
'select()' returned many:1 mapping between keys and columns
Populating genes table:
genes table filled
Populating gene_info table:
gene_info table filled
Populating chromosome table:
chromosome table filled
Populating go table:
go table filled
table metadata filled
'select()' returned many:1 mapping between keys and columns
Dropping GO IDs that are too new for the current GO.db
Populating go table:
go table filled
Populating go_bp table:
go_bp table filled
Populating go_cc table:
go_cc table filled
Populating go_mf table:
go_mf table filled
'select()' returned many:1 mapping between keys and columns
Populating go_bp_all table:
go_bp_all table filled
Populating go_cc_all table:
go_cc_all table filled
Populating go_mf_all table:
go_mf_all table filled
Populating go_all table:
go_all table filled
Creating package in /tmp/RtmpCjKoy1/file1d0756311a7af3/org.Tguttata.eg.db 
Timing stopped at: 0.656 0.026 0.711
Error in .makeAnnDbPkg(x, dbfile, dest_dir = dest_dir, no.man = no.man,  : 
  cannot copy file '/tmp/RtmpCjKoy1/file1d0756311a7af3/org.Tguttata.eg.sqlite' to '/tmp/RtmpCjKoy1/file1d0756311a7af3/org.Tguttata.eg.db/inst/extdata/org.Tguttata.eg.sqlite'
In addition: Warning message:
In file.append(to[okay], from[okay]) : write error during file append


RUNIT TEST PROTOCOL -- Tue Mar 25 07:12:26 2025 
*********************************************** 
Number of test functions: 4 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
AnnotationForge RUnit Tests - 4 test functions, 1 error, 0 failures
ERROR in test_makeOrgPackage: Error in .makeAnnDbPkg(x, dbfile, dest_dir = dest_dir, no.man = no.man,  : 
  cannot copy file '/tmp/RtmpCjKoy1/file1d0756311a7af3/org.Tguttata.eg.sqlite' to '/tmp/RtmpCjKoy1/file1d0756311a7af3/org.Tguttata.eg.db/inst/extdata/org.Tguttata.eg.sqlite'

Test files with failing tests

   test_makeOrgPackage.R 
     test_makeOrgPackage 


Error in BiocGenerics:::testPackage("AnnotationForge") : 
  unit tests failed for package AnnotationForge
Calls: <Anonymous> -> <Anonymous>
Execution halted