##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:AnnotationDbi.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings AnnotationDbi_1.69.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/AnnotationDbi.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 ‘AnnotationDbi/DESCRIPTION’ ... OK
* this is package ‘AnnotationDbi’ version ‘1.69.0’
* 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 ‘AnnotationDbi’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  8.3Mb
  sub-directories of 1Mb or more:
    R         1.0Mb
    extdata   6.0Mb
* 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 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 object imported by a ':::' call: ‘BiocGenerics:::testPackage’
  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 ... NOTE
createORGANISMSeeds: no visible global function definition for
  ‘makeAnnDbMapSeeds’
Undefined global functions or variables:
  makeAnnDbMapSeeds
* checking Rd files ... WARNING
checkRd: (5) AnnDbObj-class.Rd:58-61: \item in \describe must have non-empty label
checkRd: (5) AnnDbObj-class.Rd:64-68: \item in \describe must have non-empty label
checkRd: (5) AnnDbObj-class.Rd:71-75: \item in \describe must have non-empty label
checkRd: (5) AnnDbObj-class.Rd:78-89: \item in \describe must have non-empty label
checkRd: (5) AnnDbObj-class.Rd:92-96: \item in \describe must have non-empty label
checkRd: (5) Bimap.Rd:79-82: \item in \describe must have non-empty label
checkRd: (5) Bimap.Rd:84-87: \item in \describe must have non-empty label
checkRd: (-1) inpIDMapper.Rd:91: Escaped LaTeX specials: \#
checkRd: (-1) inpIDMapper.Rd:95: Escaped LaTeX specials: \#
checkRd: (-1) inpIDMapper.Rd:99: Escaped LaTeX specials: \#
* 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 ‘AnnotationDbi-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AnnotationDb-objects
> ### Title: AnnotationDb objects and their progeny, methods etc.
> ### Aliases: AnnotationDb class:AnnotationDb AnnotationDb-class
> ###   ChipDb-class GODb-class InparanoidDb-class OrgDb-class
> ###   ReactomeDb-class OrthologyDb-class loadDb dbconn,AnnotationDb-method
> ###   saveDb saveDb,AnnotationDb-method show,AnnotationDb-method
> ###   metadata,AnnotationDb-method names,AnnotationDb-method species
> ###   species,AnnotationDb-method dbfile,AnnotationDb-method taxonomyId
> ###   taxonomyId,AnnotationDb-method cols columns
> ###   columns,AnnotationDb-method columns,OrgDb-method
> ###   columns,ChipDb-method columns,GODb-method columns,InparanoidDb-method
> ###   columns,Inparanoid8Db-method columns,ReactomeDb-method
> ###   columns,OrthologyDb-method keytypes keytypes,OrgDb-method
> ###   keytypes,ChipDb-method keytypes,GODb-method
> ###   keytypes,InparanoidDb-method keytypes,Inparanoid8Db-method
> ###   keytypes,ReactomeDb-method keytypes,OrthologyDb-method keys
> ###   keys,OrgDb-method keys,ChipDb-method keys,GODb-method
> ###   keys,InparanoidDb-method keys,Inparanoid8Db-method
> ###   keys,ReactomeDb-method keys,OrthologyDb-method select
> ###   select,OrgDb-method select,ChipDb-method select,GODb-method
> ###   select,InparanoidDb-method select,Inparanoid8Db-method
> ###   select,ReactomeDb-method select,OrthologyDb-method mapIds
> ###   mapIds,AnnotationDb-method
> ### Keywords: classes methods
> 
> ### ** Examples
> 
> require(hgu95av2.db)
Loading required package: hgu95av2.db
Loading required package: org.Hs.eg.db
> ## display the columns
> columns(hgu95av2.db)
 [1] "ACCNUM"       "ALIAS"        "ENSEMBL"      "ENSEMBLPROT"  "ENSEMBLTRANS"
 [6] "ENTREZID"     "ENZYME"       "EVIDENCE"     "EVIDENCEALL"  "GENENAME"    
[11] "GENETYPE"     "GO"           "GOALL"        "IPI"          "MAP"         
[16] "OMIM"         "ONTOLOGY"     "ONTOLOGYALL"  "PATH"         "PFAM"        
[21] "PMID"         "PROBEID"      "PROSITE"      "REFSEQ"       "SYMBOL"      
[26] "UCSCKG"       "UNIPROT"     
> ## get the 1st 6 possible keys
> keys <- head( keys(hgu95av2.db) )
> keys
[1] "1000_at"   "1001_at"   "1002_f_at" "1003_s_at" "1004_at"   "1005_at"  
> ## lookup gene symbol and gene type for the 1st 6 keys
> select(hgu95av2.db, keys=keys, columns = c("SYMBOL","GENETYPE"))
'select()' returned 1:1 mapping between keys and columns
    PROBEID  SYMBOL       GENETYPE
1   1000_at   MAPK3 protein-coding
2   1001_at    TIE1 protein-coding
3 1002_f_at CYP2C19 protein-coding
4 1003_s_at   CXCR5 protein-coding
5   1004_at   CXCR5 protein-coding
6   1005_at   DUSP1 protein-coding
> 
> ## get keys based on RefSeq
> keyref <- head( keys(hgu95av2.db, keytype="REFSEQ") )
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'head': database or disk is full
Calls: head ... dbFetch -> .local -> result_fetch -> .handleSimpleError -> h
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
AnnDbPkg-checker 35.593  0.689  37.818
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘AnnotationDbi_unit_tests.R’
 ERROR
Running the tests in ‘tests/AnnotationDbi_unit_tests.R’ failed.
Last 13 lines of output:
       test_select2 
  
     test_select_NOSCHEMA.R 
       test_columns 
       test_keys 
       test_keysLow 
       test_keytypes 
       test_select 
       test_selectLow 
  
  
  Error in BiocGenerics:::testPackage("AnnotationDbi") : 
    unit tests failed for package AnnotationDbi
  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 ‘AnnotationDbi.Rnw’ using knitr

Quitting from AnnotationDbi.Rnw:172-175 [QAlisting]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! database or disk is full
---
Backtrace:
     x
  1. +-utils::capture.output(hgu95av2())
  2. | \-base::withVisible(...elt(i))
  3. \-hgu95av2.db::hgu95av2()
  4.   \-AnnotationDbi::showQCData("hgu95av2", datacache)
  5.     +-base::cat(...)
  6.     +-methods (local) length(map[[1]])
  7.     \-AnnotationDbi (local) length(map[[1]])
  8.       +-AnnotationDbi::Rlength(x)
  9.       \-AnnotationDbi::Rlength(x)
 10.         \-AnnotationDbi:::dbCountUniqueVals(...)
 11.           \-AnnotationDbi:::dbQuery(conn, SQL, 1)
 12.             +-DBI::dbGetQuery(conn, SQL)
 13.             \-DBI::dbGetQuery(conn, SQL)
 14.               \-DBI (local) .local(conn, statement, ...)
 15.                 +-DBI::dbSendQuery(conn, statement, ...)
 16.                 \-RSQLite::dbSendQuery(conn, statement, ...)
 17.                   \-RSQLite (local) .local(conn, statement, ...)
 18.                     +-methods::new(...)
 19.                     | +-methods::initialize(value, ...)
 20.                     | \-methods::initialize(value, ...)
 21.                     \-RSQLite:::result_create(conn@ptr, statement)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

--- re-building ‘IntroToAnnotationPackages.Rnw’ using knitr
--- finished re-building ‘IntroToAnnotationPackages.Rnw’

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

Error: Vignette re-building failed.
Execution halted

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

Status: 3 ERRORs, 1 WARNING, 2 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/AnnotationDbi.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL AnnotationDbi
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’
* installing *source* package ‘AnnotationDbi’ ...
** this is package ‘AnnotationDbi’ version ‘1.69.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘packageName’ in package ‘AnnotationDbi’
Creating a generic function for ‘ls’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘eapply’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘exists’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘sample’ from package ‘base’ in package ‘AnnotationDbi’
** 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 (AnnotationDbi)

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("AnnotationDbi") || stop("unable to load AnnotationDbi package")
Loading required package: AnnotationDbi
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: 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: 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
> 
> AnnotationDbi:::.test()
Loading required package: org.Hs.eg.db

Error : database or disk is full

'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
Loading required package: RSQLite
Loading required package: org.At.tair.db

Loading required package: org.Sc.sgd.db

Loading required package: GO.db

Loading required package: hgu95av2.db
'select()' returned many:many mapping between keys and columns
Timing stopped at: 0.308 0.003 0.315
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'head': database or disk is full
In addition: Warning message:
call dbDisconnect() when finished working with a connection 
Timing stopped at: 0.257 0.011 0.27
Error : database or disk is full
'select()' returned many:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned many:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned many:1 mapping between keys and columns
Timing stopped at: 0.262 0.009 0.272
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'head': database or disk is full
'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 1:1 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 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
Timing stopped at: 0.123 0.004 0.126
Error : database or disk is full
In addition: Warning messages:
1: In .deprecatedColsMessage() :
  Accessing gene location information via 'CHR','CHRLOC','CHRLOCEND' is
  deprecated. Please use a range based accessor like genes(), or select() with
  columns values like TXCHROM and TXSTART on a TxDb or OrganismDb object
  instead.
2: In .deprecatedColsMessage() :
  Accessing gene location information via 'CHR','CHRLOC','CHRLOCEND' is
  deprecated. Please use a range based accessor like genes(), or select() with
  columns values like TXCHROM and TXSTART on a TxDb or OrganismDb object
  instead.
3: In .deprecatedColsMessage() :
  Accessing gene location information via 'CHR','CHRLOC','CHRLOCEND' is
  deprecated. Please use a range based accessor like genes(), or select() with
  columns values like TXCHROM and TXSTART on a TxDb or OrganismDb object
  instead.
Timing stopped at: 0.178 0 0.182
Error : database or disk is full
'select()' returned 1:1 mapping between keys and columns
Warning: You have selected the following columns that can have a many to one
  relationship with the primary key: ACCNUM, ALIAS, ENSEMBL,
  ENSEMBLPROT, ENSEMBLTRANS, ENZYME, EVIDENCE, EVIDENCEALL, GO, GOALL,
  IPI, MAP, OMIM, ONTOLOGY, ONTOLOGYALL, PATH, PFAM, PMID, PROSITE,
  REFSEQ, UCSCKG, UNIPROT . Because you have selected more than a few
  such columns there is a risk that this selection may balloon up into
  a very large result as the number of rows returned multiplies
  accordingly. To experience smaller/more manageable results and faster
  retrieval times, you might want to consider selecting these columns
  separately.
Timing stopped at: 0.155 0.011 0.173
Error : database or disk is full
Timing stopped at: 0.183 0.001 0.184
Error : database or disk is full
Timing stopped at: 0.245 0.005 0.25
Error : database or disk is full
'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 many:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned many:1 mapping between keys and columns
Timing stopped at: 0.01 0 0.011
Error : .onLoad failed in loadNamespace() for 'org.testing.db', details:
  call: NULL
  error: database disk image is malformed
In addition: Warning messages:
1: Couldn't set cache size: database disk image is malformed
Use `cache_size` = NULL to turn off this warning. 
2: Couldn't set synchronous mode: database disk image is malformed
Use `synchronous` = NULL to turn off this warning. 
3: Couldn't set cache size: database disk image is malformed
Use `cache_size` = NULL to turn off this warning. 
4: Couldn't set synchronous mode: database disk image is malformed
Use `synchronous` = NULL to turn off this warning. 
Timing stopped at: 0 0 0.001
Error in loadNamespace(x) : there is no package called 'org.testing.db'
Timing stopped at: 0 0 0
Error in loadNamespace(x) : there is no package called 'org.testing.db'
Timing stopped at: 0 0 0
Error in loadNamespace(x) : there is no package called 'org.testing.db'
Timing stopped at: 0 0 0
Error in loadNamespace(x) : there is no package called 'org.testing.db'
Timing stopped at: 0 0 0.001
Error in loadNamespace(x) : there is no package called 'org.testing.db'
Loading required package: reactome.db
'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


RUNIT TEST PROTOCOL -- Fri Apr  4 07:12:31 2025 
*********************************************** 
Number of test functions: 49 
Number of errors: 15 
Number of failures: 0 

 
1 Test Suite : 
AnnotationDbi RUnit Tests - 49 test functions, 15 errors, 0 failures
ERROR in /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/AnnotationDbi/unitTests/test_bimap.R: Error while sourcing  /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/AnnotationDbi/unitTests/test_bimap.R : Error : database or disk is full
ERROR in test_keys: Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'head': database or disk is full
ERROR in test_keys_advancedArgs: Error : database or disk is full
ERROR in test_select1: Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'head': database or disk is full
ERROR in test_select12: Error : database or disk is full
ERROR in test_select13: Error : database or disk is full
ERROR in test_select15: Error : database or disk is full
ERROR in test_select16: Error : database or disk is full
ERROR in test_select2: Error : database or disk is full
ERROR in test_columns: Error : .onLoad failed in loadNamespace() for 'org.testing.db', details:
  call: NULL
  error: database disk image is malformed
ERROR in test_keys: Error in loadNamespace(x) : there is no package called 'org.testing.db'
ERROR in test_keysLow: Error in loadNamespace(x) : there is no package called 'org.testing.db'
ERROR in test_keytypes: Error in loadNamespace(x) : there is no package called 'org.testing.db'
ERROR in test_select: Error in loadNamespace(x) : there is no package called 'org.testing.db'
ERROR in test_selectLow: Error in loadNamespace(x) : there is no package called 'org.testing.db'

Test files with failing tests

   test_bimap.R 
     /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/AnnotationDbi/unitTests/test_bimap.R 

   test_select.R 
     test_keys 
     test_keys_advancedArgs 
     test_select1 
     test_select12 
     test_select13 
     test_select15 
     test_select16 
     test_select2 

   test_select_NOSCHEMA.R 
     test_columns 
     test_keys 
     test_keysLow 
     test_keytypes 
     test_select 
     test_selectLow 


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