| Back to Rapid builds (Linux only) of a subset of BioC 3.21 Report updated every 6 hours |
This page was generated on 2025-04-04 07:38 -0400 (Fri, 04 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 871 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 11/217 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | |||||||
| annotate 1.85.0 (landing page) Bioconductor Package Maintainer
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||
|
To the developers/maintainers of the annotate package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: annotate |
| Version: 1.85.0 |
| Command: /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:annotate.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings annotate_1.85.0.tar.gz |
| StartedAt: 2025-04-04 07:10:17 -0400 (Fri, 04 Apr 2025) |
| EndedAt: 2025-04-04 07:13:29 -0400 (Fri, 04 Apr 2025) |
| EllapsedTime: 192.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: annotate.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:annotate.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings annotate_1.85.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/annotate.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 ‘annotate/DESCRIPTION’ ... OK
* this is package ‘annotate’ version ‘1.85.0’
* 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 ‘annotate’ can be installed ... OK
* 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 whether startup messages can be suppressed ... 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) chrCats.Rd:13: Escaped LaTeX specials: \_
checkRd: (-1) chrCats.Rd:14: Escaped LaTeX specials: \_
checkRd: (-1) chrCats.Rd:47: Escaped LaTeX specials: \_
checkRd: (-1) chrCats.Rd:53: Escaped LaTeX specials: \_
checkRd: (-1) chrCats.Rd:60: Escaped LaTeX specials: \_
checkRd: (-1) chrCats.Rd:69: Escaped LaTeX specials: \_ \_
checkRd: (-1) chrCats.Rd:77: Escaped LaTeX specials: \_
checkRd: (-1) htmlpage.Rd:56: Escaped LaTeX specials: \_
checkRd: (-1) htmlpage.Rd:57: 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
chrCats 6.843 0.046 6.894
blastSequences 0.162 0.002 31.852
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘annotate_unit_tests.R’
ERROR
Running the tests in ‘tests/annotate_unit_tests.R’ failed.
Last 13 lines of output:
1 Test Suite :
annotate RUnit Tests - 1 test function, 1 error, 0 failures
ERROR in test_getAnnMap: Error : database or disk is full
Test files with failing tests
test_getAnnMap.R
test_getAnnMap
Error in BiocGenerics:::testPackage("annotate") :
unit tests failed for package annotate
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 ‘chromLOC.Rmd’ using rmarkdown
--- finished re-building ‘chromLOC.Rmd’
--- re-building ‘useDataPkgs.Rmd’ using rmarkdown
--- finished re-building ‘useDataPkgs.Rmd’
--- re-building ‘GOusage.Rnw’ using Sweave
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
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
Loading required package: XML
Attaching package: ‘graph’
The following object is masked from ‘package:XML’:
addNode
Attaching package: ‘Rgraphviz’
The following object is masked from ‘package:annotate’:
toFile
The following objects are masked from ‘package:IRanges’:
from, to
The following objects are masked from ‘package:S4Vectors’:
from, to
Loading required package: org.Hs.eg.db
--- finished re-building ‘GOusage.Rnw’
--- re-building ‘annotate.Rnw’ using Sweave
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
Loading required package: XML
Loading required package: org.Hs.eg.db
Error: processing vignette 'annotate.Rnw' failed with diagnostics:
chunk 2 (label = qc)
Error : database or disk is full
--- failed re-building ‘annotate.Rnw’
--- re-building ‘prettyOutput.Rnw’ using Sweave
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
Loading required package: XML
--- finished re-building ‘prettyOutput.Rnw’
--- re-building ‘query.Rnw’ using Sweave
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
Loading required package: XML
Loading required package: org.Hs.eg.db
Read 4 items
Read 3402 items
--- finished re-building ‘query.Rnw’
--- re-building ‘useProbeInfo.Rnw’ using Sweave
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
Loading required package: XML
Loading required package: org.Rn.eg.db
Loading required package: XVector
Loading required package: GenomeInfoDb
Attaching package: ‘Biostrings’
The following object is masked from ‘package:base’:
strsplit
--- finished re-building ‘useProbeInfo.Rnw’
SUMMARY: processing the following file failed:
‘annotate.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/annotate.Rcheck/00check.log’
for details.
annotate.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL annotate ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’ * installing *source* package ‘annotate’ ... ** this is package ‘annotate’ version ‘1.85.0’ ** using staged installation ** R ** data ** 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 (annotate)
annotate.Rcheck/tests/annotate_unit_tests.Rout.fail
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.
> BiocGenerics:::testPackage("annotate")
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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
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: org.Hs.eg.db
Timing stopped at: 0.716 0.083 0.808
Error : database or disk is full
RUNIT TEST PROTOCOL -- Fri Apr 4 07:12:31 2025
***********************************************
Number of test functions: 1
Number of errors: 1
Number of failures: 0
1 Test Suite :
annotate RUnit Tests - 1 test function, 1 error, 0 failures
ERROR in test_getAnnMap: Error : database or disk is full
Test files with failing tests
test_getAnnMap.R
test_getAnnMap
Error in BiocGenerics:::testPackage("annotate") :
unit tests failed for package annotate
Execution halted
annotate.Rcheck/annotate-Ex.timings
| name | user | system | elapsed | |
| ACCNUMStats | 0.935 | 0.053 | 0.989 | |
| GO2heatmap | 0.095 | 0.004 | 0.099 | |
| GOmnplot | 0.032 | 0.000 | 0.032 | |
| HTMLPage-class | 0 | 0 | 0 | |
| LL2homology | 0.001 | 0.000 | 0.000 | |
| PMIDAmat | 0.06 | 0.00 | 0.06 | |
| PWAmat | 0.906 | 0.028 | 0.935 | |
| UniGeneQuery | 0.001 | 0.000 | 0.001 | |
| accessionToUID | 0.304 | 0.013 | 1.660 | |
| annPkgName | 0 | 0 | 0 | |
| aqListGOIDs | 0.089 | 0.008 | 0.097 | |
| blastSequences | 0.162 | 0.002 | 31.852 | |
| buildChromLocation | 0.460 | 0.012 | 0.472 | |
| buildPubMedAbst | 0.044 | 0.002 | 0.474 | |
| chrCats | 6.843 | 0.046 | 6.894 | |
| chromLocation-class | 0.435 | 0.030 | 0.466 | |
| compatibleVersions | 0.018 | 0.000 | 0.018 | |
| dropECode | 0.021 | 0.002 | 0.022 | |
| entrezGeneByID | 0.001 | 0.000 | 0.001 | |
| entrezGeneQuery | 0 | 0 | 0 | |
| filterGOByOntology | 0.028 | 0.003 | 0.031 | |
| findNeighbors | 0.012 | 0.002 | 0.013 | |
| genbank | 0.134 | 0.003 | 0.597 | |
| getAnnMap | 0.015 | 0.000 | 0.016 | |
| getEvidence | 0.029 | 0.000 | 0.029 | |
| getGOTerm | 0.103 | 0.004 | 0.108 | |
| getOntology | 0.024 | 0.000 | 0.025 | |
| getPMInfo | 0.254 | 0.002 | 0.688 | |
| getSYMBOL | 0.066 | 0.007 | 0.073 | |
| getSeq4Acc | 0.032 | 0.001 | 0.325 | |
| hasGOannote | 0.014 | 0.001 | 0.015 | |
| hgByChroms | 0.012 | 0.001 | 0.014 | |
| hgCLengths | 0.000 | 0.001 | 0.001 | |
| hgu95Achroloc | 0.043 | 0.000 | 0.043 | |
| hgu95Achrom | 0.029 | 0.003 | 0.031 | |
| hgu95All | 0.036 | 0.001 | 0.037 | |
| hgu95Asym | 0.036 | 0.002 | 0.038 | |
| homoData-class | 0.002 | 0.000 | 0.001 | |
| htmlpage | 0.012 | 0.001 | 0.012 | |
| isValidkey | 0 | 0 | 0 | |
| makeAnchor | 0 | 0 | 0 | |
| organism | 0.468 | 0.001 | 0.470 | |
| p2LL | 0 | 0 | 0 | |
| pm.abstGrep | 0.609 | 0.006 | 1.340 | |
| pm.getabst | 0.720 | 0.031 | 1.474 | |
| pm.titles | 0.633 | 0.017 | 1.401 | |
| pmAbst2HTML | 0.147 | 0.002 | 0.515 | |
| pmid2MIAME | 0 | 0 | 0 | |
| pmidQuery | 0.000 | 0.000 | 0.001 | |
| pubMedAbst-class | 0.045 | 0.004 | 0.399 | |
| pubmed | 0.035 | 0.002 | 0.484 | |
| readGEOAnn | 0 | 0 | 0 | |
| serializeEnv | 0.001 | 0.000 | 0.002 | |
| setRepository | 0.000 | 0.000 | 0.001 | |
| updateSymbolsToValidKeys | 0 | 0 | 0 | |
| usedChromGenes | 0.055 | 0.004 | 0.059 | |