| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-31 05:44:29 -0000 (Wed, 31 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4219 |
| 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 | ||||
|
To the developers/maintainers of the annotate package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/annotate.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 66/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| annotate 1.79.0 (landing page) Bioconductor Package Maintainer
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: annotate |
| Version: 1.79.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:annotate.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings annotate_1.79.0.tar.gz |
| StartedAt: 2023-05-30 00:25:22 -0000 (Tue, 30 May 2023) |
| EndedAt: 2023-05-30 00:32:25 -0000 (Tue, 30 May 2023) |
| EllapsedTime: 423.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: annotate.Rcheck |
| Warnings: 0 |
##############################################################################
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### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:annotate.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings annotate_1.79.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/annotate.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘annotate/DESCRIPTION’ ... OK
* this is package ‘annotate’ version ‘1.79.0’
* 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 R 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 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 14.142 0.264 14.406
pm.abstGrep 1.343 0.020 5.191
accessionToUID 1.282 0.048 10.218
blastSequences 1.107 0.024 26.612
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘annotate_unit_tests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘GOusage.Rnw’... OK
‘annotate.Rnw’... OK
‘chromLoc.Rnw’... OK
‘prettyOutput.Rnw’... OK
‘query.Rnw’... OK
‘useDataPkgs.Rnw’... OK
‘useProbeInfo.Rnw’... OK
OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/annotate.Rcheck/00check.log’
for details.
annotate.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL annotate ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘annotate’ ... ** 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
R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
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: '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, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, 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
'select()' returned 1:many mapping between keys and columns
RUNIT TEST PROTOCOL -- Tue May 30 00:29:12 2023
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
annotate RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
10.798 0.549 11.332
annotate.Rcheck/annotate-Ex.timings
| name | user | system | elapsed | |
| ACCNUMStats | 1.666 | 0.019 | 1.686 | |
| GO2heatmap | 0.162 | 0.000 | 0.162 | |
| GOmnplot | 0.050 | 0.000 | 0.051 | |
| HTMLPage-class | 0 | 0 | 0 | |
| LL2homology | 0 | 0 | 0 | |
| PMIDAmat | 0.099 | 0.003 | 0.108 | |
| PWAmat | 2.352 | 0.231 | 2.584 | |
| UniGeneQuery | 0.001 | 0.000 | 0.001 | |
| accessionToUID | 1.282 | 0.048 | 10.218 | |
| annPkgName | 0.000 | 0.001 | 0.001 | |
| aqListGOIDs | 0.153 | 0.034 | 0.189 | |
| blastSequences | 1.107 | 0.024 | 26.612 | |
| buildChromLocation | 0.901 | 0.016 | 0.917 | |
| buildPubMedAbst | 0.223 | 0.012 | 1.811 | |
| chrCats | 14.142 | 0.264 | 14.406 | |
| chromLocation-class | 1.216 | 0.032 | 1.248 | |
| compatibleVersions | 0.038 | 0.000 | 0.038 | |
| dropECode | 0.044 | 0.002 | 0.046 | |
| entrezGeneByID | 0 | 0 | 0 | |
| entrezGeneQuery | 0.001 | 0.000 | 0.001 | |
| filterGOByOntology | 0.065 | 0.000 | 0.065 | |
| findNeighbors | 0.019 | 0.004 | 0.031 | |
| genbank | 0.376 | 0.008 | 3.164 | |
| getAnnMap | 0.022 | 0.003 | 0.027 | |
| getEvidence | 0.057 | 0.000 | 0.057 | |
| getGOTerm | 0.272 | 0.020 | 0.294 | |
| getOntology | 0.043 | 0.000 | 0.044 | |
| getPMInfo | 0.598 | 0.004 | 2.347 | |
| getSYMBOL | 0.120 | 0.004 | 0.128 | |
| getSeq4Acc | 0.205 | 0.000 | 1.596 | |
| hasGOannote | 0.025 | 0.000 | 0.026 | |
| hgByChroms | 0.013 | 0.000 | 0.013 | |
| hgCLengths | 0.001 | 0.000 | 0.001 | |
| hgu95Achroloc | 0.058 | 0.004 | 0.061 | |
| hgu95Achrom | 0.051 | 0.000 | 0.051 | |
| hgu95All | 0.056 | 0.000 | 0.056 | |
| hgu95Asym | 0.057 | 0.000 | 0.058 | |
| homoData-class | 0.003 | 0.000 | 0.003 | |
| htmlpage | 0.019 | 0.003 | 0.022 | |
| isValidkey | 0 | 0 | 0 | |
| makeAnchor | 0.000 | 0.000 | 0.001 | |
| organism | 0.805 | 0.014 | 0.819 | |
| p2LL | 0 | 0 | 0 | |
| pm.abstGrep | 1.343 | 0.020 | 5.191 | |
| pm.getabst | 1.274 | 0.012 | 4.229 | |
| pm.titles | 1.336 | 0.028 | 4.806 | |
| pmAbst2HTML | 0.239 | 0.003 | 1.732 | |
| pmid2MIAME | 0 | 0 | 0 | |
| pmidQuery | 0.001 | 0.000 | 0.000 | |
| pubMedAbst-class | 0.230 | 0.000 | 1.726 | |
| pubmed | 0.214 | 0.000 | 2.011 | |
| readGEOAnn | 0.000 | 0.000 | 0.001 | |
| serializeEnv | 0.002 | 0.001 | 0.002 | |
| setRepository | 0.000 | 0.001 | 0.001 | |
| updateSymbolsToValidKeys | 0.000 | 0.001 | 0.000 | |
| usedChromGenes | 0.071 | 0.004 | 0.075 | |