| Back to First build/check report with an "external build node" |
This page was generated on 2023-06-01 18:17:19 -0400 (Thu, 01 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| xps15 | Linux (Ubuntu 23.04) | x86_64 | 4.3.0 Patched (2023-05-23 r84466) -- "Already Tomorrow" | 544 |
| 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: 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 4/91 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||||
| annotate 1.79.0 (landing page) Bioconductor Package Maintainer
| xps15 | Linux (Ubuntu 23.04) / x86_64 | OK | OK | OK | ||||||||
| Package: annotate |
| Version: 1.79.0 |
| Command: /home/hpages/bbs-3.18-bioc/R/bin/R CMD check --install=check:annotate.install-out.txt --library=/home/hpages/bbs-3.18-bioc-testing/Rlibs --timings annotate_1.79.0.tar.gz |
| StartedAt: 2023-06-01 12:57:19 -0700 (Thu, 01 Jun 2023) |
| EndedAt: 2023-06-01 13:03:45 -0700 (Thu, 01 Jun 2023) |
| EllapsedTime: 385.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: annotate.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/hpages/bbs-3.18-bioc/R/bin/R CMD check --install=check:annotate.install-out.txt --library=/home/hpages/bbs-3.18-bioc-testing/Rlibs --timings annotate_1.79.0.tar.gz
###
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* using log directory ‘/home/hpages/bbs-3.18-bioc-testing/meat/annotate.Rcheck’
* using R version 4.3.0 Patched (2023-05-23 r84466)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 12.2.0-17ubuntu1) 12.2.0
GNU Fortran (Ubuntu 12.2.0-17ubuntu1) 12.2.0
* running under: Ubuntu 23.04
* 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 7.343 0.068 7.413
accessionToUID 0.617 0.028 6.421
blastSequences 0.561 0.003 47.246
* 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/hpages/bbs-3.18-bioc-testing/meat/annotate.Rcheck/00check.log’
for details.
annotate.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/hpages/bbs-3.18-bioc/R/bin/R CMD INSTALL annotate ### ############################################################################## ############################################################################## * installing to library ‘/home/hpages/bbs-3.18-bioc-testing/Rlibs’ * 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 Patched (2023-05-23 r84466) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 -- Thu Jun 1 13:00:51 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
9.145 0.506 9.632
annotate.Rcheck/annotate-Ex.timings
| name | user | system | elapsed | |
| ACCNUMStats | 1.555 | 0.028 | 1.594 | |
| GO2heatmap | 0.153 | 0.001 | 0.155 | |
| GOmnplot | 0.06 | 0.00 | 0.06 | |
| HTMLPage-class | 0 | 0 | 0 | |
| LL2homology | 0 | 0 | 0 | |
| PMIDAmat | 0.085 | 0.000 | 0.089 | |
| PWAmat | 1.932 | 0.024 | 1.957 | |
| UniGeneQuery | 0.001 | 0.000 | 0.001 | |
| accessionToUID | 0.617 | 0.028 | 6.421 | |
| annPkgName | 0.000 | 0.000 | 0.001 | |
| aqListGOIDs | 0.123 | 0.016 | 0.139 | |
| blastSequences | 0.561 | 0.003 | 47.246 | |
| buildChromLocation | 0.577 | 0.000 | 0.576 | |
| buildPubMedAbst | 0.093 | 0.000 | 0.945 | |
| chrCats | 7.343 | 0.068 | 7.413 | |
| chromLocation-class | 0.605 | 0.008 | 0.613 | |
| compatibleVersions | 0.033 | 0.000 | 0.033 | |
| dropECode | 0.043 | 0.000 | 0.043 | |
| entrezGeneByID | 0 | 0 | 0 | |
| entrezGeneQuery | 0.001 | 0.000 | 0.001 | |
| filterGOByOntology | 0.038 | 0.012 | 0.050 | |
| findNeighbors | 0.022 | 0.000 | 0.035 | |
| genbank | 0.347 | 0.004 | 2.283 | |
| getAnnMap | 0.027 | 0.008 | 0.034 | |
| getEvidence | 0.074 | 0.000 | 0.084 | |
| getGOTerm | 0.288 | 0.004 | 0.293 | |
| getOntology | 0.051 | 0.000 | 0.051 | |
| getPMInfo | 0.320 | 0.004 | 1.485 | |
| getSYMBOL | 0.095 | 0.008 | 0.119 | |
| getSeq4Acc | 0.057 | 0.004 | 1.327 | |
| hasGOannote | 0.025 | 0.000 | 0.025 | |
| hgByChroms | 0.019 | 0.000 | 0.018 | |
| hgCLengths | 0.001 | 0.000 | 0.001 | |
| hgu95Achroloc | 0.368 | 0.004 | 0.373 | |
| hgu95Achrom | 0.055 | 0.000 | 0.055 | |
| hgu95All | 0.059 | 0.003 | 0.063 | |
| hgu95Asym | 0.065 | 0.000 | 0.065 | |
| homoData-class | 0.002 | 0.000 | 0.002 | |
| htmlpage | 0.018 | 0.000 | 0.018 | |
| isValidkey | 0 | 0 | 0 | |
| makeAnchor | 0.000 | 0.000 | 0.001 | |
| organism | 0.506 | 0.000 | 0.507 | |
| p2LL | 0 | 0 | 0 | |
| pm.abstGrep | 1.058 | 0.004 | 3.454 | |
| pm.getabst | 0.81 | 0.02 | 2.62 | |
| pm.titles | 1.143 | 0.036 | 3.326 | |
| pmAbst2HTML | 0.094 | 0.004 | 1.182 | |
| pmid2MIAME | 0 | 0 | 0 | |
| pmidQuery | 0.001 | 0.000 | 0.001 | |
| pubMedAbst-class | 0.082 | 0.012 | 1.212 | |
| pubmed | 0.074 | 0.004 | 1.483 | |
| readGEOAnn | 0.001 | 0.000 | 0.000 | |
| serializeEnv | 0.003 | 0.000 | 0.002 | |
| setRepository | 0.001 | 0.000 | 0.001 | |
| updateSymbolsToValidKeys | 0 | 0 | 0 | |
| usedChromGenes | 0.110 | 0.000 | 0.111 | |