| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:06:55 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 56/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| annotate 1.73.0 (landing page) Bioconductor Package Maintainer
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: annotate |
| Version: 1.73.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:annotate.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings annotate_1.73.0.tar.gz |
| StartedAt: 2022-03-17 18:26:14 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:29:10 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 176.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: annotate.Rcheck |
| Warnings: 0 |
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### Running command:
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### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:annotate.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings annotate_1.73.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/annotate.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'annotate/DESCRIPTION' ... OK
* this is package 'annotate' version '1.73.0'
* 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 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 dependencies in R code ... OK
* 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 ... 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 6.54 0.02 6.56
blastSequences 0.14 0.02 43.53
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
annotate.Rcheck/00install.out
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### Running command:
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### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL annotate
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'annotate' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'annotate'
finding HTML links ... done
ACCNUMStats html
GO2heatmap html
GOmnplot html
HTMLPage-class html
LL2homology html
PMIDAmat html
PWAmat html
UniGeneQuery html
accessionToUID html
annPkgName html
annotate-defunct html
aqListGOIDs html
blastSequences html
buildChromLocation html
buildPubMedAbst html
chrCats html
chromLocation-class html
compatibleVersions html
dropECode html
entrezGeneByID html
entrezGeneQuery html
filterGOByOntology html
findNeighbors html
genbank html
getAnnMap html
getEvidence html
getGOTerm html
getOntology html
getPMInfo html
getSYMBOL html
getSeq4Acc html
getTDRows html
hasGOannote html
hgByChroms html
hgCLengths html
hgu95AProbLocs html
hgu95Achroloc html
hgu95Achrom html
hgu95All html
hgu95Asym html
homoData-class html
htmlpage html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-annotate/00new/annotate/help/htmlpage.html
isValidkey html
makeAnchor html
mapOrgs html
organism html
p2LL html
pm.abstGrep html
pm.getabst html
pm.titles html
pmAbst2HTML html
pmid2MIAME html
pmidQuery html
pubMedAbst-class html
pubmed html
readGEOAnn html
serializeEnv html
setRepository html
updateSymbolsToValidKeys html
usedChromGenes html
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'RCM' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'TCseq' is missing or broken
done
annotate.Rcheck/tests/annotate_unit_tests.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, 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 objects are masked from 'package:base':
I, expand.grid, unname
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: org.Hs.eg.db
'select()' returned 1:many mapping between keys and columns
RUNIT TEST PROTOCOL -- Thu Mar 17 18:28:59 2022
***********************************************
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
5.21 0.65 5.85
annotate.Rcheck/annotate-Ex.timings
| name | user | system | elapsed | |
| ACCNUMStats | 1.22 | 0.06 | 1.28 | |
| GO2heatmap | 0.09 | 0.00 | 0.09 | |
| GOmnplot | 0.03 | 0.02 | 0.05 | |
| HTMLPage-class | 0 | 0 | 0 | |
| LL2homology | 0 | 0 | 0 | |
| PMIDAmat | 0.06 | 0.02 | 0.08 | |
| PWAmat | 1.49 | 0.03 | 1.51 | |
| UniGeneQuery | 0.01 | 0.00 | 0.02 | |
| accessionToUID | 0.22 | 0.03 | 3.50 | |
| annPkgName | 0 | 0 | 0 | |
| aqListGOIDs | 0.14 | 0.01 | 0.16 | |
| blastSequences | 0.14 | 0.02 | 43.53 | |
| buildChromLocation | 0.44 | 0.00 | 0.44 | |
| buildPubMedAbst | 0.02 | 0.00 | 0.73 | |
| chrCats | 6.54 | 0.02 | 6.56 | |
| chromLocation-class | 0.30 | 0.18 | 0.49 | |
| compatibleVersions | 0.02 | 0.02 | 0.03 | |
| dropECode | 0.03 | 0.00 | 0.03 | |
| entrezGeneByID | 0 | 0 | 0 | |
| entrezGeneQuery | 0 | 0 | 0 | |
| filterGOByOntology | 0.04 | 0.00 | 0.05 | |
| findNeighbors | 0.02 | 0.00 | 0.15 | |
| genbank | 0.13 | 0.00 | 1.11 | |
| getAnnMap | 0.03 | 0.00 | 0.10 | |
| getEvidence | 0.05 | 0.00 | 0.05 | |
| getGOTerm | 0.12 | 0.00 | 0.12 | |
| getOntology | 0.04 | 0.00 | 0.03 | |
| getPMInfo | 0.20 | 0.00 | 1.02 | |
| getSYMBOL | 0.06 | 0.03 | 0.09 | |
| getSeq4Acc | 0.00 | 0.00 | 0.68 | |
| hasGOannote | 0.02 | 0.00 | 0.01 | |
| hgByChroms | 0.01 | 0.00 | 0.02 | |
| hgCLengths | 0 | 0 | 0 | |
| hgu95Achroloc | 0.06 | 0.00 | 0.06 | |
| hgu95Achrom | 0.05 | 0.00 | 0.05 | |
| hgu95All | 0.05 | 0.00 | 0.04 | |
| hgu95Asym | 0.05 | 0.00 | 0.05 | |
| homoData-class | 0.01 | 0.00 | 0.02 | |
| htmlpage | 0 | 0 | 0 | |
| isValidkey | 0 | 0 | 0 | |
| makeAnchor | 0.02 | 0.00 | 0.01 | |
| organism | 0.40 | 0.05 | 0.45 | |
| p2LL | 0 | 0 | 0 | |
| pm.abstGrep | 0.49 | 0.00 | 1.61 | |
| pm.getabst | 0.54 | 0.01 | 1.83 | |
| pm.titles | 0.82 | 0.02 | 2.00 | |
| pmAbst2HTML | 0.03 | 0.01 | 1.86 | |
| pmid2MIAME | 0 | 0 | 0 | |
| pmidQuery | 0 | 0 | 0 | |
| pubMedAbst-class | 0.01 | 0.00 | 0.83 | |
| pubmed | 0.02 | 0.00 | 0.83 | |
| readGEOAnn | 0 | 0 | 0 | |
| serializeEnv | 0 | 0 | 0 | |
| setRepository | 0 | 0 | 0 | |
| updateSymbolsToValidKeys | 0 | 0 | 0 | |
| usedChromGenes | 0.03 | 0.05 | 0.08 | |