Bioconductor Package Maintainer
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/annotate |
| Branch: RELEASE_3_10 |
| Last Commit: e272e0b |
| Last Changed Date: 2019-10-29 13:07:20 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:03:56 -0400 (Wed, 15 Apr 2020).
| Package 60/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| annotate 1.64.0 Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: annotate |
| Version: 1.64.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:annotate.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings annotate_1.64.0.tar.gz |
| StartedAt: 2020-04-15 00:09:12 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 00:13:29 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 257.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: annotate.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:annotate.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings annotate_1.64.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/annotate.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘annotate/DESCRIPTION’ ... OK
* this is package ‘annotate’ version ‘1.64.0’
* 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 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 or elapsed time > 5s
user system elapsed
chrCats 13.304 0.004 13.434
blastSequences 1.624 0.212 118.517
* 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
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL annotate ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-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 ** 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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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, 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:base':
expand.grid
Loading required package: org.Hs.eg.db
'select()' returned 1:many mapping between keys and columns
RUNIT TEST PROTOCOL -- Wed Apr 15 00:13:24 2020
***********************************************
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
6.664 0.248 6.957
annotate.Rcheck/annotate-Ex.timings
| name | user | system | elapsed | |
| ACCNUMStats | 1.432 | 0.028 | 1.471 | |
| GO2heatmap | 0.176 | 0.000 | 0.252 | |
| GOmnplot | 0.092 | 0.000 | 0.094 | |
| HTMLPage-class | 0.004 | 0.000 | 0.000 | |
| LL2homology | 0 | 0 | 0 | |
| PMIDAmat | 0.120 | 0.008 | 0.510 | |
| PWAmat | 2.056 | 0.040 | 2.103 | |
| UniGeneQuery | 0 | 0 | 0 | |
| accessionToUID | 0.692 | 0.028 | 1.788 | |
| annPkgName | 0 | 0 | 0 | |
| aqListGOIDs | 0.340 | 0.024 | 0.363 | |
| blastSequences | 1.624 | 0.212 | 118.517 | |
| buildChromLocation | 0.972 | 0.008 | 0.985 | |
| buildPubMedAbst | 0.136 | 0.000 | 0.447 | |
| chrCats | 13.304 | 0.004 | 13.434 | |
| chromLocation-class | 0.700 | 0.008 | 0.714 | |
| compatibleVersions | 0.052 | 0.000 | 0.052 | |
| dropECode | 0.060 | 0.008 | 0.068 | |
| entrezGeneByID | 0.004 | 0.000 | 0.001 | |
| entrezGeneQuery | 0.000 | 0.000 | 0.001 | |
| filterGOByOntology | 0.108 | 0.008 | 0.115 | |
| findNeighbors | 0.032 | 0.000 | 0.109 | |
| genbank | 0.288 | 0.008 | 0.672 | |
| getAnnMap | 0.040 | 0.012 | 1.056 | |
| getEvidence | 0.068 | 0.000 | 0.069 | |
| getGOTerm | 0.332 | 0.008 | 0.606 | |
| getOntology | 0.052 | 0.008 | 0.061 | |
| getPMInfo | 0.552 | 0.000 | 1.181 | |
| getSYMBOL | 0.124 | 0.008 | 0.357 | |
| getSeq4Acc | 0.080 | 0.008 | 0.285 | |
| hasGOannote | 0.036 | 0.000 | 0.035 | |
| hgByChroms | 0.020 | 0.000 | 0.022 | |
| hgCLengths | 0.000 | 0.000 | 0.002 | |
| hgu95Achroloc | 0.100 | 0.000 | 0.097 | |
| hgu95Achrom | 0.076 | 0.004 | 0.082 | |
| hgu95All | 0.084 | 0.004 | 0.089 | |
| hgu95Asym | 0.084 | 0.004 | 0.086 | |
| homoData-class | 0.004 | 0.000 | 0.003 | |
| htmlpage | 0.020 | 0.000 | 0.022 | |
| isValidkey | 0 | 0 | 0 | |
| makeAnchor | 0 | 0 | 0 | |
| organism | 0.712 | 0.000 | 0.711 | |
| p2LL | 0 | 0 | 0 | |
| pm.abstGrep | 1.340 | 0.000 | 2.888 | |
| pm.getabst | 1.068 | 0.012 | 1.981 | |
| pm.titles | 1.448 | 0.008 | 2.338 | |
| pmAbst2HTML | 0.116 | 0.012 | 0.523 | |
| pmid2MIAME | 0 | 0 | 0 | |
| pmidQuery | 0 | 0 | 0 | |
| pubMedAbst-class | 0.120 | 0.004 | 0.466 | |
| pubmed | 0.096 | 0.004 | 0.431 | |
| readGEOAnn | 0 | 0 | 0 | |
| serializeEnv | 0.000 | 0.000 | 0.002 | |
| setRepository | 0.000 | 0.004 | 0.001 | |
| updateSymbolsToValidKeys | 0 | 0 | 0 | |
| usedChromGenes | 0.116 | 0.004 | 0.126 | |