Bioconductor Package Maintainer
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/annotate |
| Branch: master |
| Last Commit: b8f74c5 |
| Last Changed Date: 2019-03-07 15:15:21 -0400 (Thu, 07 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 11:22:30 -0400 (Tue, 09 Apr 2019).
| Package 56/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| annotate 1.61.1 Bioconductor Package Maintainer
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK |
| Package: annotate |
| Version: 1.61.1 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:annotate.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings annotate_1.61.1.tar.gz |
| StartedAt: 2019-04-08 22:42:43 -0400 (Mon, 08 Apr 2019) |
| EndedAt: 2019-04-08 22:45:30 -0400 (Mon, 08 Apr 2019) |
| EllapsedTime: 167.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: annotate.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:annotate.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings annotate_1.61.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/annotate.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.61.1’
* 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 13.601 0.009 13.641
blastSequences 0.523 0.067 27.279
* 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-3.9-bioc/R/bin/R CMD INSTALL annotate ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-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 Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 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, colMeans, colSums, 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, rowMeans, rowSums,
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 -- Mon Apr 8 22:45:26 2019
***********************************************
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
6.874 0.244 7.123
annotate.Rcheck/annotate-Ex.timings
| name | user | system | elapsed | |
| ACCNUMStats | 1.835 | 0.036 | 1.872 | |
| GO2heatmap | 0.187 | 0.000 | 0.236 | |
| GOmnplot | 0.062 | 0.004 | 0.067 | |
| HTMLPage-class | 0.000 | 0.000 | 0.001 | |
| LL2homology | 0 | 0 | 0 | |
| PMIDAmat | 0.118 | 0.000 | 0.172 | |
| PWAmat | 1.757 | 0.028 | 1.790 | |
| UniGeneQuery | 0.001 | 0.000 | 0.002 | |
| accessionToUID | 0.587 | 0.056 | 2.046 | |
| annPkgName | 0.000 | 0.000 | 0.001 | |
| aqListGOIDs | 0.385 | 0.048 | 0.433 | |
| blastSequences | 0.523 | 0.067 | 27.279 | |
| buildChromLocation | 0.862 | 0.000 | 0.917 | |
| buildPubMedAbst | 0.123 | 0.004 | 0.491 | |
| chrCats | 13.601 | 0.009 | 13.641 | |
| chromLocation-class | 0.688 | 0.000 | 0.689 | |
| compatibleVersions | 0.057 | 0.000 | 0.057 | |
| dropECode | 0.068 | 0.000 | 0.068 | |
| entrezGeneByID | 0.001 | 0.000 | 0.000 | |
| entrezGeneQuery | 0.001 | 0.000 | 0.001 | |
| filterGOByOntology | 0.110 | 0.004 | 0.115 | |
| findNeighbors | 0.020 | 0.008 | 0.061 | |
| genbank | 0.271 | 0.004 | 1.428 | |
| getAnnMap | 0.049 | 0.008 | 0.195 | |
| getEvidence | 0.083 | 0.000 | 0.084 | |
| getGOTerm | 0.346 | 0.000 | 0.346 | |
| getOntology | 0.046 | 0.000 | 0.046 | |
| getPMInfo | 0.613 | 0.004 | 1.009 | |
| getSYMBOL | 0.180 | 0.008 | 0.268 | |
| getSeq4Acc | 0.071 | 0.008 | 0.400 | |
| hasGOannote | 0.031 | 0.000 | 0.032 | |
| hgByChroms | 0.021 | 0.000 | 0.021 | |
| hgCLengths | 0.000 | 0.001 | 0.002 | |
| hgu95Achroloc | 0.090 | 0.005 | 0.094 | |
| hgu95Achrom | 0.066 | 0.008 | 0.075 | |
| hgu95All | 0.079 | 0.004 | 0.083 | |
| hgu95Asym | 0.089 | 0.000 | 0.089 | |
| homoData-class | 0.003 | 0.000 | 0.003 | |
| htmlpage | 0.028 | 0.000 | 0.029 | |
| isValidkey | 0.001 | 0.000 | 0.000 | |
| makeAnchor | 0.001 | 0.000 | 0.001 | |
| organism | 0.760 | 0.012 | 0.772 | |
| p2LL | 0 | 0 | 0 | |
| pm.abstGrep | 1.154 | 0.016 | 2.066 | |
| pm.getabst | 1.256 | 0.020 | 2.269 | |
| pm.titles | 1.208 | 0.015 | 2.111 | |
| pmAbst2HTML | 0.136 | 0.000 | 0.566 | |
| pmid2MIAME | 0 | 0 | 0 | |
| pmidQuery | 0.001 | 0.000 | 0.001 | |
| pubMedAbst-class | 0.109 | 0.011 | 1.150 | |
| pubmed | 0.075 | 0.000 | 0.544 | |
| readGEOAnn | 0.000 | 0.000 | 0.001 | |
| serializeEnv | 0.002 | 0.000 | 0.002 | |
| setRepository | 0.000 | 0.002 | 0.002 | |
| updateSymbolsToValidKeys | 0.000 | 0.001 | 0.000 | |
| usedChromGenes | 0.096 | 0.017 | 0.112 | |