Multiple platform build/check report for BioC 3.11 - CHECK report for annotate on celaya2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:annotate.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings annotate_1.65.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/annotate.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘annotate/DESCRIPTION’ ... OK
* this is package ‘annotate’ version ‘1.65.0’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
chrCats        24.100  0.103  24.204
blastSequences  0.227  0.022  20.172
* 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

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL annotate
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/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)

Tests output


R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 -- Thu Jan 16 01:45:05 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 
 10.363   1.266  11.595

Example timings

name	user	system	elapsed
ACCNUMStats	2.381	0.137	2.517
GO2heatmap	0.326	0.028	0.355
GOmnplot	0.132	0.014	0.145
HTMLPage-class	0.000	0.000	0.001
LL2homology	0.000	0.001	0.001
PMIDAmat	0.160	0.007	0.172
PWAmat	2.824	0.135	2.959
UniGeneQuery	0.001	0.000	0.002
accessionToUID	0.473	0.098	4.125
annPkgName	0.001	0.000	0.002
aqListGOIDs	0.377	0.076	0.454
blastSequences	0.227	0.022	20.172
buildChromLocation	1.230	0.094	1.325
buildPubMedAbst	0.062	0.004	0.536
chrCats	24.100	0.103	24.204
chromLocation-class	1.147	0.155	1.302
compatibleVersions	0.078	0.005	0.082
dropECode	0.088	0.003	0.091
entrezGeneByID	0.001	0.001	0.002
entrezGeneQuery	0.002	0.000	0.001
filterGOByOntology	0.150	0.013	0.163
findNeighbors	0.040	0.006	0.049
genbank	0.271	0.055	1.003
getAnnMap	0.068	0.019	0.097
getEvidence	0.117	0.003	0.120
getGOTerm	0.400	0.023	0.449
getOntology	0.085	0.013	0.098
getPMInfo	0.682	0.020	1.276
getSYMBOL	0.159	0.023	0.186
getSeq4Acc	0.013	0.003	0.272
hasGOannote	0.041	0.001	0.042
hgByChroms	0.022	0.007	0.029
hgCLengths	0.003	0.002	0.004
hgu95Achroloc	0.096	0.016	0.112
hgu95Achrom	0.090	0.015	0.106
hgu95All	0.102	0.015	0.117
hgu95Asym	0.098	0.016	0.114
homoData-class	0.003	0.000	0.004
htmlpage	0.043	0.004	0.048
isValidkey	0.001	0.000	0.000
makeAnchor	0.002	0.000	0.002
organism	1.046	0.107	1.158
p2LL	0.000	0.001	0.001
pm.abstGrep	1.495	0.083	2.683
pm.getabst	1.364	0.082	2.462
pm.titles	1.519	0.073	2.539
pmAbst2HTML	0.092	0.007	1.060
pmid2MIAME	0	0	0
pmidQuery	0.000	0.000	0.001
pubMedAbst-class	0.061	0.004	0.503
pubmed	0.024	0.005	0.453
readGEOAnn	0.001	0.000	0.000
serializeEnv	0.002	0.001	0.003
setRepository	0.003	0.001	0.004
updateSymbolsToValidKeys	0.000	0.001	0.001
usedChromGenes	0.139	0.012	0.151

CHECK report for annotate on celaya2

Summary

Command output

Installation output

Tests output

Example timings