Multiple platform build/check report for BioC 3.10 - CHECK report for annotate on merida1

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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_1.64.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/annotate.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.64.0’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
chrCats        15.417  0.059  15.591
blastSequences  0.286  0.015  18.756
* 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/3.6/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 version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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 -- Wed Apr 15 00:24:20 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 
  7.521   0.659   8.336

Example timings

name	user	system	elapsed
ACCNUMStats	2.349	0.065	2.433
GO2heatmap	0.230	0.011	0.244
GOmnplot	0.064	0.004	0.070
HTMLPage-class	0.000	0.001	0.001
LL2homology	0.000	0.000	0.001
PMIDAmat	0.126	0.004	0.130
PWAmat	2.096	0.064	2.173
UniGeneQuery	0.001	0.000	0.002
accessionToUID	0.353	0.039	1.790
annPkgName	0.001	0.000	0.001
aqListGOIDs	0.344	0.030	0.375
blastSequences	0.286	0.015	18.756
buildChromLocation	1.084	0.058	1.153
buildPubMedAbst	0.053	0.002	0.357
chrCats	15.417	0.059	15.591
chromLocation-class	0.924	0.049	0.981
compatibleVersions	0.028	0.002	0.029
dropECode	0.041	0.002	0.043
entrezGeneByID	0.001	0.000	0.002
entrezGeneQuery	0.001	0.000	0.001
filterGOByOntology	0.090	0.004	0.095
findNeighbors	0.019	0.002	0.022
genbank	0.167	0.020	0.611
getAnnMap	0.041	0.010	0.052
getEvidence	0.053	0.003	0.055
getGOTerm	0.265	0.011	0.277
getOntology	0.042	0.002	0.045
getPMInfo	0.464	0.009	0.842
getSYMBOL	0.141	0.010	0.153
getSeq4Acc	0.010	0.002	0.266
hasGOannote	0.028	0.001	0.028
hgByChroms	0.016	0.003	0.018
hgCLengths	0.001	0.001	0.002
hgu95Achroloc	0.076	0.005	0.082
hgu95Achrom	0.061	0.008	0.070
hgu95All	0.068	0.007	0.074
hgu95Asym	0.072	0.004	0.077
homoData-class	0.003	0.000	0.002
htmlpage	0.021	0.001	0.022
isValidkey	0.000	0.001	0.000
makeAnchor	0.000	0.000	0.001
organism	0.781	0.028	0.821
p2LL	0.001	0.000	0.001
pm.abstGrep	1.139	0.042	2.443
pm.getabst	1.168	0.045	2.202
pm.titles	1.264	0.040	2.292
pmAbst2HTML	0.068	0.004	1.398
pmid2MIAME	0.000	0.000	0.001
pmidQuery	0.001	0.000	0.001
pubMedAbst-class	0.048	0.003	0.424
pubmed	0.023	0.003	0.434
readGEOAnn	0	0	0
serializeEnv	0.002	0.001	0.002
setRepository	0.002	0.000	0.003
updateSymbolsToValidKeys	0	0	0
usedChromGenes	0.107	0.007	0.115

CHECK report for annotate on merida1

Summary

Command output

Installation output

Tests output

Example timings