Package: annotate

Version: 1.61.1

Command: /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_1.61.1.tar.gz

StartedAt: 2019-04-08 23:50:25 -0400 (Mon, 08 Apr 2019)

EndedAt: 2019-04-08 23:54:02 -0400 (Mon, 08 Apr 2019)

EllapsedTime: 217.1 seconds

RetCode: 0

Status:  OK

CheckDir: annotate.Rcheck

Warnings: 0

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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_1.61.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/annotate.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.61.1’
* 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 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        21.242  0.079  21.321
blastSequences  0.281  0.021  23.353
* 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

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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)

R Under development (unstable) (2019-03-18 r76245) -- "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, 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 23:53:53 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 
  8.246   0.997   9.373 

name	user	system	elapsed
ACCNUMStats	2.565	0.113	2.679
GO2heatmap	0.217	0.019	0.237
GOmnplot	0.069	0.015	0.085
HTMLPage-class	0.001	0.000	0.000
LL2homology	0.000	0.001	0.001
PMIDAmat	0.111	0.006	0.122
PWAmat	2.675	0.112	2.786
UniGeneQuery	0.002	0.000	0.002
accessionToUID	0.382	0.075	1.955
annPkgName	0.001	0.000	0.002
aqListGOIDs	0.429	0.073	0.502
blastSequences	0.281	0.021	23.353
buildChromLocation	0.885	0.095	0.980
buildPubMedAbst	0.051	0.007	0.472
chrCats	21.242	0.079	21.321
chromLocation-class	0.972	0.122	1.094
compatibleVersions	0.052	0.004	0.055
dropECode	0.078	0.003	0.081
entrezGeneByID	0.001	0.000	0.001
entrezGeneQuery	0.002	0.000	0.003
filterGOByOntology	0.156	0.016	0.171
findNeighbors	0.028	0.006	0.040
genbank	0.225	0.040	0.802
getAnnMap	0.058	0.017	0.082
getEvidence	0.110	0.003	0.113
getGOTerm	0.408	0.026	0.439
getOntology	0.080	0.003	0.084
getPMInfo	0.585	0.008	1.104
getSYMBOL	0.155	0.022	0.180
getSeq4Acc	0.013	0.002	0.311
hasGOannote	0.041	0.002	0.043
hgByChroms	0.023	0.007	0.030
hgCLengths	0.003	0.002	0.005
hgu95Achroloc	0.071	0.009	0.079
hgu95Achrom	0.074	0.010	0.084
hgu95All	0.087	0.013	0.101
hgu95Asym	0.089	0.013	0.101
homoData-class	0.002	0.000	0.003
htmlpage	0.036	0.004	0.041
isValidkey	0.000	0.001	0.000
makeAnchor	0.001	0.000	0.001
organism	0.925	0.078	1.004
p2LL	0.001	0.000	0.000
pm.abstGrep	1.566	0.069	3.028
pm.getabst	1.623	0.063	2.873
pm.titles	1.734	0.065	2.991
pmAbst2HTML	0.081	0.007	1.004
pmid2MIAME	0.000	0.000	0.001
pmidQuery	0.001	0.001	0.001
pubMedAbst-class	0.061	0.004	0.480
pubmed	0.030	0.004	0.448
readGEOAnn	0.001	0.001	0.000
serializeEnv	0.003	0.001	0.002
setRepository	0.003	0.001	0.003
updateSymbolsToValidKeys	0.000	0.000	0.001
usedChromGenes	0.121	0.015	0.136