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CHECK report for annotate on merida1

This page was generated on 2019-04-16 11:53:56 -0400 (Tue, 16 Apr 2019).

Package 53/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
annotate 1.60.1
Bioconductor Package Maintainer
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/annotate
Branch: RELEASE_3_8
Last Commit: 9d8f87d
Last Changed Date: 2019-03-07 16:23:45 -0400 (Thu, 07 Mar 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: annotate
Version: 1.60.1
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_1.60.1.tar.gz
StartedAt: 2019-04-15 22:20:40 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 22:23:51 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 190.9 seconds
RetCode: 0
Status:  OK 
CheckDir: annotate.Rcheck
Warnings: 0

Command output

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### Running 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_1.60.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/annotate.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.60.1’
* 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        17.671  0.068  17.941
blastSequences  0.263  0.013  37.777
* 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

annotate.Rcheck/00install.out

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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/3.5/Resources/library’
* installing *source* package ‘annotate’ ...
** 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
* DONE (annotate)

Tests output

annotate.Rcheck/tests/annotate_unit_tests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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, lengths, 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 15 22:23:45 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 
  7.027   0.489   7.578 

Example timings

annotate.Rcheck/annotate-Ex.timings

nameusersystemelapsed
ACCNUMStats2.4960.0582.617
GO2heatmap0.1560.0090.167
GOmnplot0.0710.0130.085
HTMLPage-class0.0000.0000.001
LL2homology0.0010.0000.001
PMIDAmat0.1390.0050.145
PWAmat2.5150.0612.612
UniGeneQuery0.0010.0000.001
accessionToUID0.3420.0354.528
annPkgName0.0010.0010.001
aqListGOIDs0.3890.0400.432
blastSequences 0.263 0.01337.777
buildChromLocation0.7390.0510.793
buildPubMedAbst0.0480.0030.487
chrCats17.671 0.06817.941
chromLocation-class0.6090.0300.642
compatibleVersions0.0360.0020.038
dropECode0.0460.0010.048
entrezGeneByID0.0010.0000.002
entrezGeneQuery0.0010.0000.001
filterGOByOntology0.1260.0110.137
findNeighbors0.0230.0030.027
genbank0.1800.0170.594
getAnnMap0.0400.0100.052
getEvidence0.0680.0030.071
getGOTerm0.3260.0150.344
getOntology0.0450.0020.047
getPMInfo0.5190.0071.216
getSYMBOL0.1450.0130.158
getSeq4Acc0.0130.0020.272
hasGOannote0.0260.0010.027
hgByChroms0.0170.0040.021
hgCLengths0.0010.0020.004
hgu95Achroloc0.0850.0080.096
hgu95Achrom0.0500.0070.056
hgu95All0.0700.0070.078
hgu95Asym0.0690.0050.077
homoData-class0.0030.0000.002
htmlpage0.0280.0010.030
isValidkey000
makeAnchor0.0010.0000.002
organism0.7210.0310.761
p2LL000
pm.abstGrep1.2300.0512.269
pm.getabst1.2440.0332.229
pm.titles1.3470.0352.330
pmAbst2HTML0.0630.0040.458
pmid2MIAME000
pmidQuery0.0010.0010.000
pubMedAbst-class0.0490.0020.445
pubmed0.0280.0020.420
readGEOAnn0.0010.0010.000
serializeEnv0.0030.0000.003
setRepository0.0020.0000.003
updateSymbolsToValidKeys000
usedChromGenes0.1040.0160.123