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CHECK report for annotate on merida1

This page was generated on 2021-01-24 11:56:36 -0500 (Sun, 24 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE annotate PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 61/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
annotate 1.68.0
Bioconductor Package Maintainer
Snapshot Date: 2021-01-23 14:40:16 -0500 (Sat, 23 Jan 2021)
URL: https://git.bioconductor.org/packages/annotate
Branch: RELEASE_3_12
Last Commit: 98cdb12
Last Changed Date: 2020-10-27 10:21:39 -0500 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.5 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: annotate
Version: 1.68.0
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_1.68.0.tar.gz
StartedAt: 2021-01-23 23:04:04 -0500 (Sat, 23 Jan 2021)
EndedAt: 2021-01-23 23:07:48 -0500 (Sat, 23 Jan 2021)
EllapsedTime: 223.9 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_1.68.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/annotate.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘annotate/DESCRIPTION’ ... OK
* this is package ‘annotate’ version ‘1.68.0’
* 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        17.40  0.085  17.534
blastSequences  0.27  0.014  33.126
* 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:
###
###   /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

annotate.Rcheck/tests/annotate_unit_tests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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.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 -- Sat Jan 23 23:07:38 2021 
*********************************************** 
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 
  8.484   0.627   9.145 

Example timings

annotate.Rcheck/annotate-Ex.timings

nameusersystemelapsed
ACCNUMStats2.6620.0962.761
GO2heatmap0.2120.0090.224
GOmnplot0.0670.0050.072
HTMLPage-class0.0000.0000.001
LL2homology000
PMIDAmat0.1330.0050.141
PWAmat2.3940.0542.450
UniGeneQuery0.0010.0010.001
accessionToUID0.4320.0432.795
annPkgName0.0010.0000.002
aqListGOIDs0.2600.0150.275
blastSequences 0.270 0.01433.126
buildChromLocation1.0260.0341.062
buildPubMedAbst0.0480.0023.896
chrCats17.400 0.08517.534
chromLocation-class0.8160.0450.863
compatibleVersions0.0430.0030.046
dropECode0.0410.0020.043
entrezGeneByID0.0010.0000.001
entrezGeneQuery0.0010.0000.001
filterGOByOntology0.0600.0040.064
findNeighbors0.0240.0030.028
genbank0.1810.0160.980
getAnnMap0.0490.0120.062
getEvidence0.0610.0030.065
getGOTerm0.2410.0090.255
getOntology0.0530.0040.057
getPMInfo0.5390.0181.224
getSYMBOL0.1730.0210.196
getSeq4Acc0.0130.0020.427
hasGOannote0.0280.0010.029
hgByChroms0.0190.0030.021
hgCLengths0.0010.0010.003
hgu95Achroloc0.0720.0050.079
hgu95Achrom0.0570.0040.102
hgu95All0.0670.0040.136
hgu95Asym0.0700.0050.075
homoData-class0.0040.0010.005
htmlpage0.0330.0020.035
isValidkey000
makeAnchor0.0010.0010.001
organism0.9070.0250.932
p2LL0.0000.0000.001
pm.abstGrep1.2730.0382.479
pm.getabst1.3710.0452.714
pm.titles1.4580.0382.543
pmAbst2HTML0.0840.0050.605
pmid2MIAME0.0010.0000.000
pmidQuery0.0010.0000.001
pubMedAbst-class0.0610.0030.533
pubmed0.0320.0020.906
readGEOAnn0.0000.0010.000
serializeEnv0.0020.0010.002
setRepository0.0010.0010.002
updateSymbolsToValidKeys000
usedChromGenes0.0950.0060.102