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CHECK report for annotate on malbec1

This page was generated on 2021-01-25 11:48:01 -0500 (Mon, 25 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: 2021-01-24 14:40:16 -0500 (Sun, 24 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: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:annotate.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings annotate_1.68.0.tar.gz
StartedAt: 2021-01-24 23:25:12 -0500 (Sun, 24 Jan 2021)
EndedAt: 2021-01-24 23:28:22 -0500 (Sun, 24 Jan 2021)
EllapsedTime: 190.4 seconds
RetCode: 0
Status:  OK 
CheckDir: annotate.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:annotate.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings annotate_1.68.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/annotate.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
chrCats        19.680  0.004  19.708
blastSequences  0.408  0.032  26.548
* 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:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL annotate
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/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-pc-linux-gnu (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 -- Sun Jan 24 23:28:17 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 
  7.768   0.200   8.073 

Example timings

annotate.Rcheck/annotate-Ex.timings

nameusersystemelapsed
ACCNUMStats2.0800.0682.148
GO2heatmap0.2120.0000.230
GOmnplot0.080.000.08
HTMLPage-class000
LL2homology000
PMIDAmat0.1480.0000.214
PWAmat2.2360.0282.270
UniGeneQuery0.0000.0000.001
accessionToUID0.7480.0323.473
annPkgName0.0000.0000.002
aqListGOIDs0.2760.0120.292
blastSequences 0.408 0.03226.548
buildChromLocation0.6920.0000.694
buildPubMedAbst0.1040.0121.003
chrCats19.680 0.00419.708
chromLocation-class0.9000.0160.915
compatibleVersions0.0640.0000.062
dropECode0.0760.0000.077
entrezGeneByID0.0000.0000.001
entrezGeneQuery0.0040.0000.001
filterGOByOntology0.1000.0000.102
findNeighbors0.0320.0040.084
genbank0.3160.0081.297
getAnnMap0.0600.0001.153
getEvidence0.0880.0040.093
getGOTerm0.3400.0000.951
getOntology0.0760.0000.077
getPMInfo0.5280.0041.074
getSYMBOL0.1880.0080.523
getSeq4Acc0.0720.0160.436
hasGOannote0.040.000.04
hgByChroms0.0160.0040.022
hgCLengths0.0040.0000.001
hgu95Achroloc0.0920.0040.096
hgu95Achrom0.0800.0040.083
hgu95All0.0880.0040.090
hgu95Asym0.0920.0040.094
homoData-class0.0000.0040.004
htmlpage0.0360.0000.033
isValidkey000
makeAnchor0.0040.0000.002
organism0.8000.0160.818
p2LL000
pm.abstGrep1.5160.0242.643
pm.getabst1.3440.0082.488
pm.titles1.4080.0242.556
pmAbst2HTML0.1640.0040.651
pmid2MIAME000
pmidQuery0.0000.0000.001
pubMedAbst-class0.1160.0120.858
pubmed0.0960.0080.646
readGEOAnn000
serializeEnv0.0040.0000.001
setRepository000
updateSymbolsToValidKeys000
usedChromGenes0.1080.0080.125