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CHECK report for annotate on malbec1

This page was generated on 2020-08-06 11:27:56 -0400 (Thu, 06 Aug 2020).

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 57/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
annotate 1.67.0
Bioconductor Package Maintainer
Snapshot Date: 2020-08-05 14:50:59 -0400 (Wed, 05 Aug 2020)
URL: https://git.bioconductor.org/packages/annotate
Branch: master
Last Commit: 9a6f339
Last Changed Date: 2020-04-27 14:07:46 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
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: 1.67.0
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_1.67.0.tar.gz
StartedAt: 2020-08-05 22:23:49 -0400 (Wed, 05 Aug 2020)
EndedAt: 2020-08-05 22:27:02 -0400 (Wed, 05 Aug 2020)
EllapsedTime: 192.1 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_1.67.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/annotate.Rcheck’
* using R version 4.0.2 (2020-06-22)
* 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 ‘1.67.0’
* 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 ... NOTE
getGOChildren: no visible global function definition for ‘setNames’
getGOParents: no visible global function definition for ‘setNames’
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
* 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        16.304  0.000  16.329
accessionToUID  0.672  0.020   7.675
blastSequences  0.644  0.048  46.028
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/annotate.Rcheck/00check.log’
for details.



Installation output

annotate.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL annotate
###
##############################################################################
##############################################################################


* 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 4.0.2 (2020-06-22) -- "Taking Off Again"
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 -- Wed Aug  5 22:26:57 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 
  6.392   0.196   6.615 

Example timings

annotate.Rcheck/annotate-Ex.timings

nameusersystemelapsed
ACCNUMStats1.1880.0401.254
GO2heatmap0.1800.0040.183
GOmnplot0.1040.0000.102
HTMLPage-class000
LL2homology000
PMIDAmat0.1400.0040.343
PWAmat2.4600.0522.515
UniGeneQuery0.0040.0000.002
accessionToUID0.6720.0207.675
annPkgName0.0000.0000.001
aqListGOIDs0.2760.0080.281
blastSequences 0.644 0.04846.028
buildChromLocation1.0400.0001.053
buildPubMedAbst0.1200.0040.520
chrCats16.304 0.00016.329
chromLocation-class0.6360.0040.642
compatibleVersions0.0400.0000.037
dropECode0.0440.0000.041
entrezGeneByID000
entrezGeneQuery000
filterGOByOntology0.0480.0000.045
findNeighbors0.0240.0000.060
genbank0.2400.0040.760
getAnnMap0.0520.0080.442
getEvidence0.0800.0000.079
getGOTerm0.3480.0080.555
getOntology0.0680.0000.066
getPMInfo0.6320.0000.961
getSYMBOL0.1280.0120.184
getSeq4Acc0.0800.0040.383
hasGOannote0.0440.0000.041
hgByChroms0.0240.0000.022
hgCLengths0.0000.0000.001
hgu95Achroloc0.0960.0000.098
hgu95Achrom0.0760.0080.082
hgu95All0.0880.0000.089
hgu95Asym0.0960.0000.094
homoData-class0.0040.0000.004
htmlpage0.0320.0000.033
isValidkey000
makeAnchor0.0000.0000.001
organism0.8360.0000.844
p2LL000
pm.abstGrep1.2680.0082.734
pm.getabst1.0560.0042.215
pm.titles1.1480.0202.038
pmAbst2HTML0.1320.0040.470
pmid2MIAME000
pmidQuery0.0040.0000.001
pubMedAbst-class0.1120.0000.446
pubmed0.1160.0000.492
readGEOAnn000
serializeEnv0.0040.0000.003
setRepository0.0040.0000.001
updateSymbolsToValidKeys000
usedChromGenes0.1120.0120.125