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CHECK report for annotate on malbec1

This page was generated on 2018-04-12 13:06:50 -0400 (Thu, 12 Apr 2018).

Package 49/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
annotate 1.56.2
Bioconductor Package Maintainer
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/annotate
Branch: RELEASE_3_6
Last Commit: 95ec3b0
Last Changed Date: 2018-03-20 17:08:59 -0400 (Tue, 20 Mar 2018)
malbec1 Linux (Ubuntu 16.04.1 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
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: annotate
Version: 1.56.2
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings annotate_1.56.2.tar.gz
StartedAt: 2018-04-11 21:26:06 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 21:28:34 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 148.3 seconds
RetCode: 0
Status:  OK 
CheckDir: annotate.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings annotate_1.56.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/annotate.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.56.2’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
chrCats        12.248   0.00  12.256
blastSequences  0.456   0.12  27.859
* 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

* installing *source* package ‘annotate’ ...
** R
** data
** inst
** preparing 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 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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, cbind, colMeans, colSums, colnames, 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 -- Wed Apr 11 21:28:31 2018 
*********************************************** 
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 
  5.520   0.152   5.671 

Example timings

annotate.Rcheck/annotate-Ex.timings

nameusersystemelapsed
ACCNUMStats1.6480.0201.670
GO2heatmap0.1960.0000.196
GOmnplot0.0560.0080.065
HTMLPage-class000
LL2homology0.0000.0000.001
PMIDAmat0.0840.0080.414
PWAmat1.8720.0001.873
UniGeneQuery0.0000.0000.002
accessionToUID1.1160.0402.710
annPkgName0.0000.0000.002
aqListGOIDs0.2960.0040.301
blastSequences 0.456 0.12027.859
buildChromLocation0.5280.0040.531
buildPubMedAbst0.1640.0160.695
chrCats12.248 0.00012.256
chromLocation-class0.4600.0040.464
compatibleVersions0.0440.0000.047
dropECode0.0440.0000.046
entrezGeneByID0.0000.0000.001
entrezGeneQuery0.0000.0000.001
filterGOByOntology0.0720.0000.072
findNeighbors0.0280.0000.271
genbank0.2600.0040.662
getAnnMap0.0600.0040.250
getEvidence0.1640.0000.171
getGOTerm0.4680.0000.503
getOntology0.0640.0000.065
getPMInfo0.7840.0041.219
getSYMBOL0.1400.0080.292
getSeq4Acc0.0640.0120.417
hasGOannote0.0280.0000.028
hgByChroms0.0160.0000.015
hgCLengths0.0040.0000.001
hgu95Achroloc0.0640.0040.068
hgu95Achrom0.0520.0040.055
hgu95All0.060.000.06
hgu95Asym0.0600.0040.062
homoData-class0.0040.0000.003
htmlpage0.4600.0000.461
isValidkey0.0000.0000.001
makeAnchor000
organism0.5880.0000.587
p2LL000
pm.abstGrep0.9280.0041.930
pm.getabst1.1080.0002.124
pm.titles1.0200.0082.049
pmAbst2HTML0.1440.0000.517
pmid2MIAME000
pmidQuery0.0000.0000.001
pubMedAbst-class0.1320.0000.661
pubmed0.1240.0000.637
readGEOAnn0.0000.0000.001
serializeEnv0.0000.0000.002
setRepository0.0040.0000.003
updateSymbolsToValidKeys0.0000.0000.001
usedChromGenes0.0800.0000.083