Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-12-06 13:05:49 -0500 (Mon, 06 Dec 2021).

CHECK results for annotate on machv2

To the developers/maintainers of the annotate package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/annotate.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 59/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
annotate 1.72.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2021-12-05 01:55:05 -0500 (Sun, 05 Dec 2021)
git_url: https://git.bioconductor.org/packages/annotate
git_branch: RELEASE_3_14
git_last_commit: 67ac76a
git_last_commit_date: 2021-10-26 11:45:29 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: annotate
Version: 1.72.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:annotate.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings annotate_1.72.0.tar.gz
StartedAt: 2021-12-05 11:42:29 -0500 (Sun, 05 Dec 2021)
EndedAt: 2021-12-05 11:46:27 -0500 (Sun, 05 Dec 2021)
EllapsedTime: 237.8 seconds
RetCode: 0
Status:   OK  
CheckDir: annotate.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:annotate.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings annotate_1.72.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/annotate.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.72.0’
* 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        18.752  0.109  18.904
blastSequences  0.260  0.020  17.267
* 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/Resources/bin/R CMD INSTALL annotate
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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: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 objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: org.Hs.eg.db

'select()' returned 1:many mapping between keys and columns


RUNIT TEST PROTOCOL -- Sun Dec  5 11:46:14 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 
 10.087   0.642  10.718 

Example timings

annotate.Rcheck/annotate-Ex.timings

nameusersystemelapsed
ACCNUMStats2.5760.0392.617
GO2heatmap0.1820.0090.192
GOmnplot0.0630.0050.069
HTMLPage-class0.0000.0000.001
LL2homology0.0000.0000.001
PMIDAmat0.1560.0040.162
PWAmat2.5980.0522.652
UniGeneQuery0.0010.0000.002
accessionToUID0.4690.0453.529
annPkgName0.0000.0010.001
aqListGOIDs0.1920.0180.212
blastSequences 0.260 0.02017.267
buildChromLocation1.1530.0671.242
buildPubMedAbst0.0630.0020.730
chrCats18.752 0.10918.904
chromLocation-class1.0420.0581.101
compatibleVersions0.0620.0030.066
dropECode0.0750.0020.078
entrezGeneByID0.0010.0000.001
entrezGeneQuery0.0010.0000.001
filterGOByOntology0.0820.0030.085
findNeighbors0.0300.0030.035
genbank0.2780.0201.101
getAnnMap0.0530.0130.067
getEvidence0.0670.0030.070
getGOTerm0.3050.0070.313
getOntology0.0700.0040.074
getPMInfo0.5930.0061.131
getSYMBOL0.1480.0210.171
getSeq4Acc0.0220.0020.607
hasGOannote0.0350.0020.037
hgByChroms0.0210.0020.024
hgCLengths0.0020.0020.003
hgu95Achroloc0.0700.0030.073
hgu95Achrom0.0730.0050.078
hgu95All0.0910.0060.096
hgu95Asym0.0920.0060.098
homoData-class0.0040.0010.005
htmlpage0.0280.0030.030
isValidkey0.0000.0010.000
makeAnchor0.0010.0010.001
organism1.0960.0481.145
p2LL0.0010.0010.001
pm.abstGrep1.2850.0362.350
pm.getabst1.2580.0422.201
pm.titles1.3600.0502.415
pmAbst2HTML0.0780.0050.695
pmid2MIAME0.0000.0010.000
pmidQuery0.0010.0000.001
pubMedAbst-class0.0640.0030.708
pubmed0.0370.0030.630
readGEOAnn0.0010.0000.000
serializeEnv0.0020.0010.002
setRepository0.0010.0010.002
updateSymbolsToValidKeys0.0000.0000.001
usedChromGenes0.0990.0070.107