Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:22:32 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for annotate on merida1


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? 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 56/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
annotate 1.74.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/annotate
git_branch: RELEASE_3_15
git_last_commit: 200c717
git_last_commit_date: 2022-04-26 10:54:23 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: annotate
Version: 1.74.0
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_1.74.0.tar.gz
StartedAt: 2022-10-18 23:09:33 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 23:14:48 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 314.8 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_1.74.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/annotate.Rcheck’
* using R version 4.2.1 (2022-06-23)
* 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 ‘1.74.0’
* 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        22.436  0.127  22.625
accessionToUID  6.195  0.384   8.879
genbank         0.314  0.020   7.028
blastSequences  0.302  0.016  37.121
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL annotate
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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 -- Tue Oct 18 23:14:36 2022 
*********************************************** 
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 
 13.194   0.739  13.973 

Example timings

annotate.Rcheck/annotate-Ex.timings

nameusersystemelapsed
ACCNUMStats3.2080.0323.244
GO2heatmap0.2400.0090.249
GOmnplot0.1010.0060.106
HTMLPage-class0.0000.0010.000
LL2homology0.0000.0000.001
PMIDAmat0.1810.0050.188
PWAmat3.2590.0423.304
UniGeneQuery0.0010.0000.002
accessionToUID6.1950.3848.879
annPkgName0.0000.0000.001
aqListGOIDs0.2230.0170.240
blastSequences 0.302 0.01637.121
buildChromLocation1.4250.0841.536
buildPubMedAbst0.0640.0030.507
chrCats22.436 0.12722.625
chromLocation-class1.3200.0601.382
compatibleVersions0.0630.0040.067
dropECode0.0740.0030.078
entrezGeneByID0.0000.0000.001
entrezGeneQuery0.0010.0000.001
filterGOByOntology0.0860.0030.088
findNeighbors0.0300.0030.036
genbank0.3140.0207.028
getAnnMap0.0950.0140.110
getEvidence0.0900.0030.095
getGOTerm0.3390.0060.347
getOntology0.0600.0030.062
getPMInfo0.6900.0041.293
getSYMBOL0.2060.0140.222
getSeq4Acc0.0250.0020.466
hasGOannote0.0410.0010.042
hgByChroms0.0220.0020.025
hgCLengths0.0010.0010.003
hgu95Achroloc0.1020.0040.107
hgu95Achrom0.0890.0050.095
hgu95All0.0960.0050.101
hgu95Asym0.0990.0050.103
homoData-class0.0030.0000.003
htmlpage0.0330.0020.034
isValidkey0.0000.0010.000
makeAnchor0.0010.0000.001
organism1.3100.0241.336
p2LL000
pm.abstGrep1.6080.0352.320
pm.getabst1.5730.0312.735
pm.titles1.6070.0312.382
pmAbst2HTML0.0850.0040.600
pmid2MIAME000
pmidQuery0.0010.0000.001
pubMedAbst-class0.1630.0160.669
pubmed0.0380.0030.725
readGEOAnn000
serializeEnv0.0020.0010.004
setRepository0.0020.0000.002
updateSymbolsToValidKeys0.0000.0010.001
usedChromGenes0.1250.0060.132