Back to Multiple platform build/check report for BioC 3.14
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-10-23 14:06:52 -0400 (Sat, 23 Oct 2021).

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? 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 1.71.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2021-10-22 14:50:11 -0400 (Fri, 22 Oct 2021)
git_url: https://git.bioconductor.org/packages/annotate
git_branch: master
git_last_commit: f4b8119
git_last_commit_date: 2021-05-19 11:32:35 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: annotate
Version: 1.71.0
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_1.71.0.tar.gz
StartedAt: 2021-10-23 00:40:04 -0400 (Sat, 23 Oct 2021)
EndedAt: 2021-10-23 00:44:12 -0400 (Sat, 23 Oct 2021)
EllapsedTime: 247.9 seconds
RetCode: 0
Status:   OK  
CheckDir: annotate.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.71.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/annotate.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* 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 ‘1.71.0’
* 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         16.729  0.108  16.877
blastSequences   0.262  0.021  34.229
buildPubMedAbst  0.054  0.003   6.451
* 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/4.1/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 4.1.1 Patched (2021-08-22 r80813) -- "Kick Things"
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 -- Sat Oct 23 00:44:01 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 
  9.840   0.645  10.464 

Example timings

annotate.Rcheck/annotate-Ex.timings

nameusersystemelapsed
ACCNUMStats2.5440.0392.588
GO2heatmap0.1980.0080.206
GOmnplot0.0690.0060.075
HTMLPage-class000
LL2homology000
PMIDAmat0.1500.0050.156
PWAmat2.3870.0432.434
UniGeneQuery0.0010.0010.001
accessionToUID0.3890.0513.442
annPkgName0.0010.0000.001
aqListGOIDs0.1910.0150.205
blastSequences 0.262 0.02134.229
buildChromLocation0.9550.0471.007
buildPubMedAbst0.0540.0036.451
chrCats16.729 0.10816.877
chromLocation-class0.8760.0570.934
compatibleVersions0.0550.0030.059
dropECode0.0550.0020.057
entrezGeneByID0.0000.0010.001
entrezGeneQuery0.0010.0000.001
filterGOByOntology0.0580.0020.060
findNeighbors0.0220.0020.025
genbank0.2410.0230.769
getAnnMap0.0460.0090.057
getEvidence0.0820.0030.085
getGOTerm0.2930.0060.301
getOntology0.0620.0030.064
getPMInfo0.5300.0041.086
getSYMBOL0.1520.0130.168
getSeq4Acc0.0190.0010.407
hasGOannote0.0310.0000.032
hgByChroms0.0190.0020.020
hgCLengths0.0010.0010.002
hgu95Achroloc0.0680.0030.071
hgu95Achrom0.0520.0030.055
hgu95All0.0730.0040.078
hgu95Asym0.0700.0030.074
homoData-class0.0020.0010.002
htmlpage0.0210.0010.022
isValidkey000
makeAnchor0.0010.0000.001
organism0.9380.0340.974
p2LL000
pm.abstGrep1.1510.0442.090
pm.getabst1.0820.0302.006
pm.titles1.1150.0401.789
pmAbst2HTML0.0620.0050.619
pmid2MIAME000
pmidQuery0.0010.0000.001
pubMedAbst-class0.0440.0030.674
pubmed0.0300.0030.519
readGEOAnn000
serializeEnv0.0020.0010.002
setRepository0.0000.0000.001
updateSymbolsToValidKeys000
usedChromGenes0.0930.0050.098