Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-22 11:05:24 -0500 (Sat, 22 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
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 nebbiolo1


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 56/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
annotate 1.73.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2022-01-21 13:55:18 -0500 (Fri, 21 Jan 2022)
git_url: https://git.bioconductor.org/packages/annotate
git_branch: master
git_last_commit: bd601f0
git_last_commit_date: 2021-10-26 11:45:29 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    NA    NA  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'AnnotationDbi' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: annotate
Version: 1.73.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:annotate.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings annotate_1.73.0.tar.gz
StartedAt: 2022-01-21 18:10:41 -0500 (Fri, 21 Jan 2022)
EndedAt: 2022-01-21 18:13:33 -0500 (Fri, 21 Jan 2022)
EllapsedTime: 172.6 seconds
RetCode: 0
Status:   OK  
CheckDir: annotate.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:annotate.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings annotate_1.73.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/annotate.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* 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 ‘1.73.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
chrCats        8.861  0.404   9.265
blastSequences 0.165  0.012  42.210
* 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:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL annotate
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-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 Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 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: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 -- Fri Jan 21 18:13:29 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 
  6.559   0.340   6.885 

Example timings

annotate.Rcheck/annotate-Ex.timings

nameusersystemelapsed
ACCNUMStats1.0760.0321.108
GO2heatmap0.1070.0080.115
GOmnplot0.0400.0040.044
HTMLPage-class000
LL2homology000
PMIDAmat0.0790.0000.082
PWAmat1.7390.0281.766
UniGeneQuery0.0000.0010.001
accessionToUID0.3620.0232.481
annPkgName0.0010.0000.001
aqListGOIDs0.1290.0320.162
blastSequences 0.165 0.01242.210
buildChromLocation0.7190.0710.791
buildPubMedAbst0.0460.0110.477
chrCats8.8610.4049.265
chromLocation-class0.5110.0440.555
compatibleVersions0.0350.0040.039
dropECode0.0390.0060.045
entrezGeneByID0.0010.0000.000
entrezGeneQuery0.0010.0000.001
filterGOByOntology0.0560.0040.060
findNeighbors0.0160.0070.026
genbank0.1910.0201.948
getAnnMap0.0390.0130.066
getEvidence0.0470.0000.048
getGOTerm0.1870.0120.199
getOntology0.0360.0000.036
getPMInfo0.3100.0000.743
getSYMBOL0.0950.0200.116
getSeq4Acc0.0190.0000.305
hasGOannote0.0360.0000.037
hgByChroms0.0230.0000.023
hgCLengths0.0010.0010.002
hgu95Achroloc0.0830.0040.089
hgu95Achrom0.0560.0000.055
hgu95All0.0720.0000.072
hgu95Asym0.0600.0020.062
homoData-class0.0020.0000.003
htmlpage0.0190.0000.019
isValidkey0.0010.0000.000
makeAnchor0.0000.0000.001
organism0.6180.0180.637
p2LL0.0000.0000.001
pm.abstGrep0.7820.0201.571
pm.getabst0.7090.0081.424
pm.titles0.8210.0321.775
pmAbst2HTML0.0580.0000.387
pmid2MIAME0.0000.0000.001
pmidQuery0.0000.0000.001
pubMedAbst-class0.0420.0040.366
pubmed0.0270.0040.374
readGEOAnn0.0010.0000.001
serializeEnv0.0020.0000.002
setRepository0.0010.0000.001
updateSymbolsToValidKeys0.0010.0000.001
usedChromGenes0.0930.0030.096