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This page was generated on 2021-09-22 15:05:44 -0400 (Wed, 22 Sep 2021).

CHECK results for GenomeInfoDb on machv2

To the developers/maintainers of the GenomeInfoDb package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomeInfoDb.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 736/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomeInfoDb 1.28.4  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2021-09-21 04:50:12 -0400 (Tue, 21 Sep 2021)
git_url: https://git.bioconductor.org/packages/GenomeInfoDb
git_branch: RELEASE_3_13
git_last_commit: 3de2a41
git_last_commit_date: 2021-09-03 15:49:43 -0400 (Fri, 03 Sep 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: GenomeInfoDb
Version: 1.28.4
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GenomeInfoDb.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GenomeInfoDb_1.28.4.tar.gz
StartedAt: 2021-09-21 19:27:52 -0400 (Tue, 21 Sep 2021)
EndedAt: 2021-09-21 19:41:38 -0400 (Tue, 21 Sep 2021)
EllapsedTime: 826.8 seconds
RetCode: 0
Status:   OK  
CheckDir: GenomeInfoDb.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GenomeInfoDb.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GenomeInfoDb_1.28.4.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/GenomeInfoDb.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomeInfoDb/DESCRIPTION’ ... OK
* this is package ‘GenomeInfoDb’ version ‘1.28.4’
* package encoding: UTF-8
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GenomeInfoDb’ 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 ... NOTE
Unexported object imported by a ':::' call: ‘utils:::.roman2numeric’
  See the note in ?`:::` about the use of this operator.
* 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 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
loadTaxonomyDb          10.996  0.187  11.188
GenomeDescription-class  9.304  0.321   9.632
seqlevels-wrappers       6.714  0.306   7.023
seqinfo                  6.531  0.291   6.955
seqlevelsStyle           5.051  0.273  12.637
getChromInfoFromUCSC     2.355  0.577   6.818
getChromInfoFromEnsembl  0.623  0.145  43.276
getChromInfoFromNCBI     0.212  0.065   7.247
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/GenomeInfoDb.Rcheck/00check.log’
for details.



Installation output

GenomeInfoDb.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GenomeInfoDb
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘GenomeInfoDb’ ...
** using staged installation
** R
** 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 (GenomeInfoDb)

Tests output

GenomeInfoDb.Rcheck/tests/run_unitTests.Rout


R version 4.1.1 (2021-08-10) -- "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.

> require("GenomeInfoDb") || stop("unable to load GenomeInfoDb package")
Loading required package: GenomeInfoDb
Loading required package: BiocGenerics
Loading required package: parallel

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, 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

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
[1] TRUE
> GenomeInfoDb:::.test()


RUNIT TEST PROTOCOL -- Tue Sep 21 19:41:25 2021 
*********************************************** 
Number of test functions: 21 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GenomeInfoDb RUnit Tests - 21 test functions, 0 errors, 0 failures
Number of test functions: 21 
Number of errors: 0 
Number of failures: 0 
There were 50 or more warnings (use warnings() to see the first 50)
> 
> proc.time()
   user  system elapsed 
466.320  15.031 630.246 

Example timings

GenomeInfoDb.Rcheck/GenomeInfoDb-Ex.timings

nameusersystemelapsed
GenomeDescription-class9.3040.3219.632
Seqinfo-class0.4090.0440.454
fetchExtendedChromInfoFromUCSC0.0000.0010.001
getChromInfoFromEnsembl 0.623 0.14543.276
getChromInfoFromNCBI0.2120.0657.247
getChromInfoFromUCSC2.3550.5776.818
loadTaxonomyDb10.996 0.18711.188
mapGenomeBuilds0.0760.0220.099
rankSeqlevels0.1750.0140.192
seqinfo6.5310.2916.955
seqlevels-wrappers6.7140.3067.023
seqlevelsStyle 5.051 0.27312.637