Back to Multiple platform build/check report for BioC 3.13
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-09-24 15:05:39 -0400 (Fri, 24 Sep 2021).

CHECK results for AnnotationDbi on nebbiolo1

To the developers/maintainers of the AnnotationDbi package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/AnnotationDbi.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 62/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AnnotationDbi 1.54.1  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2021-09-23 04:50:12 -0400 (Thu, 23 Sep 2021)
git_url: https://git.bioconductor.org/packages/AnnotationDbi
git_branch: RELEASE_3_13
git_last_commit: 0040118
git_last_commit_date: 2021-06-07 12:36:06 -0400 (Mon, 07 Jun 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: AnnotationDbi
Version: 1.54.1
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:AnnotationDbi.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings AnnotationDbi_1.54.1.tar.gz
StartedAt: 2021-09-23 08:49:32 -0400 (Thu, 23 Sep 2021)
EndedAt: 2021-09-23 08:52:57 -0400 (Thu, 23 Sep 2021)
EllapsedTime: 204.8 seconds
RetCode: 0
Status:   OK  
CheckDir: AnnotationDbi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:AnnotationDbi.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings AnnotationDbi_1.54.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/AnnotationDbi.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AnnotationDbi/DESCRIPTION’ ... OK
* this is package ‘AnnotationDbi’ version ‘1.54.1’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘AnnotationDbi’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   4.3Mb
* 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 ... NOTE
createORGANISMSeeds: no visible global function definition for
  ‘makeAnnDbMapSeeds’
Undefined global functions or variables:
  makeAnnDbMapSeeds
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
AnnDbPkg-checker 44.407  0.752  45.178
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘AnnotationDbi_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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/AnnotationDbi.Rcheck/00check.log’
for details.



Installation output

AnnotationDbi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL AnnotationDbi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘AnnotationDbi’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘packageName’ in package ‘AnnotationDbi’
Creating a generic function for ‘ls’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘eapply’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘exists’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘sample’ from package ‘base’ in package ‘AnnotationDbi’
** 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 (AnnotationDbi)

Tests output

AnnotationDbi.Rcheck/tests/AnnotationDbi_unit_tests.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.

> require("AnnotationDbi") || stop("unable to load AnnotationDbi package")
Loading required package: AnnotationDbi
Loading required package: stats4
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: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

[1] TRUE
> 
> AnnotationDbi:::.test()
Loading required package: org.Hs.eg.db

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

'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
Loading required package: RSQLite
Loading required package: org.At.tair.db

Loading required package: org.Sc.sgd.db

Loading required package: GO.db

Loading required package: hgu95av2.db
'select()' returned many:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned many:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned many:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned many:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
Warning: You have selected the following columns that can have a many to one
  relationship with the primary key: ACCNUM, ALIAS, ENSEMBL,
  ENSEMBLPROT, ENSEMBLTRANS, ENZYME, EVIDENCE, EVIDENCEALL, GO, GOALL,
  IPI, MAP, OMIM, ONTOLOGY, ONTOLOGYALL, PATH, PFAM, PMID, PROSITE,
  REFSEQ, UCSCKG, UNIPROT . Because you have selected more than a few
  such columns there is a risk that this selection may balloon up into
  a very large result as the number of rows returned multiplies
  accordingly. To experience smaller/more manageable results and faster
  retrieval times, you might want to consider selecting these columns
  separately.
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned many:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned many:1 mapping between keys and columns

'select()' returned 1:1 mapping between keys and columns
'select()' returned many:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
Loading required package: reactome.db
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns


RUNIT TEST PROTOCOL -- Thu Sep 23 08:52:53 2021 
*********************************************** 
Number of test functions: 63 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
AnnotationDbi RUnit Tests - 63 test functions, 0 errors, 0 failures
Number of test functions: 63 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In .local(x, ...) : returned vector has duplicated names
2: In .local(x, ...) : returned vector has duplicated names
3: call dbDisconnect() when finished working with a connection 
4: In .deprecatedColsMessage() :
  Accessing gene location information via 'CHR','CHRLOC','CHRLOCEND' is
  deprecated. Please use a range based accessor like genes(), or select()
  with columns values like TXCHROM and TXSTART on a TxDb or OrganismDb
  object instead.
5: In .deprecatedColsMessage() :
  Accessing gene location information via 'CHR','CHRLOC','CHRLOCEND' is
  deprecated. Please use a range based accessor like genes(), or select()
  with columns values like TXCHROM and TXSTART on a TxDb or OrganismDb
  object instead.
6: In .deprecatedColsMessage() :
  Accessing gene location information via 'CHR','CHRLOC','CHRLOCEND' is
  deprecated. Please use a range based accessor like genes(), or select()
  with columns values like TXCHROM and TXSTART on a TxDb or OrganismDb
  object instead.
> 
> proc.time()
   user  system elapsed 
 46.645   2.541  49.275 

Example timings

AnnotationDbi.Rcheck/AnnotationDbi-Ex.timings

nameusersystemelapsed
AnnDbObj-class0.3400.0120.352
AnnDbPkg-checker44.407 0.75245.178
AnnotationDb-class1.5330.1541.689
Bimap-direction2.6800.8533.533
Bimap-envirAPI0.4131.0561.470
Bimap-keys0.5990.0320.631
Bimap-toTable1.8160.0601.879
Bimap1.4530.4561.910
BimapFiltering0.130.000.13
BimapFormatting0.3140.0040.318
GOColsAndKeytypes0.1380.0120.150
GOFrame1.1170.3521.474
GOTerms-class0.0000.0000.001
KEGGFrame0.0350.0041.549
colsAndKeytypes0.1950.0080.204
createSimpleBimap0.0900.0040.094
inpIDMapper0.0010.0000.001
makeGOGraph0.2140.0120.226
make_eg_to_go_map0.1300.0120.142
organismKEGGFrame0.1690.0043.865
print.probetable0.5380.7201.257
toSQLStringSet0.0010.0000.001
unlist20.1520.0570.209