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CHECK report for AnnotationDbi on tokay1

This page was generated on 2018-04-12 13:18:30 -0400 (Thu, 12 Apr 2018).

Package 50/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AnnotationDbi 1.40.0
Bioconductor Package Maintainer
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/AnnotationDbi
Branch: RELEASE_3_6
Last Commit: e34dff0
Last Changed Date: 2017-10-30 12:39:18 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: AnnotationDbi
Version: 1.40.0
Command: rm -rf AnnotationDbi.buildbin-libdir AnnotationDbi.Rcheck && mkdir AnnotationDbi.buildbin-libdir AnnotationDbi.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AnnotationDbi.buildbin-libdir AnnotationDbi_1.40.0.tar.gz >AnnotationDbi.Rcheck\00install.out 2>&1 && cp AnnotationDbi.Rcheck\00install.out AnnotationDbi-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=AnnotationDbi.buildbin-libdir --install="check:AnnotationDbi-install.out" --force-multiarch --no-vignettes --timings AnnotationDbi_1.40.0.tar.gz
StartedAt: 2018-04-11 22:11:38 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 22:22:54 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 676.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: AnnotationDbi.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf AnnotationDbi.buildbin-libdir AnnotationDbi.Rcheck && mkdir AnnotationDbi.buildbin-libdir AnnotationDbi.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AnnotationDbi.buildbin-libdir AnnotationDbi_1.40.0.tar.gz >AnnotationDbi.Rcheck\00install.out 2>&1 && cp AnnotationDbi.Rcheck\00install.out AnnotationDbi-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=AnnotationDbi.buildbin-libdir --install="check:AnnotationDbi-install.out" --force-multiarch --no-vignettes --timings AnnotationDbi_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/AnnotationDbi.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'AnnotationDbi/DESCRIPTION' ... OK
* this is package 'AnnotationDbi' version '1.40.0'
* 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 whether package 'AnnotationDbi' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.5Mb
  sub-directories of 1Mb or more:
    extdata   6.0Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods' 'utils' 'stats4' 'BiocGenerics' 'Biobase' 'IRanges' 'DBI' 'RSQLite'
A package should be listed in only one of these fields.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
'library' or 'require' calls in package code:
  'GO.db' 'KEGG.db' 'RSQLite' 'graph'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.selectInp8: no visible global function definition for '.resort'
annotMessage: no visible binding for global variable 'pkgName'
createORGANISMSeeds: no visible global function definition for
  'makeAnnDbMapSeeds'
makeGOGraph: no visible binding for global variable 'GOBPPARENTS'
makeGOGraph: no visible binding for global variable 'GOMFPARENTS'
makeGOGraph: no visible binding for global variable 'GOCCPARENTS'
makeGOGraph: no visible global function definition for 'ftM2graphNEL'
Undefined global functions or variables:
  .resort GOBPPARENTS GOCCPARENTS GOMFPARENTS ftM2graphNEL
  makeAnnDbMapSeeds pkgName
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
AnnDbPkg-checker          28.89   0.45  134.17
Bimap-direction            4.37   1.65    6.03
InparanoidColsAndKeytypes  4.09   0.08  166.89
Bimap-toTable              3.65   0.17    5.86
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
AnnDbPkg-checker          34.37   0.31   34.69
InparanoidColsAndKeytypes  5.21   0.25    5.47
print.probetable           4.99   0.19    5.17
* checking for unstated dependencies in 'tests' ... WARNING
'library' or 'require' call not declared from: 'org.testing.db'
* checking tests ...
** running tests for arch 'i386' ...
  Running 'AnnotationDbi_unit_tests.R'
 OK
** running tests for arch 'x64' ...
  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: 1 WARNING, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/AnnotationDbi.Rcheck/00check.log'
for details.

Installation output

AnnotationDbi.Rcheck/00install.out


install for i386

* installing *source* package 'AnnotationDbi' ...
** R
** inst
** preparing package for lazy loading
in method for 'initialize' with signature '"L2Rlink"': no definition for class "L2Rlink"
in method for 'toString' with signature '"L2Rlink"': no definition for class "L2Rlink"
in method for 'show' with signature '"L2Rlink"': no definition for class "L2Rlink"
in method for 'rev' with signature '"L2Rlink"': no definition for class "L2Rlink"
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
  converting help for package 'AnnotationDbi'
    finding HTML links ... done
    AnnDbObj-class                          html  
    AnnDbPkg-checker                        html  
    AnnotationDb-class                      html  
    AnnotationDbi-internals                 html  
    Bimap-direction                         html  
    Bimap-envirAPI                          html  
    Bimap-keys                              html  
    Bimap-toTable                           html  
    Bimap                                   html  
    BimapFiltering                          html  
    BimapFormatting                         html  
    GOColsAndKeytypes                       html  
    GOFrame                                 html  
    GOTerms-class                           html  
    InparanoidColsAndKeytypes               html  
    KEGGFrame                               html  
    colsAndKeytypes                         html  
    createSimpleBimap                       html  
    inpIDMapper                             html  
    makeGOGraph                             html  
    make_eg_to_go_map                       html  
    orgPackageName                          html  
    print.probetable                        html  
    toSQLStringSet                          html  
    unlist2                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'AnnotationDbi' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AnnotationDbi' as AnnotationDbi_1.40.0.zip
* DONE (AnnotationDbi)
In R CMD INSTALL
In R CMD INSTALL

Tests output

AnnotationDbi.Rcheck/tests_i386/AnnotationDbi_unit_tests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    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 object is masked from 'package:base':

    expand.grid

[1] TRUE
>     if (!require(org.testing.db))
+     {
+         install.packages(system.file("extdata", "org.testing.db",
+           package="AnnotationDbi"), repos=NULL,
+           type="source", INSTALL_opts="--no-test-load")
+         library(org.testing.db)
+     }
Loading required package: org.testing.db
Installing package into 'C:/Users/biocbuild/bbs-3.6-bioc/meat/AnnotationDbi.buildbin-libdir'
(as 'lib' is unspecified)
* installing *source* package 'org.testing.db' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'org.testing.db'
    finding HTML links ... done
    org.TguttataTestingSubset.egBASE        html  
    org.TguttataTestingSubset.egORGANISM    html  
    org.TguttataTestingSubset.eg_dbconn     html  
** building package indices
* DONE (org.testing.db)
In R CMD INSTALL

Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'org.testing.db'
> 
> 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
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
'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: hom.Hs.inp.db

'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
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 -- Wed Apr 11 22:21:27 2018 
*********************************************** 
Number of test functions: 71 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
AnnotationDbi RUnit Tests - 71 test functions, 0 errors, 0 failures
Number of test functions: 71 
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 
  65.65    1.28   75.43

AnnotationDbi.Rcheck/tests_x64/AnnotationDbi_unit_tests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    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 object is masked from 'package:base':

    expand.grid

[1] TRUE
>     if (!require(org.testing.db))
+     {
+         install.packages(system.file("extdata", "org.testing.db",
+           package="AnnotationDbi"), repos=NULL,
+           type="source", INSTALL_opts="--no-test-load")
+         library(org.testing.db)
+     }
Loading required package: org.testing.db

> 
> 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
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, UNIGENE, 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: hom.Hs.inp.db

'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
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 -- Wed Apr 11 22:22:49 2018 
*********************************************** 
Number of test functions: 71 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
AnnotationDbi RUnit Tests - 71 test functions, 0 errors, 0 failures
Number of test functions: 71 
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 
  78.90    2.85   81.92

Example timings

AnnotationDbi.Rcheck/examples_i386/AnnotationDbi-Ex.timings

nameusersystemelapsed
AnnDbObj-class0.640.050.69
AnnDbPkg-checker 28.89 0.45134.17
AnnotationDb-class1.190.021.30
Bimap-direction4.371.656.03
Bimap-envirAPI0.710.240.94
Bimap-keys1.080.371.45
Bimap-toTable3.650.175.86
Bimap2.331.033.36
BimapFiltering0.200.000.21
BimapFormatting0.420.020.43
GOColsAndKeytypes0.200.000.21
GOFrame2.270.553.29
GOTerms-class000
InparanoidColsAndKeytypes 4.09 0.08166.89
KEGGFrame0.210.000.20
colsAndKeytypes0.250.020.30
createSimpleBimap0.140.000.14
inpIDMapper000
makeGOGraph0.530.010.54
make_eg_to_go_map0.270.000.27
print.probetable4.700.064.76
toSQLStringSet000
unlist20.190.000.19

AnnotationDbi.Rcheck/examples_x64/AnnotationDbi-Ex.timings

nameusersystemelapsed
AnnDbObj-class0.850.000.84
AnnDbPkg-checker34.37 0.3134.69
AnnotationDb-class0.940.050.99
Bimap-direction3.631.344.97
Bimap-envirAPI0.530.170.70
Bimap-keys0.810.381.19
Bimap-toTable2.640.062.70
Bimap1.900.762.67
BimapFiltering0.240.000.23
BimapFormatting0.480.020.50
GOColsAndKeytypes0.220.000.22
GOFrame2.130.372.50
GOTerms-class000
InparanoidColsAndKeytypes5.210.255.47
KEGGFrame0.270.000.27
colsAndKeytypes0.300.000.29
createSimpleBimap0.180.000.19
inpIDMapper000
makeGOGraph0.580.000.58
make_eg_to_go_map0.310.000.32
print.probetable4.990.195.17
toSQLStringSet000
unlist20.260.010.28