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CHECK report for AnnotationForge on tokay1

This page was generated on 2020-08-06 11:54:38 -0400 (Thu, 06 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE AnnotationForge PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 60/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AnnotationForge 1.31.2
Bioconductor Package Maintainer
Snapshot Date: 2020-08-05 14:50:59 -0400 (Wed, 05 Aug 2020)
URL: https://git.bioconductor.org/packages/AnnotationForge
Branch: master
Last Commit: 7382b9a
Last Changed Date: 2020-06-01 17:00:58 -0400 (Mon, 01 Jun 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: AnnotationForge
Version: 1.31.2
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AnnotationForge.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings AnnotationForge_1.31.2.tar.gz
StartedAt: 2020-08-06 00:48:38 -0400 (Thu, 06 Aug 2020)
EndedAt: 2020-08-06 00:51:30 -0400 (Thu, 06 Aug 2020)
EllapsedTime: 171.2 seconds
RetCode: 0
Status:  OK  
CheckDir: AnnotationForge.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AnnotationForge.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings AnnotationForge_1.31.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/AnnotationForge.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'AnnotationForge/DESCRIPTION' ... OK
* this is package 'AnnotationForge' version '1.31.2'
* 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 'AnnotationForge' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    AnnDbPkg-templates   1.3Mb
    extdata              3.3Mb
* 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
* 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 ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'AnnotationForge_unit_tests.R'
 OK
** running tests for arch 'x64' ...
  Running 'AnnotationForge_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 NOTE
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/AnnotationForge.Rcheck/00check.log'
for details.



Installation output

AnnotationForge.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/AnnotationForge_1.31.2.tar.gz && rm -rf AnnotationForge.buildbin-libdir && mkdir AnnotationForge.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=AnnotationForge.buildbin-libdir AnnotationForge_1.31.2.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL AnnotationForge_1.31.2.zip && rm AnnotationForge_1.31.2.tar.gz AnnotationForge_1.31.2.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 3284k  100 3284k    0     0  44.9M      0 --:--:-- --:--:-- --:--:-- 47.8M

install for i386

* installing *source* package 'AnnotationForge' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'AnnotationForge'
    finding HTML links ... done
    AnnDbPkg-maker                          html  
    finding level-2 HTML links ... done

    available.db0pkgs                       html  
    generateSeqnames_db                     html  
    getProbeDataAffy                        html  
    getProbeData_1lq                        html  
    makeChipPackageFromDataFrames           html  
    makeInpDb                               html  
    makeOrgPackage                          html  
    makeOrgPackageFromNCBI                  html  
    makeProbePackage                        html  
    sqlForge-makeCHIPDB                     html  
    sqlForge-popDB                          html  
    sqlForge-wrapDBPackages                 html  
** 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

install for x64

* installing *source* package 'AnnotationForge' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AnnotationForge' as AnnotationForge_1.31.2.zip
* DONE (AnnotationForge)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'AnnotationForge' successfully unpacked and MD5 sums checked

Tests output

AnnotationForge.Rcheck/tests_i386/AnnotationForge_unit_tests.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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("AnnotationForge") || stop("unable to load AnnotationForge package")
Loading required package: AnnotationForge
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: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

[1] TRUE
> AnnotationForge:::.test()

'select()' returned many:1 mapping between keys and columns
'select()' returned many:1 mapping between keys and columns
Populating genes table:
genes table filled
Populating gene_info table:
gene_info table filled
Populating chromosome table:
chromosome table filled
Populating go table:
go table filled
table metadata filled
'select()' returned many:1 mapping between keys and columns
Dropping GO IDs that are too new for the current GO.db
Populating go table:
go table filled
Populating go_bp table:
go_bp table filled
Populating go_cc table:
go_cc table filled
Populating go_mf table:
go_mf table filled
'select()' returned many:1 mapping between keys and columns
Populating go_bp_all table:
go_bp_all table filled
Populating go_cc_all table:
go_cc_all table filled
Populating go_mf_all table:
go_mf_all table filled
Populating go_all table:
go_all table filled
Creating package in C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpU5gneT\file13cc4cad18a1/org.Tguttata.eg.db 
Now deleting temporary database file


RUNIT TEST PROTOCOL -- Thu Aug 06 00:51:16 2020 
*********************************************** 
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
AnnotationForge RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4 
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 
   6.43    1.10    7.87 

AnnotationForge.Rcheck/tests_x64/AnnotationForge_unit_tests.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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("AnnotationForge") || stop("unable to load AnnotationForge package")
Loading required package: AnnotationForge
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: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

[1] TRUE
> AnnotationForge:::.test()

'select()' returned many:1 mapping between keys and columns
'select()' returned many:1 mapping between keys and columns
Populating genes table:
genes table filled
Populating gene_info table:
gene_info table filled
Populating chromosome table:
chromosome table filled
Populating go table:
go table filled
table metadata filled
'select()' returned many:1 mapping between keys and columns
Dropping GO IDs that are too new for the current GO.db
Populating go table:
go table filled
Populating go_bp table:
go_bp table filled
Populating go_cc table:
go_cc table filled
Populating go_mf table:
go_mf table filled
'select()' returned many:1 mapping between keys and columns
Populating go_bp_all table:
go_bp_all table filled
Populating go_cc_all table:
go_cc_all table filled
Populating go_mf_all table:
go_mf_all table filled
Populating go_all table:
go_all table filled
Creating package in C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpYBBDUG\file2720468c18bf/org.Tguttata.eg.db 
Now deleting temporary database file


RUNIT TEST PROTOCOL -- Thu Aug 06 00:51:25 2020 
*********************************************** 
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
AnnotationForge RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4 
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 
   7.12    1.34    8.50 

Example timings

AnnotationForge.Rcheck/examples_i386/AnnotationForge-Ex.timings

nameusersystemelapsed
AnnDbPkg-maker0.060.000.06
available.db0pkgs0.150.000.22
generateSeqnames_db000
getProbeDataAffy000
getProbeData_1lq000
makeChipPackageFromDataFrames000
makeInpDb000
makeOrgPackage000
makeOrgPackageFromNCBI0.000.010.02
makeProbePackage3.150.103.72
sqlForge-makeCHIPDB000
sqlForge-popDB000
sqlForge-wrapDBPackages000

AnnotationForge.Rcheck/examples_x64/AnnotationForge-Ex.timings

nameusersystemelapsed
AnnDbPkg-maker0.060.000.06
available.db0pkgs0.130.010.17
generateSeqnames_db000
getProbeDataAffy000
getProbeData_1lq000
makeChipPackageFromDataFrames000
makeInpDb000
makeOrgPackage0.010.000.02
makeOrgPackageFromNCBI000
makeProbePackage2.610.082.81
sqlForge-makeCHIPDB000
sqlForge-popDB000
sqlForge-wrapDBPackages000