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CHECK report for AnnotationForge on tokay2

This page was generated on 2019-04-09 12:00:46 -0400 (Tue, 09 Apr 2019).

Package 59/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AnnotationForge 1.25.0
Bioconductor Package Maintainer
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/AnnotationForge
Branch: master
Last Commit: 5b53a75
Last Changed Date: 2018-10-30 11:54:30 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: AnnotationForge
Version: 1.25.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AnnotationForge.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings AnnotationForge_1.25.0.tar.gz
StartedAt: 2019-04-09 01:05:11 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 01:07:35 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 144.6 seconds
RetCode: 0
Status:  OK  
CheckDir: AnnotationForge.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AnnotationForge.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings AnnotationForge_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/AnnotationForge.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* 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 '1.25.0'
* 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 '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-3.9-bioc/meat/AnnotationForge.Rcheck/00check.log'
for details.



Installation output

AnnotationForge.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/AnnotationForge_1.25.0.tar.gz && rm -rf AnnotationForge.buildbin-libdir && mkdir AnnotationForge.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=AnnotationForge.buildbin-libdir AnnotationForge_1.25.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL AnnotationForge_1.25.0.zip && rm AnnotationForge_1.25.0.tar.gz AnnotationForge_1.25.0.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 3288k  100 3288k    0     0  34.4M      0 --:--:-- --:--:-- --:--:-- 36.9M

install for i386

* installing *source* package 'AnnotationForge' ...
** 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_1.25.0.zip
* DONE (AnnotationForge)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'AnnotationForge' successfully unpacked and MD5 sums checked

Tests output

AnnotationForge.Rcheck/tests_i386/AnnotationForge_unit_tests.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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, colMeans, colSums, 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, 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: 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
'select()' returned many:1 mapping between keys and columns
Populating go_all table:
go_all table filled
Creating package in C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpCepMHr\filec5058a51e67/org.Tguttata.eg.db 
Now deleting temporary database file


RUNIT TEST PROTOCOL -- Tue Apr 09 01:07:20 2019 
*********************************************** 
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 41 warnings (use warnings() to see them)
> 
> proc.time()
   user  system elapsed 
   6.89    1.10   10.82 

AnnotationForge.Rcheck/tests_x64/AnnotationForge_unit_tests.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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, colMeans, colSums, 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, 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: 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
'select()' returned many:1 mapping between keys and columns
Populating go_all table:
go_all table filled
Creating package in C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpoBwbtk\filec58507a1e8e/org.Tguttata.eg.db 
Now deleting temporary database file


RUNIT TEST PROTOCOL -- Tue Apr 09 01:07:30 2019 
*********************************************** 
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 41 warnings (use warnings() to see them)
> 
> proc.time()
   user  system elapsed 
   7.68    1.06    8.95 

Example timings

AnnotationForge.Rcheck/examples_i386/AnnotationForge-Ex.timings

nameusersystemelapsed
AnnDbPkg-maker0.030.020.08
available.db0pkgs0.120.010.28
generateSeqnames_db000
getProbeDataAffy000
getProbeData_1lq000
makeChipPackageFromDataFrames000
makeInpDb000
makeOrgPackage000
makeOrgPackageFromNCBI000
makeProbePackage3.080.083.89
sqlForge-makeCHIPDB000
sqlForge-popDB000
sqlForge-wrapDBPackages000

AnnotationForge.Rcheck/examples_x64/AnnotationForge-Ex.timings

nameusersystemelapsed
AnnDbPkg-maker0.020.020.03
available.db0pkgs0.090.030.28
generateSeqnames_db000
getProbeDataAffy000
getProbeData_1lq000
makeChipPackageFromDataFrames000
makeInpDb000
makeOrgPackage0.010.000.01
makeOrgPackageFromNCBI000
makeProbePackage3.050.113.66
sqlForge-makeCHIPDB000
sqlForge-popDB000
sqlForge-wrapDBPackages000