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CHECK report for LRBaseDbi on tokay2

This page was generated on 2020-10-17 11:56:58 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE LRBaseDbi PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 960/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LRBaseDbi 1.6.0
Koki Tsuyuzaki
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/LRBaseDbi
Branch: RELEASE_3_11
Last Commit: fa039d4
Last Changed Date: 2020-04-27 15:18:17 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: LRBaseDbi
Version: 1.6.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:LRBaseDbi.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings LRBaseDbi_1.6.0.tar.gz
StartedAt: 2020-10-17 05:34:07 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:36:16 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 128.4 seconds
RetCode: 0
Status:  OK  
CheckDir: LRBaseDbi.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:LRBaseDbi.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings LRBaseDbi_1.6.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/LRBaseDbi.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'LRBaseDbi/DESCRIPTION' ... OK
* this is package 'LRBaseDbi' version '1.6.0'
* 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 'LRBaseDbi' 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
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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: OK


Installation output

LRBaseDbi.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/LRBaseDbi_1.6.0.tar.gz && rm -rf LRBaseDbi.buildbin-libdir && mkdir LRBaseDbi.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=LRBaseDbi.buildbin-libdir LRBaseDbi_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL LRBaseDbi_1.6.0.zip && rm LRBaseDbi_1.6.0.tar.gz LRBaseDbi_1.6.0.zip
###
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  % 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 22084  100 22084    0     0   337k      0 --:--:-- --:--:-- --:--:--  385k

install for i386

* installing *source* package 'LRBaseDbi' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'LRBaseDbi'
    finding HTML links ... done
    FANTOM5                                 html  
    LRBaseDb                                html  
    columns                                 html  
    dbInfo                                  html  
    dbconn                                  html  
    dbfile                                  html  
    dbschema                                html  
    keys                                    html  
    keytypes                                html  
    lrListDatabases                         html  
    lrNomenclature                          html  
    lrPackageName                           html  
    lrVersion                               html  
    makeLRBasePackage                       html  
    metaFANTOM5                             html  
    select                                  html  
    species                                 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 'LRBaseDbi' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'LRBaseDbi' as LRBaseDbi_1.6.0.zip
* DONE (LRBaseDbi)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'LRBaseDbi' successfully unpacked and MD5 sums checked

Tests output

LRBaseDbi.Rcheck/tests_i386/runTests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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.

> BiocGenerics:::testPackage("LRBaseDbi")


RUNIT TEST PROTOCOL -- Sat Oct 17 05:36:04 2020 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
LRBaseDbi RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
Warning message:
In getPackageName(where) :
  Created a package name, '2020-10-17 05:36:04', when none found
> 
> proc.time()
   user  system elapsed 
   3.87    0.31    4.17 

LRBaseDbi.Rcheck/tests_x64/runTests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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.

> BiocGenerics:::testPackage("LRBaseDbi")


RUNIT TEST PROTOCOL -- Sat Oct 17 05:36:08 2020 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
LRBaseDbi RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
Warning message:
In getPackageName(where) :
  Created a package name, '2020-10-17 05:36:08', when none found
> 
> proc.time()
   user  system elapsed 
   3.29    0.12    3.39 

Example timings

LRBaseDbi.Rcheck/examples_i386/LRBaseDbi-Ex.timings

nameusersystemelapsed
FANTOM50.030.010.04
LRBaseDb000
columns000
dbInfo000
dbconn000
dbfile000
dbschema000
keys000
keytypes0.020.000.02
lrListDatabases000
lrNomenclature000
lrPackageName000
lrVersion000
makeLRBasePackage000
metaFANTOM50.000.020.02
select000
species000

LRBaseDbi.Rcheck/examples_x64/LRBaseDbi-Ex.timings

nameusersystemelapsed
FANTOM50.030.000.03
LRBaseDb000
columns000
dbInfo000
dbconn000
dbfile000
dbschema000
keys000
keytypes000
lrListDatabases000
lrNomenclature000
lrPackageName000
lrVersion000
makeLRBasePackage0.020.000.02
metaFANTOM5000
select000
species000