##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ginmappeR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ginmappeR_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ginmappeR.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘ginmappeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ginmappeR’ version ‘1.1.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ginmappeR’ 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 code 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
getCARD2KEGG           1.724  0.127  12.376
getCARD2UniProt        0.697  0.113   7.199
getNCBINucleotide2KEGG 0.450  0.047   7.084
getNCBIProtein2UniProt 0.427  0.066   5.007
getKEGG2NCBINucleotide 0.440  0.040   6.263
getNCBIGene2KEGG       0.363  0.053   7.073
getNCBIProtein2KEGG    0.256  0.052  10.973
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/ginmappeR.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL ginmappeR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘ginmappeR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** 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 (ginmappeR)

R version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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("ginmappeR")
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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, aperm, 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, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: RSQLite
Testing getKEGG2UniProt
Testing getKEGG2NCBIProtein, getKEGG2NCBINucleotide, getKEGG2NCBIGene
Testing getKEGG2CARD
Updating CARD database data...
CARD database downloaded successfully!
Located at /tmp/RtmpZne2CD/card-data
Using a CARD database version downloaded on Wed 05/15/2024 22:55:02, please consider updating it with updateCARDDataBase() function.
Using a CARD database version downloaded on Wed 05/15/2024 22:55:02, please consider updating it with updateCARDDataBase() function.
Using a CARD database version downloaded on Wed 05/15/2024 22:55:02, please consider updating it with updateCARDDataBase() function.
Using a CARD database version downloaded on Wed 05/15/2024 22:55:02, please consider updating it with updateCARDDataBase() function.
Using a CARD database version downloaded on Wed 05/15/2024 22:55:02, please consider updating it with updateCARDDataBase() function.
Using a CARD database version downloaded on Wed 05/15/2024 22:55:02, please consider updating it with updateCARDDataBase() function.
Testing getUniProtSimilarGenes
The given ID "test" is not registered in UniProt database
The given ID "test" is not registered in UniProt database
The given ID "test" is not registered in UniProt database
Testing getUniProt2KEGG
The given ID "test" is not registered in UniProt database
The given ID "test" is not registered in UniProt database
The given ID "test" is not registered in UniProt database
The given ID "test" is not registered in UniProt database
The given ID "test" is not registered in UniProt database
The given ID "test" is not registered in UniProt database
The given ID "test" is not registered in UniProt database
The given ID "test" is not registered in UniProt database
Testing getUniProt2NCBIProtein, getUniProt2NCBINucleotide, getUniProt2NCBIGene
Testing getUniProt2CARD
Using a CARD database version downloaded on Wed 05/15/2024 22:55:02, please consider updating it with updateCARDDataBase() function.
Using a CARD database version downloaded on Wed 05/15/2024 22:55:02, please consider updating it with updateCARDDataBase() function.
Using a CARD database version downloaded on Wed 05/15/2024 22:55:02, please consider updating it with updateCARDDataBase() function.
Using a CARD database version downloaded on Wed 05/15/2024 22:55:02, please consider updating it with updateCARDDataBase() function.
Using a CARD database version downloaded on Wed 05/15/2024 22:55:02, please consider updating it with updateCARDDataBase() function.


RUNIT TEST PROTOCOL -- Wed May 15 22:59:49 2024 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ginmappeR RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 24.922   2.105 307.786