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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:ginmappeR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ginmappeR_1.3.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ginmappeR.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ginmappeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ginmappeR’ version ‘1.3.3’
* 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 ... NOTE
Warning: program compiled against libxml 212 using older 211
* 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                  8.756  0.343  84.185
getKEGG2NCBIProtein           5.691  0.432 174.513
getCARD2NCBIGene              2.688  0.118  21.636
getCARD2UniProt               2.505  0.122  55.305
getNCBINucleotide2KEGG        1.133  0.076  62.095
getNCBIProtein2UniProt        0.453  0.028  20.593
getKEGG2NCBINucleotide        0.456  0.020  15.785
getNCBIGene2UniProt           0.395  0.016  11.786
getNCBINucleotide2UniProt     0.378  0.032  11.734
getNCBIProtein2CARD           0.347  0.031  26.199
getNCBIProtein2KEGG           0.344  0.025  29.601
getNCBIProtein2NCBIGene       0.324  0.032  16.981
getNCBIProtein2NCBINucleotide 0.317  0.028  15.419
getUniProt2NCBINucleotide     0.217  0.000   7.353
getNCBIGene2CARD              0.158  0.003   8.452
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/ginmappeR.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL ginmappeR
###
##############################################################################
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* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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")
Testing getKEGG2UniProt

                                                                                  

  |=.............................| Step   1: Translating from KEGG to UniProt

                                                                                  

  |==............................| Step   2: Connecting to KEGG web services

                                                                                  

  |===...........................| Step   3: Connecting to KEGG API and translating id aag:5579347 to Uniprot

                                                                                  
[1] "A0A1S4G4Z1"
Testing getKEGG2NCBIProtein, getKEGG2NCBINucleotide, getKEGG2NCBIGene

                                                                                  

  |=.............................| Step   1: Translating from KEGG to NCBI Protein

                                                                                  

  |==............................| Step   2: Trying to get a direct translation for KEGG id bha:BH0380 to NCBI

                                                                                  

  |===...........................| Step   3: Translating KEGG id bha:BH0380 to NCBI through similar genes strategy

  |====..........................| Step   4: Connecting to KEGG web services

                                                                                  

  |=====.........................| Step   5: Connecting to KEGG API and translating id bha:BH0380 to Uniprot

                                                                                  

  |======........................| Step   6: Trying to get a direct translation for KEGG id bha:BH0380 to NCBI

                                                                                  

  |=======.......................| Step   7: Translating KEGG id bha:BH0380 to NCBI through similar genes strategy

                                                                                  

  |=.............................| Step   1: Trying to get a direct translation for UniProt id Q7AJZ0 to NCBI

                                                                                  

  |==............................| Step   2: Translating UniProt id Q7AJZ0 to NCBI through similar genes strategy

                                                                                  

  |===...........................| Step   3: Trying to get a direct translation for KEGG id bha:BH0380 to NCBI

                                                                                  

  |====..........................| Step   4: Translating KEGG id bha:BH0380 to NCBI through similar genes strategy

                                                                                  
[1] NA
Test failed: 
NA != BAB04099
Testing getKEGG2CARD

                                                                                  

  |=.............................| Step   1: Translating from KEGG to CARD
Updating CARD database data...
Deleting previous versions of CARD if any.

Downloading latest version

Extracting database

CARD database downloaded successfully!
Located at /home/biocbuild/tmp/RtmpWGWzfi/card-data
CARD database version 4.0.0 (2024-12-17)

                                                                                  

  |==............................| Step   2: Searching CARD database and translating to KEGG

                                                                                  

  |===...........................| Step   3: Trying to get a direct translation for KEGG id ag:ACC85616 to CARD

                                                                                  
[1] "ARO:3002804"
Testing getUniProtSimilarGenes

                                                                                  

  |=.............................| Step   1: Accessing UniProt similar genes database

                                                                                  

  |==............................| Step   2: Connecting to UniProt API and retrieving cluster of id G9JVE6

                                                                                  

  |===...........................| Step   3: Retrieving and parsing genes of cluster UniRef100_G9JVE6

                                                                                  
[1] "UniRef100_G9JVE6"
Testing getUniProt2KEGG

                                                                                  

  |=.............................| Step   1: Translating from UniProt to KEGG

                                                                                  

  |==............................| Step   2: Trying to get a direct translation for UniProt id A0A6I6H1L5 to KEGG

                                                                                  
[1] "fls:GLV81_10715"
Testing getUniProt2NCBIProtein, getUniProt2NCBINucleotide, getUniProt2NCBIGene

                                                                                  

  |=.............................| Step   1: Translating from UniProt to NCBI Protein

                                                                                  

  |==............................| Step   2: Trying to get a direct translation for UniProt id A0A6H2TXZ6 to NCBI

                                                                                  

  |===...........................| Step   3: Translating UniProt id A0A6H2TXZ6 to NCBI through similar genes strategy

                                                                                  
[1] NA
Test failed: 
NA != QIB98918.1
Testing getUniProt2CARD

                                                                                  

  |=.............................| Step   1: Translating from UniProt to CARD
Using a CARD database version downloaded on Tue 01/28/2025 11:20:19, please consider updating it with updateCARDDataBase() function.

                                                                                  

  |==............................| Step   2: Translating Uniprot id A0A1S7BGS4 to CARD

                                                                                  

  |===...........................| Step   3: Trying to get a direct translation for Uniprot id A0A1S7BGS4 to CARD

                                                                                  
[1] "ARO:3004185"


RUNIT TEST PROTOCOL -- Tue Jan 28 11:20:43 2025 
*********************************************** 
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 
 15.253   0.706  43.140