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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:EDIRquery.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings EDIRquery_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/EDIRquery.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EDIRquery/DESCRIPTION’ ... OK
* this is package ‘EDIRquery’ version ‘1.6.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘EDIRquery’ 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 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 ... NOTE
gene_lookup : gen_filter : <anonymous>: no visible binding for global
  variable ‘hgnc_symbol’
gene_lookup : gen_filter : <anonymous>: no visible binding for global
  variable ‘ensembl_gene_id’
Undefined global functions or variables:
  ensembl_gene_id hgnc_symbol
* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/EDIRquery.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL EDIRquery
###
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* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘EDIRquery’ ...
** using staged installation
** R
** data
** 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 (EDIRquery)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(EDIRquery)
> 
> test_check("EDIRquery")
	Parameters
 Repeat length:  10 bp
 
 Gene:            ENSG00000171298 / GAA 
 Gene length:     18325 bp
 Transcript ID:   ENST00000302262
 Distance:        0-1000 bp
 Mismatch:        TRUE


  repeat_length unique_seqs tot_instances tot_structures avg_dist
1            10        1172          1227            690 500.2217
  norm_instances_bp norm_instances_Mb norm_structures_bp norm_structures_Mb
1        0.06695771          66957.71         0.03765348           37653.48


Runtime: 0.769 sec elapsed
	Parameters

 
 Gene:            ENSG00000171298 / GAA 
 Gene length:     18325 bp
 Transcript ID:   ENST00000302262
 Distance:        0-1000 bp
 Mismatch:        TRUE


   repeat_length unique_seqs tot_instances tot_structures avg_dist
1              7        5172         10460          14562 486.2603
2              8        5677          7592           7062 516.1827
3              9        3160          3461           2226 508.7588
4             10        1172          1227            690 500.2217
5             11         389           399            209 492.5263
6             12         122           124             63 454.6190
7             13          42            42             21 346.2857
8             14          14            14              7 271.1429
9             15           4             4              2  43.0000
10            16           2             2              1  42.0000
   norm_instances_bp norm_instances_Mb norm_structures_bp norm_structures_Mb
1       0.5708049113       570804.9113       7.946521e-01       794652.11460
2       0.4142974079       414297.4079       3.853752e-01       385375.17053
3       0.1888676671       188867.6671       1.214734e-01       121473.39700
4       0.0669577080        66957.7080       3.765348e-02        37653.47885
5       0.0217735334        21773.5334       1.140518e-02        11405.18417
6       0.0067667121         6766.7121       3.437926e-03         3437.92633
7       0.0022919509         2291.9509       1.145975e-03         1145.97544
8       0.0007639836          763.9836       3.819918e-04          381.99181
9       0.0002182810          218.2810       1.091405e-04          109.14052
10      0.0001091405          109.1405       5.457026e-05           54.57026


Runtime: 1.351 sec elapsed
	Parameters
 Repeat length:  10 bp
 
 Gene:            ENSG00000171298 / GAA 
 Gene length:     18325 bp
 Transcript ID:   ENST00000302262
 Distance:        0-1000 bp
 Mismatch:        FALSE


  repeat_length unique_seqs tot_instances tot_structures avg_dist
1            10          34            68             34 473.0588
  norm_instances_bp norm_instances_Mb norm_structures_bp norm_structures_Mb
1       0.003710778          3710.778        0.001855389           1855.389


Runtime: 0.779 sec elapsed
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 16 ]
> 
> proc.time()
   user  system elapsed 
 13.777   0.460  14.163