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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_1.10.0.tar.gz###############################################################################################################################################################* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/EDIRquery.Rcheck’* using R version 4.5.0 (2025-04-11)* 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 ‘EDIRquery/DESCRIPTION’ ... OK* this is package ‘EDIRquery’ version ‘1.10.0’* 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 ... NOTEgene_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* DONEStatus: 1 NOTESee  ‘/home/biocbuild/bbs-3.22-bioc/meat/EDIRquery.Rcheck/00check.log’for details.

################################################################################################################################################################## Running command:######   /home/biocbuild/R/R/bin/R CMD INSTALL EDIRquery###############################################################################################################################################################* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’* installing *source* package ‘EDIRquery’ ...** this is package ‘EDIRquery’ version ‘1.10.0’** 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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"Copyright (C) 2025 The R Foundation for Statistical ComputingPlatform: aarch64-unknown-linux-gnuR 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_dist1            10        1172          1227            690 500.2217  norm_instances_bp norm_instances_Mb norm_structures_bp norm_structures_Mb1        0.06695771          66957.71         0.03765348           37653.48Runtime: 0.519 sec elapsedParameters  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_dist1              7        5172         10460          14562 486.26032              8        5677          7592           7062 516.18273              9        3160          3461           2226 508.75884             10        1172          1227            690 500.22175             11         389           399            209 492.52636             12         122           124             63 454.61907             13          42            42             21 346.28578             14          14            14              7 271.14299             15           4             4              2  43.000010            16           2             2              1  42.0000   norm_instances_bp norm_instances_Mb norm_structures_bp norm_structures_Mb1       0.5708049113       570804.9113       7.946521e-01       794652.114602       0.4142974079       414297.4079       3.853752e-01       385375.170533       0.1888676671       188867.6671       1.214734e-01       121473.397004       0.0669577080        66957.7080       3.765348e-02        37653.478855       0.0217735334        21773.5334       1.140518e-02        11405.184176       0.0067667121         6766.7121       3.437926e-03         3437.926337       0.0022919509         2291.9509       1.145975e-03         1145.975448       0.0007639836          763.9836       3.819918e-04          381.991819       0.0002182810          218.2810       1.091405e-04          109.1405210      0.0001091405          109.1405       5.457026e-05           54.57026Runtime: 0.961 sec elapsedParameters 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_dist1            10          34            68             34 473.0588  norm_instances_bp norm_instances_Mb norm_structures_bp norm_structures_Mb1       0.003710778          3710.778        0.001855389           1855.389Runtime: 0.499 sec elapsed[ FAIL 0 | WARN 0 | SKIP 0 | PASS 16 ]> > proc.time()   user  system elapsed  11.501   0.436  11.943