* using log directory ‘/srv/hornik/tmp/CRAN/gen3DNet.Rcheck’ * using R Under development (unstable) (2024-05-15 r86556) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 18.1.4 (1) Debian flang-new version 18.1.4 (1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘gen3DNet/DESCRIPTION’ ... OK * this is package ‘gen3DNet’ version ‘1.0.0.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/3s] NOTE Maintainer: ‘Shamim Mollah ’ New submission License components with restrictions and base license permitting such: MIT + file LICENSE * 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 executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking serialization versions ... OK * checking whether package ‘gen3DNet’ can be installed ... [4s/4s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... WARNING Invalid license file pointers: LICENSE Author field differs from that derived from Authors@R Author: ‘Paul Morrison’ Authors@R: ‘Paul Morrison [aut], Tina Tang [aut] (), Charles Lu [aut] (), Shamim Mollah [aut, cre] ()’ Maintainer field differs from that derived from Authors@R Maintainer: ‘Shamim Mollah ’ Authors@R: ‘Shamim Mollah ’ * 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 ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... WARNING Missing or unexported object: ‘gen3DNet::max_kl_ward’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [6s/6s] NOTE Found if() conditions comparing class() to string: File ‘gen3DNet/R/gen3DNet.R’: if (class(object) == "data.frame") ... File ‘gen3DNet/R/gen3DNet.R’: if (class(object) == "list") ... Use inherits() (or maybe is()) instead. * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... 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 examples ... [27s/25s] NOTE Examples with CPU (user + system) or elapsed time > 5s user system elapsed gen3DNet 12.602 0.426 11.907 create_gen3DNet 12.188 0.438 11.584 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [18m/12m] ERROR Running ‘testthat.R’ [18m/12m] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(gen3DNet) Loading required package: NMF Loading required package: registry Loading required package: rngtools Loading required package: cluster NMF - BioConductor layer [OK] | Shared memory capabilities [NO: bigmemory] | Cores 2/2 | CRAN check To enable shared memory capabilities, try: install.extras(' NMF ') Attaching package: 'NMF' The following object is masked from 'package:testthat': compare > > test_check("gen3DNet") v Generating 3D network v Running NMF i Picking k from [ 2 , 30 ]. i Using k = 4 v Running PLSR v Merging data... v Writing to test_output v Generating 3D network v Running NMF i Picking k from [ 2 , 30 ]. i Using k = 2 v Running PLSR v Merging data... v Writing to gen3DNet_2024-05-16_21-19-21 v Generating 3D network v Running NMF i Picking k from [ 2 , 30 ]. i Using k = 18 v Running PLSR v Merging data... v Writing to gen3DNet_2024-05-16_21-21-47 v Generating 3D network v Running NMF i Picking k from [ 2 , 30 ]. i Using k = 24 v Running PLSR v Merging data... v Writing to gen3DNet_2024-05-16_21-24-10 v Generating 3D network v Running NMF i Picking k from [ 2 , 30 ]. i Using k = 2 v Running PLSR v Merging data... v Writing to gen3DNet_2024-05-16_21-26-33 v Generating 3D network v Running NMF i Picking k from [ 2 , 30 ]. i Using k = 2 v Running PLSR v Merging data... v Writing to gen3DNet_2024-05-16_21-28-56 v Generating 3D network v Running NMF i Picking k from [ 2 , 30 ]. i Using k = 4 v Running PLSR v Merging data... v Writing to gen3DNet_2024-05-16_21-31-20 [ FAIL 1 | WARN 2 | SKIP 1 | PASS 0 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'test-test_k_selection_functions-as_script-final.R:77:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-test_k_selection_functions-as_script-final.R:73:1'): Results match iPhDNet ── Error in `file(con, "r")`: cannot open the connection Backtrace: ▆ 1. ├─testthat::expect(verify_folders_same("test_output", "correct_output")) at test-test_k_selection_functions-as_script-final.R:73:1 2. └─gen3DNet (local) verify_folders_same("test_output", "correct_output") 3. └─base::sapply(...) at test-test_k_selection_functions-as_script-final.R:17:8 4. └─base::lapply(X = X, FUN = FUN, ...) 5. └─gen3DNet (local) FUN(X[[i]], ...) 6. └─gen3DNet (local) verify_files_same(...) at test-test_k_selection_functions-as_script-final.R:25:20 7. └─base::readLines(file_a) at test-test_k_selection_functions-as_script-final.R:43:5 8. └─base::file(con, "r") [ FAIL 1 | WARN 2 | SKIP 1 | PASS 0 ] Error: Test failures Execution halted * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... NOTE Found the following files/directories: ‘gen3DNet_2024-05-16_21-18-42’ ‘gen3DNet_2024-05-16_21-18-53’ ‘toplevelfolder’ * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 2 WARNINGs, 4 NOTEs