• using R Under development (unstable) (2026-02-23 r89469)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)     GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
• running under: Fedora Linux 42 (Workstation Edition)
• using session charset: UTF-8 * current time: 2026-02-23 21:24:36 UTC
• using option ‘--no-stop-on-test-error’
• checking for file ‘ApplyPolygenicScore/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘ApplyPolygenicScore’ version ‘4.0.1’
• 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 executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘ApplyPolygenicScore’ can be installed ... [18s/35s] OK See the install log for details.
• 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 ... [4s/11s] OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... [4s/11s] 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 ... [4s/10s] OK
• checking use of S3 registration ... 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 ... [29s/51s] OK
• checking Rd files ... 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 installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [35s/43s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [259s/296s] ERROR   Running ‘testthat.R’ [259s/296s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat);   > library(ApplyPolygenicScore);   >   > test_check('ApplyPolygenicScore');   Input data passed validation   Input data passed validation   Skipping test for >12 PGS columns as 'scales' package is available and will be used.   [1] "springgreen3"   [1] "darkturquoise"   [1] "springgreen3"   [1] "darkturquoise"   Saving _problems/test-vcf-import-266.R   Saving _problems/test-vcf-import-270.R   [ FAIL 2 | WARN 87 | SKIP 0 | PASS 653 ]      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Failure ('test-vcf-import.R:263:9'): import.vcf accurately imports INFO fields ──   Expected `ncol(select.info.test.vcf$dat)` to equal `ncol.select`.   Differences:     `actual`: 19.0   `expected`: 18.0      ── Failure ('test-vcf-import.R:267:9'): import.vcf accurately imports INFO fields ──   Expected `ncol(all.info.test.vcf$dat)` to equal `ncol.all`.   Differences:     `actual`: 32.0   `expected`: 31.0         [ FAIL 2 | WARN 87 | SKIP 0 | PASS 653 ]   Error:   ! Test failures.   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [58s/66s] OK
• checking PDF version of manual ... OK
• checking HTML version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 1 ERROR