• using R Under development (unstable) (2024-10-07 r87211)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (GCC) 14.2.0     GNU Fortran (GCC) 14.2.0
• running under: Fedora Linux 36 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘pmartR/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘pmartR’ version ‘2.4.5’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... NOTE Package suggested but not available for checking: ‘pmartRdata’
• 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 ‘pmartR’ can be installed ... [170s/119s] OK See the install log for details.
• used C++ compiler: ‘g++-14 (GCC) 14.2.0’
• checking package 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 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 ... [83s/102s] 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 line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... OK
• checking compilation flags in Makevars ... OK
• checking for GNU extensions in Makefiles ... OK
• checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking use of PKG_*FLAGS in Makefiles ... OK
• checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
• checking pragmas in C/C++ headers and code ... OK
• checking compilation flags used ... OK
• checking compiled code ... OK
• checking examples ... OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [79s/95s] ERROR   Running ‘testthat.R’ [79s/94s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(pmartR)   >   > test_check("pmartR")   [ FAIL 1 | WARN 1 | SKIP 11 | PASS 2371 ]      ══ Skipped tests (11) ══════════════════════════════════════════════════════════   • On CRAN (11): 'test_as_trelliData.R:4:3', 'test_as_trelliData.R:361:3',     'test_as_trelliData_edata.R:4:3', 'test_as_trelliData_summary.R:4:3',     'test_diffexp_seq.R:4:3', 'test_imd_anova.R:5:3',     'test_imd_anova_paired.R:5:3', 'test_plots.R:14:3', 'test_trelliPlots.R:4:3',     'test_trelliPlots_seqData.R:4:3', 'test_trelli_pvalue_filter.R:4:3'      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test_dispersion_est.R:42:3'): dispersion_est returns the correct data frame and attributes ──   Error in `data.frame(CD = D_edgeR$common.dispersion, TD = D_edgeR$trended.dispersion,       TagD = D_edgeR$tagwise.dispersion, fitD1 = fit_edgeR$var.prior,       fitD2 = fit_edgeR$var.post, AveLogCPM = fit_edgeR$AveLogCPM)`: arguments imply differing number of rows: 1, 1200, 0   Backtrace:       ▆    1. └─pmartR::dispersion_est(seqdata_grp, method = "edgeR") at test_dispersion_est.R:42:3    2. └─base::data.frame(...)      [ FAIL 1 | WARN 1 | SKIP 11 | PASS 2371 ]   Deleting unused snapshots:   • plots/plot-corres.svg   • plots/plot-cvfilt-log-scale.svg   • plots/plot-cvfilt.svg   • plots/plot-datares-bw-theme.svg   • plots/plot-datares-palette.svg   • plots/plot-datares.svg   • plots/plot-dimres.svg   • plots/plot-imdanovafilt.svg   • plots/plot-isobaricnormres-bw-theme.svg   • plots/plot-isobaricnormres-global-normalized.svg   • plots/plot-isobaricnormres-palette.svg   • plots/plot-isobaricnormres.svg   • plots/plot-isobaricpepdata.svg   • plots/plot-lipiddata.svg   • plots/plot-metabdata.svg   • plots/plot-moleculefilt-cumulative.svg   • plots/plot-moleculefilt.svg   • plots/plot-nares-bar-group-color.svg   • plots/plot-nares-bar-group-order.svg   • plots/plot-nares-scatter.svg   • plots/plot-nmrdata.svg   • plots/plot-nmrnormres-2.svg   • plots/plot-nmrnormres-color-by.svg   • plots/plot-nmrnormres.svg   • plots/plot-normres.svg   • plots/plot-pepdata.svg   • plots/plot-prodata.svg   • plots/plot-proteomicsfilt-redundancy.svg   • plots/plot-proteomicsfilt.svg   • plots/plot-rmdfilt.svg   • plots/plot-rnafilt.svg   • plots/plot-seqdata.svg   • plots/plot-spansres-bw-theme.svg   • plots/plot-spansres-color-high-color-low.svg   • plots/plot-spansres.svg   • plots/plot-statres-anova-volcano.svg   • plots/plot-statres-anova.svg   • plots/plot-statres-combined-volcano.svg   • plots/plot-statres-combined.svg   • plots/plot-statres-gtest.svg   • plots/plot-totalcountfilt.svg   Error: Test failures   Execution halted
• checking PDF version of manual ... [20s/27s] OK
• checking HTML version of manual ... [16s/28s] OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 1 ERROR, 1 NOTE