* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/pmartR.Rcheck’
* using R Under development (unstable) (2024-04-19 r86451)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-13 (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* 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 ‘2.4.4’
* 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 ... [206s/179s] OK
* used C++ compiler: ‘g++-13 (GCC) 13.2.0’
* 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 ... [89s/115s] 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 ...
  Running ‘testthat.R’ [70s/100s]
 [71s/101s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pmartR)
  > 
  > test_check("pmartR")
  [ FAIL 14 | WARN 0 | SKIP 5 | PASS 2480 ]
  
  ══ Skipped tests (5) ═══════════════════════════════════════════════════════════
  • On CRAN (5): 'test_diffexp_seq.R:4:3', 'test_imd_anova.R:5:3',
    'test_imd_anova_paired.R:5:3', 'test_trelliPlots.R:4:3',
    'test_trelliPlots_seqData.R:4:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_as_trelliData.R:374:3'): as.trelliData and trelli_panel_by returns correct data frames and attributes ──
  Error in `voom_wrapper(omicsData = omicsData, p_adjust = p_adjust, comparisons = comparisons, 
      p_cutoff = p_cutoff, ...)`: package 'edgeR' required for voom processing
  Backtrace:
      ▆
   1. └─pmartR::diffexp_seq(omicsData = seqData_omics, method = "voom") at test_as_trelliData.R:374:3
   2.   └─pmartR:::voom_wrapper(...)
  ── Error ('test_as_trelliData_edata.R:149:3'): as.trelliData.edata returns correct data frames and attributes ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'limma'
  Backtrace:
      ▆
   1. ├─pmartR::as.trelliData.edata(...) at test_as_trelliData_edata.R:149:3
   2. │ ├─base::do.call(norm_fun, normalization_params)
   3. │ └─pmartR (local) `<fn>`(method = "affy", span = 0.2, omicsData = `<lipidDat>`)
   4. └─base::loadNamespace(x)
   5.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   6.     └─base (local) withOneRestart(expr, restarts[[1L]])
   7.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test_as_trelliData_summary.R:100:3'): trelliData object summaries return the correct data frames ──
  Error in `voom_wrapper(omicsData = omicsData, p_adjust = p_adjust, comparisons = comparisons, 
      p_cutoff = p_cutoff, ...)`: package 'edgeR' required for voom processing
  Backtrace:
      ▆
   1. └─pmartR::diffexp_seq(omicsData = seqData_omics, method = "voom") at test_as_trelliData_summary.R:100:3
   2.   └─pmartR:::voom_wrapper(...)
  ── Error ('test_dispersion_est.R:38:3'): dispersion_est returns the correct data frame and attributes ──
  Error in `dispersion_est(seqdata_grp, method = "edgeR")`: package 'edgeR' required for edgeR processing
  Backtrace:
      ▆
   1. └─pmartR::dispersion_est(seqdata_grp, method = "edgeR") at test_dispersion_est.R:38:3
  ── Failure ('test_edata_structure.R:52:3'): errors are thrown for bad data structures/values ──
  `as.pepData(...)` threw an error with unexpected message.
  Expected match: "Columns 2 and 4 of e_data contain non-numeric values."
  Actual message: "there is no package called 'knitr'"
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test_edata_structure.R:52:3
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. ├─pmartR::as.pepData(...)
    7. │ └─pmartR:::.as.pepData(...)
    8. │   └─pmartR:::pre_flight(...)
    9. │     └─pmartR:::str_col(edata = e_data, edata_cname = edata_cname)
   10. │       ├─base::stop(...)
   11. │       └─base::paste(...)
   12. └─base::loadNamespace(x)
   13.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   14.     └─base (local) withOneRestart(expr, restarts[[1L]])
   15.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Failure ('test_edata_structure.R:63:3'): errors are thrown for bad data structures/values ──
  `as.lipidData(...)` threw an error with unexpected message.
  Expected match: "Column 4 of e_data contains non-numeric values."
  Actual message: "there is no package called 'knitr'"
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test_edata_structure.R:63:3
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. ├─pmartR::as.lipidData(...)
    7. │ └─pmartR:::.as.lipidData(...)
    8. │   └─pmartR:::pre_flight(...)
    9. │     └─pmartR:::str_col(edata = e_data, edata_cname = edata_cname)
   10. │       ├─base::stop(...)
   11. │       └─base::paste(...)
   12. └─base::loadNamespace(x)
   13.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   14.     └─base (local) withOneRestart(expr, restarts[[1L]])
   15.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Failure ('test_edata_structure.R:76:3'): errors are thrown for bad data structures/values ──
  `as.metabData(...)` threw an error with unexpected message.
  Expected match: "Column 3 of e_data contains infinite values."
  Actual message: "there is no package called 'knitr'"
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test_edata_structure.R:76:3
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. ├─pmartR::as.metabData(...)
    7. │ └─pmartR:::.as.metabData(...)
    8. │   └─pmartR:::pre_flight(...)
    9. │     └─pmartR:::str_col(edata = e_data, edata_cname = edata_cname)
   10. │       ├─base::stop(...)
   11. │       └─base::paste(...)
   12. └─base::loadNamespace(x)
   13.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   14.     └─base (local) withOneRestart(expr, restarts[[1L]])
   15.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Failure ('test_edata_structure.R:89:3'): errors are thrown for bad data structures/values ──
  `as.metabData(...)` threw an error with unexpected message.
  Expected match: "Columns 3 and 6 of e_data contain infinite values."
  Actual message: "there is no package called 'knitr'"
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test_edata_structure.R:89:3
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. ├─pmartR::as.metabData(...)
    7. │ └─pmartR:::.as.metabData(...)
    8. │   └─pmartR:::pre_flight(...)
    9. │     └─pmartR:::str_col(edata = e_data, edata_cname = edata_cname)
   10. │       ├─base::stop(...)
   11. │       └─base::paste(...)
   12. └─base::loadNamespace(x)
   13.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   14.     └─base (local) withOneRestart(expr, restarts[[1L]])
   15.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Failure ('test_filter_custom.R:1553:3'): custom_filter and applyFilt produce the correct output ──
  `applyFilt(filter_object = split_remove, omicsData = pairdata)` threw an error with unexpected message.
  Expected match: "The following samples should also be removed based on the input: FM_18hr_3 and AM_0hr_5. Samples in a pair must be removed together."
  Actual message: "there is no package called 'knitr'"
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test_filter_custom.R:1553:3
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. ├─pmartR::applyFilt(filter_object = split_remove, omicsData = pairdata)
    7. ├─pmartR:::applyFilt.customFilt(filter_object = split_remove, omicsData = pairdata)
    8. │ ├─base::stop(...)
    9. │ └─base::paste(...)
   10. └─base::loadNamespace(x)
   11.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   12.     └─base (local) withOneRestart(expr, restarts[[1L]])
   13.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Failure ('test_filter_custom.R:1561:3'): custom_filter and applyFilt produce the correct output ──
  `applyFilt(filter_object = split_keep, omicsData = pairdata)` threw an error with unexpected message.
  Expected match: "The following samples should also be kept based on the input: FM_18hr_5. Samples in a pair must be kept together."
  Actual message: "there is no package called 'knitr'"
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test_filter_custom.R:1561:3
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. ├─pmartR::applyFilt(filter_object = split_keep, omicsData = pairdata)
    7. ├─pmartR:::applyFilt.customFilt(filter_object = split_keep, omicsData = pairdata)
    8. │ ├─base::stop(...)
    9. │ └─base::paste(...)
   10. └─base::loadNamespace(x)
   11.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   12.     └─base (local) withOneRestart(expr, restarts[[1L]])
   13.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Failure ('test_group_designation.R:757:3'): the correct group data frame and attributes are created ──
  `group_designation(...)` threw an error with unexpected message.
  Expected match: "The following samples have main effects that differ between pairs: Mock_0hr_2 and Mock_18hr_2"
  Actual message: "there is no package called 'knitr'"
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test_group_designation.R:757:3
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. ├─pmartR::group_designation(...)
    7. │ ├─base::stop(...)
    8. │ └─base::paste(...)
    9. └─base::loadNamespace(x)
   10.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   11.     └─base (local) withOneRestart(expr, restarts[[1L]])
   12.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Failure ('test_group_designation.R:770:3'): the correct group data frame and attributes are created ──
  `group_designation(...)` threw an error with unexpected message.
  Expected match: "The following samples have covariates that differ between pairs: AM_0hr_4 and AM_18hr_4"
  Actual message: "there is no package called 'knitr'"
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test_group_designation.R:770:3
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. ├─pmartR::group_designation(...)
    7. │ ├─base::stop(...)
    8. │ └─base::paste(...)
    9. └─base::loadNamespace(x)
   10.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   11.     └─base (local) withOneRestart(expr, restarts[[1L]])
   12.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test_plots.R:1:1'): (code run outside of `test_that()`) ─────────────
  <packageNotFoundError/error/condition>
  Error in `library(vdiffr)`: there is no package called 'vdiffr'
  Backtrace:
      ▆
   1. └─base::library(vdiffr) at test_plots.R:1:1
  ── Error ('test_trelli_pvalue_filter.R:88:3'): trelli_pvalue_filter returns correct data frames and attributes ──
  Error in `voom_wrapper(omicsData = omicsData, p_adjust = p_adjust, comparisons = comparisons, 
      p_cutoff = p_cutoff, ...)`: package 'edgeR' required for voom processing
  Backtrace:
      ▆
   1. └─pmartR::diffexp_seq(omicsData = seqData_omics, method = "voom") at test_trelli_pvalue_filter.R:88:3
   2.   └─pmartR:::voom_wrapper(...)
  
  [ FAIL 14 | WARN 0 | SKIP 5 | PASS 2480 ]
  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 ... [22s/31s] OK
* checking HTML version of manual ... [15s/24s] 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
See
  ‘/data/gannet/ripley/R/packages/tests-Suggests/pmartR.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 9:09.47, 459.66 + 26.02