CRAN Package Check Results for Maintainer ‘Thijs Janzen <thijsjanzen at gmail.com>’

Last updated on 2025-03-12 08:53:37 CET.

Package ERROR NOTE OK
GenomeAdmixR 15
GUILDS 2 13
junctions 15
nLTT 12 3
nodeSub 15
simRestore 15
STEPCAM 12 3
treestats 2 4 9

Package GenomeAdmixR

Current CRAN status: NOTE: 15

Version: 2.1.7
Check: C++ specification
Result: NOTE Specified C++14: please drop specification unless essential Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-macos-arm64, r-devel-macos-x86_64, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

Version: 2.1.7
Check: Rd files
Result: NOTE checkRd: (-1) simulate_admixture.Rd:36: Lost braces 36 | \code{location}{ location of the marker under selection (in Morgan) } | ^ checkRd: (-1) simulate_ancestry.Rd:49: Lost braces 49 | \code{location}{ location of the marker under selection (in Morgan) } | ^ checkRd: (-1) simulate_ancestry_migration.Rd:59: Lost braces 59 | \code{location}{ location of the marker under selection (in Morgan) } | ^ checkRd: (-1) simulate_sequence.Rd:51: Lost braces 51 | \code{location}{ location of the marker under selection (in Morgan) } | ^ checkRd: (-1) simulate_sequence_migration.Rd:58: Lost braces 58 | \code{location}{ location of the marker under selection (in Morgan) } | ^ Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-macos-arm64, r-devel-macos-x86_64, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64

Version: 2.1.7
Check: dependencies in R code
Result: NOTE Namespace in Imports field not imported from: ‘methods’ All declared Imports should be used. Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 2.1.7
Check: installed package size
Result: NOTE installed size is 6.8Mb sub-directories of 1Mb or more: doc 2.0Mb libs 4.3Mb Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Package GUILDS

Current CRAN status: ERROR: 2, OK: 13

Version: 1.4.7
Check: examples
Result: ERROR Running examples in ‘GUILDS-Ex.R’ failed The error most likely occurred in: > ### Name: maxLikelihood.Guilds.Conditional > ### Title: Maximization of the loglikelihood under the Guilds Model, > ### conditioned on guild size. > ### Aliases: maxLikelihood.Guilds.Conditional > > ### ** Examples > > theta = 20 > alpha = 0.1 > initParams <- c(theta, alpha) > maxLikelihood.Guilds.Conditional(initParams, + model = "D0", + sadx = 1:20, + sady = 1:20, + verbose = TRUE) Error in if (fnew <= fmin) { : missing value where TRUE/FALSE needed Calls: maxLikelihood.Guilds.Conditional ... eval_f -> conditional.LogLik -> logLikguilds -> <Anonymous> Execution halted Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.4.7
Check: tests
Result: ERROR Running ‘testthat.R’ [20s/50s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(GUILDS) > test_check("GUILDS") [ FAIL 2 | WARN 0 | SKIP 0 | PASS 100 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-maxLikelihood.Guilds.Conditional.R:13:3'): maxLikelihood.GuildsConditional: use ── Error in `if (fnew <= fmin) { if (xnew < xmin) { xu <- xmin } else { xl <- xmin } xmin2 <- xmin1 fmin2 <- fmin1 xmin1 <- xmin fmin1 <- fmin xmin <- xnew fmin <- fnew } else { if (xnew < xmin) { xl <- xnew } else { xu <- xnew } if (xnew <= xmin1 || xmin1 == xmin) { xmin2 = xmin1 fmin2 = fmin1 xmin1 = xnew fmin1 = fnew } else if (xnew <= xmin2 || xmin2 == xmin || xmin2 == xmin1) { xmin2 <- xnew fmin2 <- fnew } }`: missing value where TRUE/FALSE needed Backtrace: ▆ 1. ├─GUILDS::maxLikelihood.Guilds.Conditional(...) at test-maxLikelihood.Guilds.Conditional.R:13:3 2. │ └─nloptr::nloptr(...) 3. └─nloptr (local) `<fn>`(`<dbl>`) 4. └─GUILDS (local) eval_f(x, ...) 5. └─GUILDS:::conditional.LogLik(...) 6. └─GUILDS:::logLikguilds(...) 7. └─pracma::fminbnd(f, 0, 1, maxiter = 500, tol = 1e-04) ── Error ('test-maxLikelihood.Guilds.R:14:3'): maxLikelihood.Guilds: use ─────── Error in `if (fnew <= fmin) { if (xnew < xmin) { xu <- xmin } else { xl <- xmin } xmin2 <- xmin1 fmin2 <- fmin1 xmin1 <- xmin fmin1 <- fmin xmin <- xnew fmin <- fnew } else { if (xnew < xmin) { xl <- xnew } else { xu <- xnew } if (xnew <= xmin1 || xmin1 == xmin) { xmin2 = xmin1 fmin2 = fmin1 xmin1 = xnew fmin1 = fnew } else if (xnew <= xmin2 || xmin2 == xmin || xmin2 == xmin1) { xmin2 <- xnew fmin2 <- fnew } }`: missing value where TRUE/FALSE needed Backtrace: ▆ 1. ├─GUILDS::maxLikelihood.Guilds(...) at test-maxLikelihood.Guilds.R:14:3 2. │ └─nloptr::nloptr(...) 3. └─nloptr (local) `<fn>`(`<dbl>`) 4. └─GUILDS (local) eval_f(x, ...) 5. └─GUILDS:::logLikguilds(...) 6. └─pracma::fminbnd(f, 0, 1, maxiter = 500, tol = 1e-04) [ FAIL 2 | WARN 0 | SKIP 0 | PASS 100 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.4.7
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building ‘Walkthrough.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-clang/GUILDS.Rcheck/vign_test/GUILDS/vignettes/Walkthrough_files/figure-html/unnamed-chunk-1-1.png 576x288 pixels, 8 bits/pixel, 246 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 2947 bytes Input file size = 3775 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2454 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 2452 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 2452 Output IDAT size = 2452 bytes (495 bytes decrease) Output file size = 2530 bytes (1245 bytes = 32.98% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/GUILDS.Rcheck/vign_test/GUILDS/vignettes/Walkthrough_files/figure-html/unnamed-chunk-2-1.png 576x288 pixels, 8 bits/pixel, 255 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 4642 bytes Input file size = 5497 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3998 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 3970 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 3970 Output IDAT size = 3970 bytes (672 bytes decrease) Output file size = 4048 bytes (1449 bytes = 26.36% decrease) Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.4.7
Check: tests
Result: ERROR Running ‘testthat.R’ [19s/23s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(GUILDS) > test_check("GUILDS") [ FAIL 2 | WARN 0 | SKIP 0 | PASS 100 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-maxLikelihood.Guilds.Conditional.R:13:3'): maxLikelihood.GuildsConditional: use ── Error in `if (fnew <= fmin) { if (xnew < xmin) { xu <- xmin } else { xl <- xmin } xmin2 <- xmin1 fmin2 <- fmin1 xmin1 <- xmin fmin1 <- fmin xmin <- xnew fmin <- fnew } else { if (xnew < xmin) { xl <- xnew } else { xu <- xnew } if (xnew <= xmin1 || xmin1 == xmin) { xmin2 = xmin1 fmin2 = fmin1 xmin1 = xnew fmin1 = fnew } else if (xnew <= xmin2 || xmin2 == xmin || xmin2 == xmin1) { xmin2 <- xnew fmin2 <- fnew } }`: missing value where TRUE/FALSE needed Backtrace: ▆ 1. ├─GUILDS::maxLikelihood.Guilds.Conditional(...) at test-maxLikelihood.Guilds.Conditional.R:13:3 2. │ └─nloptr::nloptr(...) 3. └─nloptr (local) `<fn>`(`<dbl>`) 4. └─GUILDS (local) eval_f(x, ...) 5. └─GUILDS:::conditional.LogLik(...) 6. └─GUILDS:::logLikguilds(...) 7. └─pracma::fminbnd(f, 0, 1, maxiter = 500, tol = 1e-04) ── Error ('test-maxLikelihood.Guilds.R:14:3'): maxLikelihood.Guilds: use ─────── Error in `if (fnew <= fmin) { if (xnew < xmin) { xu <- xmin } else { xl <- xmin } xmin2 <- xmin1 fmin2 <- fmin1 xmin1 <- xmin fmin1 <- fmin xmin <- xnew fmin <- fnew } else { if (xnew < xmin) { xl <- xnew } else { xu <- xnew } if (xnew <= xmin1 || xmin1 == xmin) { xmin2 = xmin1 fmin2 = fmin1 xmin1 = xnew fmin1 = fnew } else if (xnew <= xmin2 || xmin2 == xmin || xmin2 == xmin1) { xmin2 <- xnew fmin2 <- fnew } }`: missing value where TRUE/FALSE needed Backtrace: ▆ 1. ├─GUILDS::maxLikelihood.Guilds(...) at test-maxLikelihood.Guilds.R:14:3 2. │ └─nloptr::nloptr(...) 3. └─nloptr (local) `<fn>`(`<dbl>`) 4. └─GUILDS (local) eval_f(x, ...) 5. └─GUILDS:::logLikguilds(...) 6. └─pracma::fminbnd(f, 0, 1, maxiter = 500, tol = 1e-04) [ FAIL 2 | WARN 0 | SKIP 0 | PASS 100 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.4.7
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building ‘Walkthrough.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-devel/GUILDS.Rcheck/vign_test/GUILDS/vignettes/Walkthrough_files/figure-html/unnamed-chunk-1-1.png 576x288 pixels, 8 bits/pixel, 246 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 2947 bytes Input file size = 3775 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2454 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 2452 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 2452 Output IDAT size = 2452 bytes (495 bytes decrease) Output file size = 2530 bytes (1245 bytes = 32.98% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/GUILDS.Rcheck/vign_test/GUILDS/vignettes/Walkthrough_files/figure-html/unnamed-chunk-2-1.png 576x288 pixels, 8 bits/pixel, 255 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 4642 bytes Input file size = 5497 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3998 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 3970 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 3970 Output IDAT size = 3970 bytes (672 bytes decrease) Output file size = 4048 bytes (1449 bytes = 26.36% decrease) Flavor: r-devel-linux-x86_64-fedora-gcc

Package junctions

Current CRAN status: OK: 15

Package nLTT

Current CRAN status: NOTE: 12, OK: 3

Version: 1.4.9
Check: Rd files
Result: NOTE checkRd: (-1) check_input_event_times.Rd:16-17: Lost braces in \itemize; meant \describe ? checkRd: (-1) check_input_event_times.Rd:18-19: Lost braces in \itemize; meant \describe ? checkRd: (-1) check_time_unit.Rd:12-13: Lost braces in \itemize; meant \describe ? checkRd: (-1) check_time_unit.Rd:14-15: Lost braces in \itemize; meant \describe ? checkRd: (-1) default_params_doc.Rd:30-31: Lost braces in \itemize; meant \describe ? checkRd: (-1) default_params_doc.Rd:32-33: Lost braces in \itemize; meant \describe ? checkRd: (-1) nltt_diff_exact_brts.Rd:30: Lost braces in \itemize; meant \describe ? checkRd: (-1) nltt_diff_exact_brts.Rd:31: Lost braces in \itemize; meant \describe ? checkRd: (-1) nltt_diff_exact_brts.Rd:36-37: Lost braces in \itemize; meant \describe ? checkRd: (-1) nltt_diff_exact_brts.Rd:38-39: Lost braces in \itemize; meant \describe ? checkRd: (-1) nltt_diff_exact_extinct.Rd:31: Lost braces in \itemize; meant \describe ? checkRd: (-1) nltt_diff_exact_extinct.Rd:32: Lost braces in \itemize; meant \describe ? checkRd: (-1) nltt_diff_exact_extinct.Rd:37-38: Lost braces in \itemize; meant \describe ? checkRd: (-1) nltt_diff_exact_extinct.Rd:39-40: Lost braces in \itemize; meant \describe ? Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-macos-arm64, r-devel-macos-x86_64, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64

Package nodeSub

Current CRAN status: OK: 15

Package simRestore

Current CRAN status: OK: 15

Package STEPCAM

Current CRAN status: NOTE: 12, OK: 3

Version: 1.2
Check: Rd files
Result: NOTE checkRd: (-1) STEPCAM_ABC.Rd:19: Lost braces 19 | \code{rows}{ every row corresponds to a different plot or community} \cr | ^ checkRd: (-1) STEPCAM_ABC.Rd:20: Lost braces 20 | \code{columns}{ every column corresponds to a different species.} \cr | ^ checkRd: (-1) STEPCAM_ABC.Rd:25: Lost braces 25 | \code{rows}{ every row corresponds to a different species} \cr | ^ checkRd: (-1) STEPCAM_ABC.Rd:26: Lost braces 26 | \code{columns}{ the first column contains the name of the species, every consecutive column corresponds to a different trait} \cr | ^ checkRd: (-1) plotSTEPCAM.Rd:16: Lost braces 16 | - \code{DA}{ a vector containing the posterior distribution for the parameter dispersal assembly} \cr | ^ checkRd: (-1) plotSTEPCAM.Rd:17: Lost braces 17 | - \code{HF}{ a vector containing the posterior distribution for the parameter habitat filtering} \cr | ^ checkRd: (-1) plotSTEPCAM.Rd:18: Lost braces 18 | - \code{LS}{ a vector containing the posterior distribution for the parameter limiting similarity} \cr | ^ Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-macos-arm64, r-devel-macos-x86_64, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64

Package treestats

Current CRAN status: ERROR: 2, NOTE: 4, OK: 9

Version: 1.70.5
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building ‘Example_abc.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-clang/treestats.Rcheck/vign_test/treestats/vignettes/Example_abc_files/figure-html/plot_simpl2-1.png 576x576 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 13027 bytes Input file size = 13897 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11275 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 11235 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 11235 Output IDAT size = 11235 bytes (1792 bytes decrease) Output file size = 11313 bytes (2584 bytes = 18.59% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/treestats.Rcheck/vign_test/treestats/vignettes/Example_abc_files/figure-html/plot_simple-1.png 576x576 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 21407 bytes Input file size = 22289 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19755 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 19508 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 19508 Output IDAT size = 19508 bytes (1899 bytes decrease) Output file size = 19586 bytes (2703 bytes = 12.13% decrease) Quitting from lines 86-102 [sim_ddd] (Example_abc.Rmd) Error: processing vignette 'Example_abc.Rmd' failed with diagnostics: variable 7 appears to be constant within groups --- failed re-building ‘Example_abc.Rmd’ --- re-building ‘Example_data.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-clang/treestats.Rcheck/vign_test/treestats/vignettes/Example_data_files/figure-html/plot_size-1.png 576x576 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 7446 bytes Input file size = 8304 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6569 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 6549 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 6549 Output IDAT size = 6549 bytes (897 bytes decrease) Output file size = 6627 bytes (1677 bytes = 20.20% decrease) Quitting from lines 61-64 [corr] (Example_data.Rmd) Error: processing vignette 'Example_data.Rmd' failed with diagnostics: NA/NaN/Inf in foreign function call (arg 10) --- failed re-building ‘Example_data.Rmd’ --- re-building ‘Getting_started.Rmd’ using rmarkdown --- finished re-building ‘Getting_started.Rmd’ --- re-building ‘Speed_improvement.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-clang/treestats.Rcheck/vign_test/treestats/vignettes/Speed_improvement_files/figure-html/unnamed-chunk-2-1.png 576x576 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 11064 bytes Input file size = 11934 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10269 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10269 Output IDAT size = 10269 bytes (795 bytes decrease) Output file size = 10347 bytes (1587 bytes = 13.30% decrease) --- finished re-building ‘Speed_improvement.Rmd’ SUMMARY: processing the following files failed: ‘Example_abc.Rmd’ ‘Example_data.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.70.5
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building ‘Example_abc.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-devel/treestats.Rcheck/vign_test/treestats/vignettes/Example_abc_files/figure-html/plot_simpl2-1.png 576x576 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 13124 bytes Input file size = 13994 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11400 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 11376 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 11376 Output IDAT size = 11376 bytes (1748 bytes decrease) Output file size = 11454 bytes (2540 bytes = 18.15% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/treestats.Rcheck/vign_test/treestats/vignettes/Example_abc_files/figure-html/plot_simple-1.png 576x576 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 21165 bytes Input file size = 22047 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19673 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 19457 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 19457 Output IDAT size = 19457 bytes (1708 bytes decrease) Output file size = 19535 bytes (2512 bytes = 11.39% decrease) Quitting from lines 86-102 [sim_ddd] (Example_abc.Rmd) Error: processing vignette 'Example_abc.Rmd' failed with diagnostics: variable 7 appears to be constant within groups --- failed re-building ‘Example_abc.Rmd’ --- re-building ‘Example_data.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-devel/treestats.Rcheck/vign_test/treestats/vignettes/Example_data_files/figure-html/plot_size-1.png 576x576 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 7446 bytes Input file size = 8304 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6569 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 6549 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 6549 Output IDAT size = 6549 bytes (897 bytes decrease) Output file size = 6627 bytes (1677 bytes = 20.20% decrease) Quitting from lines 61-64 [corr] (Example_data.Rmd) Error: processing vignette 'Example_data.Rmd' failed with diagnostics: NA/NaN/Inf in foreign function call (arg 10) --- failed re-building ‘Example_data.Rmd’ --- re-building ‘Getting_started.Rmd’ using rmarkdown --- finished re-building ‘Getting_started.Rmd’ --- re-building ‘Speed_improvement.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-devel/treestats.Rcheck/vign_test/treestats/vignettes/Speed_improvement_files/figure-html/unnamed-chunk-2-1.png 576x576 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 11064 bytes Input file size = 11934 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10269 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10269 Output IDAT size = 10269 bytes (795 bytes decrease) Output file size = 10347 bytes (1587 bytes = 13.30% decrease) --- finished re-building ‘Speed_improvement.Rmd’ SUMMARY: processing the following files failed: ‘Example_abc.Rmd’ ‘Example_data.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.70.5
Check: installed package size
Result: NOTE installed size is 8.6Mb sub-directories of 1Mb or more: doc 3.1Mb libs 5.0Mb Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64