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 |
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
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
Current CRAN status: OK: 15
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
Current CRAN status: OK: 15
Current CRAN status: OK: 15
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
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