Error in digit.fixed()
Closed this issue · 4 comments
kmiddleton commented
I'm following the 3d digitizing tutorial (https://cran.r-project.org/web/packages/geomorph/vignettes/geomorph.digitize3D.html). With the example code:
library(geomorph)
data("scallopPLY")
my.ply <- scallopPLY$ply
fixed.lms1 <- digit.fixed(spec = my.ply, fixed = 5)
Right-clicking on any vertex of the scallop gives an error to the console:
Error in (0 <= wz) && (wz <= 1) :
'length = 7575' in coercion to 'logical(1)'
I think this might be related to the recent change in R 4.3:
Calling && or || with LHS or (if evaluated) RHS of length greater than one is now always an error, with a report of the form 'length = 4' in coercion to 'logical(1)'
as the error message looks similar.
My sessionInfo:
R version 4.3.0 beta (2023-04-11 r84222)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.3.1
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/Chicago
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] geomorph_4.0.5.999 Matrix_1.5-4 rgl_1.1.3 RRPP_1.3.1
loaded via a namespace (and not attached):
[1] gtable_0.3.3 xfun_0.39 ggplot2_3.4.2 htmlwidgets_1.6.2 devtools_2.4.5
[6] remotes_2.4.2 processx_3.8.1 lattice_0.21-8 callr_3.7.3 vctrs_0.6.2
[11] tools_4.3.0 ps_1.7.5 generics_0.1.3 curl_5.0.0 parallel_4.3.0
[16] tibble_3.2.1 fansi_1.0.4 pkgconfig_2.0.3 desc_1.4.2 lifecycle_1.0.3
[21] compiler_4.3.0 stringr_1.5.0 munsell_0.5.0 httpuv_1.6.11 htmltools_0.5.5
[26] usethis_2.1.6 later_1.3.1 pillar_1.9.0 crayon_1.5.2 urlchecker_1.0.1
[31] ellipsis_0.3.2 cachem_1.0.8 sessioninfo_1.2.2 nlme_3.1-162 mime_0.12
[36] tidyselect_1.2.0 digest_0.6.31 stringi_1.7.12 dplyr_1.1.2 purrr_1.0.1
[41] rprojroot_2.0.3 fastmap_1.1.1 grid_4.3.0 colorspace_2.1-0 cli_3.6.1
[46] magrittr_2.0.3 base64enc_0.1-3 pkgbuild_1.4.0 utf8_1.2.3 ape_5.7-1
[51] withr_2.5.0 prettyunits_1.1.1 scales_1.2.1 promises_1.2.0.1 jpeg_0.1-10
[56] memoise_2.0.1 shiny_1.7.4 knitr_1.42 miniUI_0.1.1.1 profvis_0.3.8
[61] rlang_1.1.1 Rcpp_1.0.10 xtable_1.8-4 glue_1.6.2 pkgload_1.3.2
[66] rstudioapi_0.14 jsonlite_1.8.4 R6_2.5.1 fs_1.6.2
deanadams commented
Thanks. I can replicate the error. I will investigate solutions soon.
Dean
Dr. Dean C. Adams (he/him)
Distinguished Professor of Evolutionary Biology
Department of Ecology, Evolution, and Organismal Biology
Iowa State University
https://faculty.sites.iastate.edu/dcadams/
phone: 515-294-3834
From: Kevin Middleton ***@***.***>
Sent: Friday, May 26, 2023 6:30 PM
To: geomorphR/geomorph ***@***.***>
Cc: Subscribed ***@***.***>
Subject: [geomorphR/geomorph] Error in digit.fixed() (Issue #43)
I'm following the 3d digitizing tutorial (https://cran.r-project.org/web/packages/geomorph/vignettes/geomorph.digitize3D.html). With the example code:
library(geomorph)
data("scallopPLY")
my.ply <- scallopPLY$ply
fixed.lms1 <- digit.fixed(spec = my.ply, fixed = 5)
Right-clicking on any vertex of the scallop gives an error to the console:
Error in (0 <= wz) && (wz <= 1) :
'length = 7575' in coercion to 'logical(1)'
I think this might be related to the recent change in R 4.3<https://cran.r-project.org/bin/windows/base/NEWS.R-4.3.0.html>:
Calling && or || with LHS or (if evaluated) RHS of length greater than one is now always an error, with a report of the form 'length = 4' in coercion to 'logical(1)'
as the error message looks similar.
My sessionInfo:
R version 4.3.0 beta (2023-04-11 r84222)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.3.1
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/Chicago
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] geomorph_4.0.5.999 Matrix_1.5-4 rgl_1.1.3 RRPP_1.3.1
loaded via a namespace (and not attached):
[1] gtable_0.3.3 xfun_0.39 ggplot2_3.4.2 htmlwidgets_1.6.2 devtools_2.4.5
[6] remotes_2.4.2 processx_3.8.1 lattice_0.21-8 callr_3.7.3 vctrs_0.6.2
[11] tools_4.3.0 ps_1.7.5 generics_0.1.3 curl_5.0.0 parallel_4.3.0
[16] tibble_3.2.1 fansi_1.0.4 pkgconfig_2.0.3 desc_1.4.2 lifecycle_1.0.3
[21] compiler_4.3.0 stringr_1.5.0 munsell_0.5.0 httpuv_1.6.11 htmltools_0.5.5
[26] usethis_2.1.6 later_1.3.1 pillar_1.9.0 crayon_1.5.2 urlchecker_1.0.1
[31] ellipsis_0.3.2 cachem_1.0.8 sessioninfo_1.2.2 nlme_3.1-162 mime_0.12
[36] tidyselect_1.2.0 digest_0.6.31 stringi_1.7.12 dplyr_1.1.2 purrr_1.0.1
[41] rprojroot_2.0.3 fastmap_1.1.1 grid_4.3.0 colorspace_2.1-0 cli_3.6.1
[46] magrittr_2.0.3 base64enc_0.1-3 pkgbuild_1.4.0 utf8_1.2.3 ape_5.7-1
[51] withr_2.5.0 prettyunits_1.1.1 scales_1.2.1 promises_1.2.0.1 jpeg_0.1-10
[56] memoise_2.0.1 shiny_1.7.4 knitr_1.42 miniUI_0.1.1.1 profvis_0.3.8
[61] rlang_1.1.1 Rcpp_1.0.10 xtable_1.8-4 glue_1.6.2 pkgload_1.3.2
[66] rstudioapi_0.14 jsonlite_1.8.4 R6_2.5.1 fs_1.6.2
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deanadams commented
Kevin,
I traced this back to an RGL function. I cannot fix this: the RGL folks must do so. As some of them are part of the CRAN team, I assume they are aware of the issue, but you may wish to notify them also.
Dean
Dr. Dean C. Adams (he/him)
Distinguished Professor of Evolutionary Biology
Department of Ecology, Evolution, and Organismal Biology
Iowa State University
https://faculty.sites.iastate.edu/dcadams/
phone: 515-294-3834
From: Kevin Middleton ***@***.***>
Sent: Friday, May 26, 2023 6:30 PM
To: geomorphR/geomorph ***@***.***>
Cc: Subscribed ***@***.***>
Subject: [geomorphR/geomorph] Error in digit.fixed() (Issue #43)
I'm following the 3d digitizing tutorial (https://cran.r-project.org/web/packages/geomorph/vignettes/geomorph.digitize3D.html). With the example code:
library(geomorph)
data("scallopPLY")
my.ply <- scallopPLY$ply
fixed.lms1 <- digit.fixed(spec = my.ply, fixed = 5)
Right-clicking on any vertex of the scallop gives an error to the console:
Error in (0 <= wz) && (wz <= 1) :
'length = 7575' in coercion to 'logical(1)'
I think this might be related to the recent change in R 4.3<https://cran.r-project.org/bin/windows/base/NEWS.R-4.3.0.html>:
Calling && or || with LHS or (if evaluated) RHS of length greater than one is now always an error, with a report of the form 'length = 4' in coercion to 'logical(1)'
as the error message looks similar.
My sessionInfo:
R version 4.3.0 beta (2023-04-11 r84222)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.3.1
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/Chicago
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] geomorph_4.0.5.999 Matrix_1.5-4 rgl_1.1.3 RRPP_1.3.1
loaded via a namespace (and not attached):
[1] gtable_0.3.3 xfun_0.39 ggplot2_3.4.2 htmlwidgets_1.6.2 devtools_2.4.5
[6] remotes_2.4.2 processx_3.8.1 lattice_0.21-8 callr_3.7.3 vctrs_0.6.2
[11] tools_4.3.0 ps_1.7.5 generics_0.1.3 curl_5.0.0 parallel_4.3.0
[16] tibble_3.2.1 fansi_1.0.4 pkgconfig_2.0.3 desc_1.4.2 lifecycle_1.0.3
[21] compiler_4.3.0 stringr_1.5.0 munsell_0.5.0 httpuv_1.6.11 htmltools_0.5.5
[26] usethis_2.1.6 later_1.3.1 pillar_1.9.0 crayon_1.5.2 urlchecker_1.0.1
[31] ellipsis_0.3.2 cachem_1.0.8 sessioninfo_1.2.2 nlme_3.1-162 mime_0.12
[36] tidyselect_1.2.0 digest_0.6.31 stringi_1.7.12 dplyr_1.1.2 purrr_1.0.1
[41] rprojroot_2.0.3 fastmap_1.1.1 grid_4.3.0 colorspace_2.1-0 cli_3.6.1
[46] magrittr_2.0.3 base64enc_0.1-3 pkgbuild_1.4.0 utf8_1.2.3 ape_5.7-1
[51] withr_2.5.0 prettyunits_1.1.1 scales_1.2.1 promises_1.2.0.1 jpeg_0.1-10
[56] memoise_2.0.1 shiny_1.7.4 knitr_1.42 miniUI_0.1.1.1 profvis_0.3.8
[61] rlang_1.1.1 Rcpp_1.0.10 xtable_1.8-4 glue_1.6.2 pkgload_1.3.2
[66] rstudioapi_0.14 jsonlite_1.8.4 R6_2.5.1 fs_1.6.2
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bernb commented
Dear Dean,
could you specify the issue within the RGL package? I would like to open a bug report, but for that more information on the issue is needed.
With best regards
Bern
deanadams commented
I do not see the problem any longer. I attempted to digitize a ply file without error. Perhaps RGL updated.