feat: Compatibility with upcoming igraph 2.1.2 #282
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krlmlr
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krlmlr
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Hi @krlmlr and thank you very much for your PR! I tested locally that devtools::check("C:/Users/user/Documents/git-stuff/sfnetworks/")
#> ══ Documenting ═════════════════════════════════════════════════════════════════
#> ℹ Updating sfnetworks documentation
#> ℹ Loading sfnetworks
#>
#> ══ Building ════════════════════════════════════════════════════════════════════
#> Setting env vars:
#> • CFLAGS : -Wall -pedantic
#> • CXXFLAGS : -Wall -pedantic
#> • CXX11FLAGS: -Wall -pedantic
#> • CXX14FLAGS: -Wall -pedantic
#> • CXX17FLAGS: -Wall -pedantic
#> • CXX20FLAGS: -Wall -pedantic
#> ── R CMD build ─────────────────────────────────────────────────────────────────
#> checking for file 'C:\Users\user\Documents\git-stuff\sfnetworks/DESCRIPTION' ... ✔ checking for file 'C:\Users\user\Documents\git-stuff\sfnetworks/DESCRIPTION' (441ms)
#> ─ preparing 'sfnetworks': (829ms)
#> checking DESCRIPTION meta-information ... checking DESCRIPTION meta-information ... ✔ checking DESCRIPTION meta-information
#> ─ installing the package to build vignettes (405ms)
#> creating vignettes ... creating vignettes ... E creating vignettes (1m 34.3s)
#> --- re-building 'sfn01_structure.Rmd' using rmarkdown
#> --- finished re-building 'sfn01_structure.Rmd'
#>
#> --- re-building 'sfn02_preprocess_clean.Rmd' using rmarkdown
#>
#> Quitting from lines 293-299 [unnamed-chunk-10] (sfn02_preprocess_clean.Rmd)
#> Error: processing vignette 'sfn02_preprocess_clean.Rmd' failed with diagnostics:
#> inherits(x, "sfc_MULTILINESTRING") is not TRUE
#> --- failed re-building 'sfn02_preprocess_clean.Rmd'
#>
#> --- re-building 'sfn03_join_filter.Rmd' using rmarkdown
#> --- finished re-building 'sfn03_join_filter.Rmd'
#>
#> --- re-building 'sfn04_routing.Rmd' using rmarkdown
#> --- finished re-building 'sfn04_routing.Rmd'
#>
#> --- re-building 'sfn05_morphers.Rmd' using rmarkdown
#>
#> Quitting from lines 312-317 [unnamed-chunk-14] (sfn05_morphers.Rmd)
#> Error: processing vignette 'sfn05_morphers.Rmd' failed with diagnostics:
#> Invalid vertex name(s)
#> --- failed re-building 'sfn05_morphers.Rmd'
#>
#> SUMMARY: processing the following files failed:
#> 'sfn02_preprocess_clean.Rmd' 'sfn05_morphers.Rmd'
#>
#> Error: Vignette re-building failed.
#> Execution halted
#>
#> Error in c("(function (command = NULL, args = character(), error_on_status = TRUE, ", : ! System command 'Rcmd.exe' failedCreated on 2024-12-04 with reprex v2.0.2 Session infosessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
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#> collate English_United Kingdom.utf8
#> ctype English_United Kingdom.utf8
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#> date 2024-12-04
#> pandoc 3.2 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> ! package * version date (UTC) lib source
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#> cachem 1.1.0 2024-05-16 [1] CRAN (R 4.3.3)
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#> class 7.3-22 2023-05-03 [2] CRAN (R 4.3.1)
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#> cli 3.6.3.9001 2024-11-18 [1] Github (r-lib/cli@007c388)
#> colorspace 2.1-1 2024-07-26 [1] CRAN (R 4.3.1)
#> crayon 1.5.3 2024-06-20 [1] CRAN (R 4.3.3)
#> DBI 1.2.3 2024-06-02 [1] CRAN (R 4.3.1)
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#> goftest 1.2-3 2021-10-07 [1] CRAN (R 4.3.1)
#> gtable 0.3.6 2024-10-25 [1] CRAN (R 4.3.1)
#> htmltools 0.5.8.1 2024-04-04 [1] CRAN (R 4.3.3)
#> htmlwidgets 1.6.4 2023-12-06 [1] CRAN (R 4.3.3)
#> httpuv 1.6.15 2024-03-26 [1] CRAN (R 4.3.3)
#> igraph 2.1.2 2024-12-04 [1] Github (igraph/rigraph@7414602)
#> KernSmooth 2.23-21 2023-05-03 [2] CRAN (R 4.3.1)
#> knitr 1.49 2024-11-08 [1] CRAN (R 4.3.1)
#> later 1.3.2 2023-12-06 [1] CRAN (R 4.3.3)
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#> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.3.1)
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#> memoise 2.0.1 2021-11-26 [1] CRAN (R 4.3.1)
#> mgcv 1.9-1 2023-12-21 [1] CRAN (R 4.3.1)
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#> pillar 1.9.0 2023-03-22 [1] CRAN (R 4.3.1)
#> pkgbuild 1.4.4 2024-03-17 [1] CRAN (R 4.3.3)
#> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.3.1)
#> pkgload 1.3.4 2024-01-16 [1] CRAN (R 4.3.3)
#> polyclip 1.10-7 2024-07-23 [1] CRAN (R 4.3.1)
#> processx 3.8.4 2024-03-16 [1] CRAN (R 4.3.3)
#> profvis 0.3.8 2023-05-02 [1] CRAN (R 4.3.1)
#> promises 1.3.0 2024-04-05 [1] CRAN (R 4.3.3)
#> proxy 0.4-27 2022-06-09 [1] CRAN (R 4.3.1)
#> ps 1.7.6 2024-01-18 [1] CRAN (R 4.3.3)
#> purrr 1.0.2 2023-08-10 [1] CRAN (R 4.3.1)
#> R.cache 0.16.0 2022-07-21 [1] CRAN (R 4.3.1)
#> R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.3.1)
#> R.oo 1.25.0 2022-06-12 [1] CRAN (R 4.3.1)
#> R.utils 2.12.2 2022-11-11 [1] CRAN (R 4.3.1)
#> R6 2.5.1 2021-08-19 [1] CRAN (R 4.3.1)
#> Rcpp 1.0.13 2024-07-17 [1] CRAN (R 4.3.1)
#> remotes 2.5.0 2024-03-17 [1] CRAN (R 4.3.1)
#> reprex 2.0.2 2022-08-17 [1] CRAN (R 4.3.1)
#> rlang 1.1.4 2024-06-04 [1] CRAN (R 4.3.1)
#> rmarkdown 2.28 2024-08-17 [1] CRAN (R 4.3.1)
#> roxygen2 7.3.1 2024-12-04 [1] Github (r-lib/roxygen2@d97643a)
#> rpart 4.1.19 2022-10-21 [2] CRAN (R 4.3.1)
#> rprojroot 2.0.4 2023-11-05 [1] CRAN (R 4.3.1)
#> rstudioapi 0.16.0 2024-03-24 [1] CRAN (R 4.3.1)
#> scales 1.3.0 2023-11-28 [1] CRAN (R 4.3.1)
#> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.3.1)
#> sf 1.0-19 2024-11-05 [1] CRAN (R 4.3.1)
#> sfheaders 0.4.4 2024-01-17 [1] CRAN (R 4.3.3)
#> VP sfnetworks * 0.6.4 2024-11-23 [?] load_all() (on disk 1.0.0)
#> shiny 1.8.1.1 2024-04-02 [1] CRAN (R 4.3.1)
#> spatstat.data 3.1-2 2024-06-21 [1] CRAN (R 4.3.1)
#> spatstat.explore 3.3-2 2024-08-21 [1] CRAN (R 4.3.1)
#> spatstat.geom 3.3-3 2024-09-18 [1] CRAN (R 4.3.1)
#> spatstat.linnet 3.2-2 2024-09-20 [1] CRAN (R 4.3.1)
#> spatstat.model 3.3-2 2024-09-19 [1] CRAN (R 4.3.1)
#> spatstat.random 3.3-2 2024-09-18 [1] CRAN (R 4.3.1)
#> spatstat.sparse 3.1-0 2024-06-21 [1] CRAN (R 4.3.1)
#> spatstat.univar 3.0-1 2024-09-05 [1] CRAN (R 4.3.1)
#> spatstat.utils 3.1-0 2024-08-17 [1] CRAN (R 4.3.1)
#> stringi 1.8.3 2023-12-11 [1] CRAN (R 4.3.2)
#> stringr 1.5.1 2023-11-14 [1] CRAN (R 4.3.1)
#> styler 1.10.2 2023-08-29 [1] CRAN (R 4.3.1)
#> tensor 1.5 2012-05-05 [1] CRAN (R 4.3.1)
#> tibble 3.2.1 2023-03-20 [1] CRAN (R 4.3.1)
#> tidygraph 1.3.1 2024-01-30 [1] CRAN (R 4.3.1)
#> tidyr 1.3.0 2023-01-24 [1] CRAN (R 4.3.1)
#> tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.3.1)
#> units 0.8-5.4 2024-06-03 [1] local
#> urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.3.1)
#> usethis 2.2.3 2024-02-19 [1] CRAN (R 4.3.1)
#> utf8 1.2.4 2023-10-22 [1] CRAN (R 4.3.1)
#> vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.3.2)
#> withr 3.0.2 2024-10-28 [1] CRAN (R 4.3.1)
#> xfun 0.49 2024-10-31 [1] CRAN (R 4.3.1)
#> xml2 1.3.6 2023-12-04 [1] CRAN (R 4.3.2)
#> xtable 1.8-4 2019-04-21 [1] CRAN (R 4.3.1)
#> yaml 2.3.9 2024-07-05 [1] CRAN (R 4.3.3)
#>
#> [1] C:/Users/user/AppData/Local/R/win-library/4.3
#> [2] C:/Program Files/R/R-4.3.1/library
#>
#> V ── Loaded and on-disk version mismatch.
#> P ── Loaded and on-disk path mismatch.
#>
#> ──────────────────────────────────────────────────────────────────────────────Everything works fine (apart from easy-to-fix deprecation warnings) with the patch you provided (which can be applied without any problem): devtools::check("C:/Users/user/Documents/git-stuff/sfnetworks/")
#> ══ Documenting ═════════════════════════════════════════════════════════════════
#> ℹ Updating sfnetworks documentation
#> ℹ Loading sfnetworks
#>
#> ══ Building ════════════════════════════════════════════════════════════════════
#> Setting env vars:
#> • CFLAGS : -Wall -pedantic
#> • CXXFLAGS : -Wall -pedantic
#> • CXX11FLAGS: -Wall -pedantic
#> • CXX14FLAGS: -Wall -pedantic
#> • CXX17FLAGS: -Wall -pedantic
#> • CXX20FLAGS: -Wall -pedantic
#> ── R CMD build ─────────────────────────────────────────────────────────────────
#> checking for file 'C:\Users\user\Documents\git-stuff\sfnetworks/DESCRIPTION' ... ✔ checking for file 'C:\Users\user\Documents\git-stuff\sfnetworks/DESCRIPTION'
#> ─ preparing 'sfnetworks': (693ms)
#> checking DESCRIPTION meta-information ... checking DESCRIPTION meta-information ... ✔ checking DESCRIPTION meta-information
#> ─ installing the package to build vignettes
#> creating vignettes ... creating vignettes ... ✔ creating vignettes (51.2s)
#> ─ checking for LF line-endings in source and make files and shell scripts (446ms)
#> ─ checking for empty or unneeded directories
#> ─ building 'sfnetworks_0.6.4.tar.gz'
#>
#> ══ Checking ════════════════════════════════════════════════════════════════════
#> Setting env vars:
#> • _R_CHECK_CRAN_INCOMING_REMOTE_ : FALSE
#> • _R_CHECK_CRAN_INCOMING_ : FALSE
#> • _R_CHECK_FORCE_SUGGESTS_ : FALSE
#> • _R_CHECK_PACKAGES_USED_IGNORE_UNUSED_IMPORTS_: FALSE
#> • NOT_CRAN : true
#> ── R CMD check ─────────────────────────────────────────────────────────────────
#> ─ using log directory 'C:/Users/user/AppData/Local/Temp/RtmpeMp5WO/filefec42494ad7/sfnetworks.Rcheck'
#> ─ using R version 4.3.1 (2023-06-16 ucrt)
#> ─ using platform: x86_64-w64-mingw32 (64-bit)
#> ─ R was compiled by
#> gcc.exe (GCC) 12.2.0
#> GNU Fortran (GCC) 12.2.0
#> ─ running under: Windows 11 x64 (build 22631)
#> ─ using session charset: UTF-8
#> ─ using options '--no-manual --as-cran' (348ms)
#> ✔ checking for file 'sfnetworks/DESCRIPTION'
#> ─ this is package 'sfnetworks' version '0.6.4'
#> ─ package encoding: UTF-8
#> ✔ checking package namespace information
#> ✔ checking package dependencies (992ms)
#> ✔ checking if this is a source package
#> ✔ checking if there is a namespace
#> ✔ checking for executable files (1.8s)
#> ✔ checking for hidden files and directories
#> ✔ checking for portable file names
#> ✔ checking whether package 'sfnetworks' can be installed (9s)
#> ✔ checking installed package size
#> ✔ checking package directory
#> N checking for future file timestamps
#> unable to verify current time
#> ✔ checking 'build' directory
#> ✔ checking DESCRIPTION meta-information (339ms)
#> N checking top-level files
#> Non-standard file/directory found at top level:
#> '31b00e9346449aee75ac217170b06654f2e280c5.patch'
#> ✔ checking for left-over files
#> ✔ checking index information (340ms)
#> ✔ checking package subdirectories (403ms)
#> ✔ checking R files for non-ASCII characters
#> ✔ checking R files for syntax errors
#> ✔ checking whether the package can be loaded (2.4s)
#> ✔ checking whether the package can be loaded with stated dependencies (2.4s)
#> ✔ checking whether the package can be unloaded cleanly (2.5s)
#> ✔ checking whether the namespace can be loaded with stated dependencies (2.8s)
#> ✔ checking whether the namespace can be unloaded cleanly (2.7s)
#> ✔ checking loading without being on the library search path (1.4s)
#> ✔ checking startup messages can be suppressed (4.9s)
#> ✔ checking dependencies in R code (3.2s)
#> ✔ checking S3 generic/method consistency (2.8s)
#> ✔ checking replacement functions (2.4s)
#> ✔ checking foreign function calls (2.2s)
#> ─ checking R code for possible problems ... [16s] OK (16s)
#> ✔ checking Rd files (545ms)
#> ✔ checking Rd metadata
#> ✔ checking Rd line widths
#> ✔ checking Rd cross-references
#> ✔ checking for missing documentation entries (2.2s)
#> ✔ checking for code/documentation mismatches (6.3s)
#> ✔ checking Rd \usage sections (2.5s)
#> ✔ checking Rd contents
#> ✔ checking for unstated dependencies in examples (434ms)
#> ✔ checking contents of 'data' directory
#> ✔ checking data for non-ASCII characters
#> ✔ checking LazyData
#> ✔ checking data for ASCII and uncompressed saves
#> ✔ checking installed files from 'inst/doc'
#> ✔ checking files in 'vignettes'
#> ─ checking examples ... [11s] OK (11.7s)
#> ✔ checking for unstated dependencies in 'tests'
#> ─ checking tests
#> Running 'testthat.R' [15s] [15s] OK
#> * checking for unstated dependencies in vignettes ... OK
#> * checking package vignettes in 'inst/doc' ... OK
#> * checking re-building of vignette outputs ... [54s] OK
#> * checking for non-standard things in the check directory ... OK
#> * checking for detritus in the temp directory ... OK
#> * DONE
#>
#> Status: 2 NOTEs
#> See
#> 'C:/Users/user/AppData/Local/Temp/RtmpeMp5WO/filefec42494ad7/sfnetworks.Rcheck/00check.log'
#> for details.
#>
#>
#>
#> ── R CMD check results ─────────────────────────────────── sfnetworks 0.6.4 ────
#> Duration: 2m 35.5s
#>
#> ❯ checking for future file timestamps ... NOTE
#> unable to verify current time
#>
#> ❯ checking top-level files ... NOTE
#> Non-standard file/directory found at top level:
#> '31b00e9346449aee75ac217170b06654f2e280c5.patch'
#>
#> 0 errors ✔ | 0 warnings ✔ | 2 notes ✖Created on 2024-12-04 with reprex v2.0.2 Session infosessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.3.1 (2023-06-16 ucrt)
#> os Windows 11 x64 (build 22631)
#> system x86_64, mingw32
#> ui RTerm
#> language (EN)
#> collate English_United Kingdom.utf8
#> ctype English_United Kingdom.utf8
#> tz Europe/Rome
#> date 2024-12-04
#> pandoc 3.2 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)
#>
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#> ! package * version date (UTC) lib source
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#> cachem 1.1.0 2024-05-16 [1] CRAN (R 4.3.3)
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#> ggplot2 3.5.1 2024-04-23 [1] CRAN (R 4.3.1)
#> glue 1.8.0 2024-09-30 [1] CRAN (R 4.3.1)
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#> httpuv 1.6.15 2024-03-26 [1] CRAN (R 4.3.3)
#> igraph 2.1.2 2024-12-04 [1] Github (igraph/rigraph@7414602)
#> KernSmooth 2.23-21 2023-05-03 [2] CRAN (R 4.3.1)
#> knitr 1.49 2024-11-08 [1] CRAN (R 4.3.1)
#> later 1.3.2 2023-12-06 [1] CRAN (R 4.3.3)
#> lattice 0.21-8 2023-04-05 [2] CRAN (R 4.3.1)
#> lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.3.2)
#> lwgeom 0.2-14 2024-02-21 [1] CRAN (R 4.3.1)
#> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.3.1)
#> Matrix 1.6-1.1 2023-09-18 [1] CRAN (R 4.3.1)
#> memoise 2.0.1 2021-11-26 [1] CRAN (R 4.3.1)
#> mgcv 1.9-1 2023-12-21 [1] CRAN (R 4.3.1)
#> mime 0.12 2021-09-28 [1] CRAN (R 4.3.1)
#> miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.3.1)
#> munsell 0.5.1 2024-04-01 [1] CRAN (R 4.3.3)
#> nlme 3.1-162 2023-01-31 [2] CRAN (R 4.3.1)
#> pillar 1.9.0 2023-03-22 [1] CRAN (R 4.3.1)
#> pkgbuild 1.4.4 2024-03-17 [1] CRAN (R 4.3.3)
#> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.3.1)
#> pkgload 1.3.4 2024-01-16 [1] CRAN (R 4.3.3)
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#> vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.3.2)
#> withr 3.0.2 2024-10-28 [1] CRAN (R 4.3.1)
#> xfun 0.49 2024-10-31 [1] CRAN (R 4.3.1)
#> xml2 1.3.6 2023-12-04 [1] CRAN (R 4.3.2)
#> xopen 1.0.1 2024-04-25 [1] CRAN (R 4.3.3)
#> xtable 1.8-4 2019-04-21 [1] CRAN (R 4.3.1)
#> yaml 2.3.9 2024-07-05 [1] CRAN (R 4.3.3)
#>
#> [1] C:/Users/user/AppData/Local/R/win-library/4.3
#> [2] C:/Program Files/R/R-4.3.1/library
#>
#> V ── Loaded and on-disk version mismatch.
#> P ── Loaded and on-disk path mismatch.
#>
#> ──────────────────────────────────────────────────────────────────────────────btw: we probably also need to update @krlmlr just one question: do we need to set v2.1.2 as the minimum igraph version or the patch works with any igraph version? |
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Thanks a lot! Yes, this will work also with igraph < 2.1.2. It would be great if you could review the deprecation warning too. |
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Thanks @krlmlr! I always thought the zero-based indexing of this function was intended, and not considered a bug. If I understand correctly, the same should be done for |
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Yes, |
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@luukvdmeer: This is a hotfix on top of the currently released v0.6.4 to enable compatibility with the upcoming igraph release.
I can't easily test locally due to a broken GDAL (?) setup. The main compatibility code is borrowed from https://github.com/ropensci/targets/blob/f872e3afd96a832e62ad852e4068e77f75954d30/R/utils_igraph.R#L33, thanks @wlandau!
If you want to release this compatibility fix, perhaps as 0.6.5, continuity will be provided for CRAN users. I will ask CRAN to release igraph 2.1.2 tomorrow. Apologies for the short notice, this was a last-minute bugfix for igraph that had unanticipated consequences.
This PR doesn't cleanly apply to the main branch, but it looks like it can be ported.