CRAN Package Check Results for Maintainer Robrecht Cannoodt <rcannood at gmail.com>

CRAN Package Check Results for Maintainer ‘Robrecht Cannoodt <rcannood at gmail.com>’

Last updated on 2026-02-04 04:50:49 CET.

Package	ERROR	NOTE	OK
anndata			13
babelwhale		2	11
diffusionMap		2	11
dyndimred		5	8
dyngen	3	10
dynparam		5	8
dynutils			13
dynwrap		4	9
funkyheatmap			13
GillespieSSA			13
GillespieSSA2		4	9
incgraph			13
lmds		7	6
princurve		2	11
qsub		2	11
SCORPIUS			13

Package anndata

Current CRAN status: OK: 13

Package babelwhale

Current CRAN status: NOTE: 2, OK: 11

Version: 1.2.0
Check: DESCRIPTION meta-information
Result: NOTE Author field differs from that derived from Authors@R Author: ‘Robrecht Cannoodt [aut, cre] (<https://orcid.org/0000-0003-3641-729X>, rcannood), Wouter Saelens [aut] (<https://orcid.org/0000-0002-7114-6248>, zouter), Joel Nitta [aut] (<https://orcid.org/0000-0003-4719-7472>, joelnitta)’ Authors@R: ‘Robrecht Cannoodt [aut, cre] (ORCID: <https://orcid.org/0000-0003-3641-729X>, github: rcannood), Wouter Saelens [aut] (ORCID: <https://orcid.org/0000-0002-7114-6248>, github: zouter), Joel Nitta [aut] (ORCID: <https://orcid.org/0000-0003-4719-7472>, github: joelnitta)’ Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Package diffusionMap

Current CRAN status: NOTE: 2, OK: 11

Version: 1.2.0
Check: DESCRIPTION meta-information
Result: NOTE Author field differs from that derived from Authors@R Author: ‘Joseph Richards [aut] (joeyrichar), Robrecht Cannoodt [aut, cre] (<https://orcid.org/0000-0003-3641-729X>, rcannood)’ Authors@R: ‘Joseph Richards [aut] (github: joeyrichar), Robrecht Cannoodt [aut, cre] (ORCID: <https://orcid.org/0000-0003-3641-729X>, github: rcannood)’ Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Package dyndimred

Current CRAN status: NOTE: 5, OK: 8

Version: 1.0.4
Check: DESCRIPTION meta-information
Result: NOTE Author field differs from that derived from Authors@R Author: ‘Robrecht Cannoodt [aut, cre] (<https://orcid.org/0000-0003-3641-729X>, rcannood), Wouter Saelens [aut] (<https://orcid.org/0000-0002-7114-6248>, zouter)’ Authors@R: ‘Robrecht Cannoodt [aut, cre] (ORCID: <https://orcid.org/0000-0003-3641-729X>, github: rcannood), Wouter Saelens [aut] (ORCID: <https://orcid.org/0000-0002-7114-6248>, github: zouter)’ Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 1.0.4
Check: package dependencies
Result: NOTE Package suggested but not available for checking: ‘lle’ Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

Version: 1.0.4
Check: LazyData
Result: NOTE 'LazyData' is specified without a 'data' directory Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

Package dyngen

Current CRAN status: ERROR: 3, NOTE: 10

Additional issues

donttest

Version: 1.0.5
Check: CRAN incoming feasibility
Result: NOTE Maintainer: ‘Robrecht Cannoodt <rcannood@gmail.com>’ Package CITATION file contains call(s) to old-style citEntry(). Please use bibentry() instead. Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 1.0.5
Check: Rd files
Result: NOTE checkRd: (-1) generate_kinetics.Rd:57: Lost braces; missing escapes or markup? 57 | By default, sampled from {-1, 1} with probabilities {.25, .75}. | ^ checkRd: (-1) generate_kinetics.Rd:57: Lost braces; missing escapes or markup? 57 | By default, sampled from {-1, 1} with probabilities {.25, .75}. | ^ 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-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: 1.0.5
Check: examples
Result: ERROR Running examples in ‘dyngen-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: get_timings > ### Title: Return the timings of each of the dyngen steps > ### Aliases: get_timings > > ### ** Examples > > data("example_model") > timings <- get_timings(example_model) Error in `summarise()`: ℹ In argument: `task = .data$task[-length(.data$task)]`. ℹ In group 2: `group = "2_tf_network"`. Caused by error: ! `task` must be size 1, not 2. ℹ To return more or less than 1 row per group, use `reframe()`. Backtrace: ▆ 1. ├─dyngen::get_timings(example_model) 2. │ └─model$timings %>% group_by(.data$group) %>% ... 3. ├─dplyr::summarise(...) 4. ├─dplyr:::summarise.grouped_df(...) 5. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise") 6. │ └─base::withCallingHandlers(...) 7. ├─dplyr:::dplyr_internal_error(...) 8. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data) 9. │ └─rlang:::signal_abort(cnd, .file) 10. │ └─base::signalCondition(cnd) 11. └─dplyr (local) `<fn>`(`<dpl:::__>`) 12. └─dplyr (local) handler(cnd) 13. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.0.5
Check: examples
Result: ERROR Running examples in ‘dyngen-Ex.R’ failed The error most likely occurred in: > ### Name: get_timings > ### Title: Return the timings of each of the dyngen steps > ### Aliases: get_timings > > ### ** Examples > > data("example_model") > timings <- get_timings(example_model) Error in `summarise()`: ℹ In argument: `task = .data$task[-length(.data$task)]`. ℹ In group 2: `group = "2_tf_network"`. Caused by error: ! `task` must be size 1, not 2. ℹ To return more or less than 1 row per group, use `reframe()`. Backtrace: ▆ 1. ├─dyngen::get_timings(example_model) 2. │ └─model$timings %>% group_by(.data$group) %>% ... 3. ├─dplyr::summarise(...) 4. ├─dplyr:::summarise.grouped_df(...) 5. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise") 6. │ └─base::withCallingHandlers(...) 7. ├─dplyr:::dplyr_internal_error(...) 8. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data) 9. │ └─rlang:::signal_abort(cnd, .file) 10. │ └─base::signalCondition(cnd) 11. └─dplyr (local) `<fn>`(`<dpl:::__>`) 12. └─dplyr (local) handler(cnd) 13. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) Execution halted Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Package dynparam

Current CRAN status: NOTE: 5, OK: 8

Version: 1.0.2
Check: CRAN incoming feasibility
Result: NOTE Maintainer: ‘Robrecht Cannoodt <rcannood@gmail.com>’ Package CITATION file contains call(s) to old-style citEntry(). Please use bibentry() instead. Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 1.0.2
Check: DESCRIPTION meta-information
Result: NOTE Author field differs from that derived from Authors@R Author: ‘Robrecht Cannoodt [aut, cre] (<https://orcid.org/0000-0003-3641-729X>, rcannood), Wouter Saelens [aut] (<https://orcid.org/0000-0002-7114-6248>, zouter)’ Authors@R: ‘Robrecht Cannoodt [aut, cre] (ORCID: <https://orcid.org/0000-0003-3641-729X>, github: rcannood), Wouter Saelens [aut] (ORCID: <https://orcid.org/0000-0002-7114-6248>, github: zouter)’ Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 1.0.2
Check: LazyData
Result: NOTE 'LazyData' is specified without a 'data' directory Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

Package dynutils

Current CRAN status: OK: 13

Package dynwrap

Current CRAN status: NOTE: 4, OK: 9

Version: 1.2.5
Check: relative paths in package URLs
Result: NOTE Found the following (possibly) invalid URLs: URL: ../create_ti_method_script From: inst/doc/create_ti_method_container.html URL: ../create_ti_method_container From: inst/doc/create_ti_method_definition.html URL: ../create_ti_method_wrappers From: inst/doc/create_ti_method_definition.html URL: ../create_ti_method_wrappers From: inst/doc/create_ti_method_r.html Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 1.2.5
Check: R code for possible problems
Result: NOTE get_ti_methods: no visible binding for global variable ‘id’ simplify_replace_edges: no visible binding for global variable ‘id’ simplify_trajectory: no visible binding for global variable ‘id’ Undefined global functions or variables: id Flavors: r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Package funkyheatmap

Current CRAN status: OK: 13

Package GillespieSSA

Current CRAN status: OK: 13

Package GillespieSSA2

Current CRAN status: NOTE: 4, OK: 9

Version: 0.3.0
Check: CRAN incoming feasibility
Result: NOTE Maintainer: ‘Robrecht Cannoodt <rcannood@gmail.com>’ Package CITATION file contains call(s) to old-style citEntry(). Please use bibentry() instead. Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 0.3.0
Check: installed package size
Result: NOTE installed size is 5.7Mb sub-directories of 1Mb or more: doc 1.7Mb libs 3.4Mb Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Package incgraph

Current CRAN status: OK: 13

Package lmds

Current CRAN status: NOTE: 7, OK: 6

Version: 0.1.0
Check: DESCRIPTION meta-information
Result: NOTE Author field differs from that derived from Authors@R Author: ‘Robrecht Cannoodt [aut, cre] (<https://orcid.org/0000-0003-3641-729X>, rcannood), Wouter Saelens [aut] (<https://orcid.org/0000-0002-7114-6248>, zouter)’ Authors@R: ‘Robrecht Cannoodt [aut, cre] (ORCID: <https://orcid.org/0000-0003-3641-729X>, github: rcannood), Wouter Saelens [aut] (ORCID: <https://orcid.org/0000-0002-7114-6248>, github: zouter)’ Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 0.1.0
Check: dependencies in R code
Result: NOTE Namespace in Imports field not imported from: ‘Matrix’ All declared Imports should be used. Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 0.1.0
Check: LazyData
Result: NOTE 'LazyData' is specified without a 'data' directory Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

Package princurve

Current CRAN status: NOTE: 2, OK: 11

Version: 2.1.6
Check: CRAN incoming feasibility
Result: NOTE Maintainer: ‘Robrecht Cannoodt <rcannood@gmail.com>’ Package CITATION file contains call(s) to old-style citEntry(). Please use bibentry() instead. Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 2.1.6
Check: DESCRIPTION meta-information
Result: NOTE Author field differs from that derived from Authors@R Author: ‘Trevor Hastie [aut], Andreas Weingessel [aut], Kurt Hornik [aut] (<https://orcid.org/0000-0003-4198-9911>), Henrik Bengtsson [ctb] (HenrikBengtsson), Robrecht Cannoodt [aut, cre] (<https://orcid.org/0000-0003-3641-729X>, rcannood)’ Authors@R: ‘Trevor Hastie [aut], Andreas Weingessel [aut], Kurt Hornik [aut] (ORCID: <https://orcid.org/0000-0003-4198-9911>), Henrik Bengtsson [ctb] (github: HenrikBengtsson), Robrecht Cannoodt [aut, cre] (ORCID: <https://orcid.org/0000-0003-3641-729X>, github: rcannood)’ Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Package qsub

Current CRAN status: NOTE: 2, OK: 11

Version: 1.1.3
Check: CRAN incoming feasibility
Result: NOTE Maintainer: ‘Robrecht Cannoodt <rcannood@gmail.com>’ Package CITATION file contains call(s) to old-style citEntry(). Please use bibentry() instead. Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 1.1.3
Check: DESCRIPTION meta-information
Result: NOTE Author field differs from that derived from Authors@R Author: ‘Robrecht Cannoodt [aut, cre] (<https://orcid.org/0000-0003-3641-729X>, rcannood), Wouter Saelens [aut] (<https://orcid.org/0000-0002-7114-6248>, zouter)’ Authors@R: ‘Robrecht Cannoodt [aut, cre] (ORCID: <https://orcid.org/0000-0003-3641-729X>, github: rcannood), Wouter Saelens [aut] (ORCID: <https://orcid.org/0000-0002-7114-6248>, github: zouter)’ Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Package SCORPIUS

Current CRAN status: OK: 13