Fatal error after Rstudio and R Update

Question

Fatal error after Rstudio and R Update

Closed this issue a year ago · 7 comments

hello again,
In order to try to make the KEGG visualisation working on my Macbook, I updated my Rstudio to Version 2023.06.0+421 and R to 4.3.1 and now I get a fatal error when I try to run pathfindR (see image). Any recommendations/suggestions?
Thanks again for your help!

Answer 1 · 2023-07-26T12:03:45.000Z

what version of pathfindR are you using? Can you share the output of sessionInfo()?

Answer 2 · 2023-07-29T16:38:21.000Z

Dear Ege, I tired to run it again and it gives me the same error. Here is what I get when I put sessionInfo(). See below. I am not sure if I should downgrade to a previous R and Rstudio version. Best and thanks, H

sessionInfo()

R version 4.3.1 (2023-06-16) Platform: x86_64-apple-darwin20 (64-bit) Running under: macOS Big Sur 11.7.8 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-x86_64/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: Europe/Berlin tzcode source: internal attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] R.utils_2.12.2 R.oo_1.25.0 R.methodsS3_1.8.2 archive_1.1.5 [5] dplyr_1.1.2 ggplot2_3.4.2 readr_2.1.4 pathfindR_2.1.0 [9] pathfindR.data_2.0.0 loaded via a namespace (and not attached): [1] viridis_0.6.3 utf8_1.2.3 generics_0.1.3 tidyr_1.3.0 [5] hms_1.1.3 digest_0.6.32 magrittr_2.0.3 evaluate_0.21 [9] grid_4.3.1 iterators_1.0.14 fastmap_1.1.1 foreach_1.5.2 [13] doParallel_1.0.17 ggrepel_0.9.3 gridExtra_2.3 purrr_1.0.1 [17] fansi_1.0.4 viridisLite_0.4.2 scales_1.2.1 tweenr_2.0.2 [21] codetools_0.2-19 cli_3.6.1 crayon_1.5.2 rlang_1.1.1 [25] graphlayouts_1.0.0 polyclip_1.10-4 bit64_4.0.5 tidygraph_1.2.3 [29] munsell_0.5.0 withr_2.5.0 tools_4.3.1 parallel_4.3.1 [33] tzdb_0.4.0 colorspace_2.1-0 vctrs_0.6.3 R6_2.5.1 [37] lifecycle_1.0.3 bit_4.0.5 vroom_1.6.3 MASS_7.3-60 [41] ggraph_2.1.0 pkgconfig_2.0.3 pillar_1.9.0 gtable_0.3.3 [45] glue_1.6.2 Rcpp_1.0.10 ggforce_0.4.1 xfun_0.39 [49] tibble_3.2.1 tidyselect_1.2.0 rstudioapi_0.14 knitr_1.43 [53] farver_2.1.1 htmltools_0.5.5 igraph_1.5.0 rmarkdown_2.23 [57] compiler_4.3.1

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On 26. Jul 2023, at 14:03, Ege Ulgen ***@***.***> wrote: what version of pathfindR are you using? Can you share the output of sessionInfo()? — Reply to this email directly, view it on GitHub <#167 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADU6KHJN65Y7LDIGQGP4GQLXSEBSZANCNFSM6AAAAAA2NRGOW4>. You are receiving this because you authored the thread.

Answer 3 · 2023-08-02T09:16:16.000Z

Hej,
this is what I get.

sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Big Sur 11.7.8

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-x86_64/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: Europe/Berlin
tzcode source: internal

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] R.utils_2.12.2 R.oo_1.25.0 R.methodsS3_1.8.2 archive_1.1.5
[5] dplyr_1.1.2 ggplot2_3.4.2 readr_2.1.4 pathfindR_2.1.0
[9] pathfindR.data_2.0.0

loaded via a namespace (and not attached):
[1] viridis_0.6.3 utf8_1.2.3 generics_0.1.3 tidyr_1.3.0
[5] hms_1.1.3 digest_0.6.32 magrittr_2.0.3 evaluate_0.21
[9] grid_4.3.1 iterators_1.0.14 fastmap_1.1.1 foreach_1.5.2
[13] doParallel_1.0.17 ggrepel_0.9.3 gridExtra_2.3 purrr_1.0.1
[17] fansi_1.0.4 viridisLite_0.4.2 scales_1.2.1 tweenr_2.0.2
[21] codetools_0.2-19 cli_3.6.1 crayon_1.5.2 rlang_1.1.1
[25] graphlayouts_1.0.0 polyclip_1.10-4 bit64_4.0.5 tidygraph_1.2.3
[29] munsell_0.5.0 withr_2.5.0 tools_4.3.1 parallel_4.3.1
[33] tzdb_0.4.0 colorspace_2.1-0 vctrs_0.6.3 R6_2.5.1
[37] lifecycle_1.0.3 bit_4.0.5 vroom_1.6.3 MASS_7.3-60
[41] ggraph_2.1.0 pkgconfig_2.0.3 pillar_1.9.0 gtable_0.3.3
[45] glue_1.6.2 Rcpp_1.0.10 ggforce_0.4.1 xfun_0.39
[49] tibble_3.2.1 tidyselect_1.2.0 rstudioapi_0.14 knitr_1.43
[53] farver_2.1.1 htmltools_0.5.5 igraph_1.5.0 rmarkdown_2.23
[57] compiler_4.3.1

Answer 4 · 2023-08-04T16:27:16.000Z

Sorry for the late reply. This might be a java-related issue. Please follow the advice in this article and let me know if that resolves the issue.

Answer 5 · 2023-08-06T18:33:20.000Z

Thank you, so far I haven’t managed to solve it. Rstudio works otherwise, just not with pathfindR. I working on fixing it. If you have other suggestion, please tell me.

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On 4. Aug 2023, at 18:27, Ege Ulgen ***@***.***> wrote: Sorry for the late reply. This might be a java-related issue. Please follow the advice in this article <https://solutions.posit.co/envs-pkgs/using-rjava/#setup-java-support-in-r> and let me know if that resolves the issue. — Reply to this email directly, view it on GitHub <#167 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADU6KHLPEQE4XOR3CDLSQZLXTUPG7ANCNFSM6AAAAAA2NRGOW4>. You are receiving this because you authored the thread.

Answer 6 · 2023-08-09T21:59:45.000Z

has fixing the java configuration not resolved the issue

Answer 7 · 2023-09-03T09:43:04.000Z

hello @kratzera, has re-configuring java resolved the issue? I'm closing this, if it persists, please re-open it