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Inferring, interpreting and visualising trajectories using a streamlined set of packages 🦕
https://dynverse.github.io/dyno
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fail to run infer_trajectory #105

Open ch8316f5eyu opened 3 years ago

ch8316f5eyu commented 3 years ago

After I called infer_trajectory, no result was return. There is the code: model <- infer_trajectory(dataset, ti_slingshot()) There is the printed message: Running singularity exec 'docker://dynverse/ti_slingshot:v1.0.3' echo hi Running /home/data/gmb23/miniconda3/bin/singularity exec --containall -B '/tmp/Rtmpl2vAot/file21cfe3600c853/:/copy_mount,/tmp/Rtmpl2vAot/file21cfe5fea4879/tmp:/tmp2' 'docker://dynverse/ti_slingshot:v1.0.3 INFO: Converting OCI blobs to SIF format INFO: Starting build... Getting image source signatures Copying blob sha256:a4d8138d0f6b5a441aaa533faf5fe0c3996a6ca42643c46f4402c7e8bda53742 Copying blob sha256:fb232e1cbf74f0fbcc4777cbfa268e7edacec9b944284fecb9a49a0717727371 Copying blob sha256:53a69644892140b394d496f0206f1e7caaffe83ac5c60245721b2d00189e0914 Copying blob sha256:0a98bf8e346bef6e92b33f0f28c5a473b6248a9ceb21686c5139485961033a8e Copying blob sha256:80070ed7cf8857a7fa54e7506039f1dc8c03beb2ce337fb45c2c7a963d6c3336 Copying blob sha256:3dda0c19343b691057ef5913c40aa79e2d65e2ffb9cfead972003f055c52854a Copying blob sha256:c8dedce96c17f919cd38e6d135303d3f2ca29bf0f73245671e1e3693bfa3169f Copying blob sha256:33199d4ff47fef1ac4cd988b1a9e63341436fdfa00e6de3578d31031555385be Copying blob sha256:7d44151ac2dae4a5c213f71c964418e5a18472aef650a4e3add71164e1d4ac82 Copying blob sha256:71c13904cc333688f9fa770fd95965f827949ea5c746b4dbb03e546fec3ad006 Copying blob sha256:a03a650d036654b42695ee1f175f5780d39ab41a25caebbd65a999aa946bc4e4 Copying blob sha256:d0e24af2427d84970f842be99c9e7320bebd79c6c408e05fdc8f98f5774cac4f Copying blob sha256:509c796290f5400effd645bb08a804ec8ce8587687552a105d0a94b0f984208d Copying blob sha256:fc7b41c3606c7d0cf3e66f4c7211f7ef0613e53fea45b733287465499f0bd216 Copying blob sha256:a0885e753793697a00322473263d6dea5c81d582b626c8cc3e6e34116de37a0b Copying config sha256:9d4bf56ab1117a1d80d714edf530fc3ba45dafe7500d196577e833522a28c677 Writing manifest to image destination Storing signatures 2021/03/09 06:58:30 info unpack layer: sha256:a4d8138d0f6b5a441aaa533faf5fe0c3996a6ca42643c46f4402c7e8bda53742 2021/03/09 06:58:31 warn rootless{usr/local/man} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers" 2021/03/09 06:58:32 info unpack layer: sha256:fb232e1cbf74f0fbcc4777cbfa268e7edacec9b944284fecb9a49a0717727371 2021/03/09 06:58:35 warn rootless{usr/local/bin/install2.r} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers" 2021/03/09 06:58:35 warn rootless{usr/local/bin/installGithub.r} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers" 2021/03/09 06:58:35 warn rootless{usr/local/bin/r} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers" 2021/03/09 06:58:37 info unpack layer: sha256:53a69644892140b394d496f0206f1e7caaffe83ac5c60245721b2d00189e0914 2021/03/09 06:58:43 warn rootless{usr/local/bin/pandoc} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers" 2021/03/09 06:58:43 warn rootless{usr/local/bin/pandoc-citeproc} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers" 2021/03/09 06:58:43 info unpack layer: sha256:0a98bf8e346bef6e92b33f0f28c5a473b6248a9ceb21686c5139485961033a8e 2021/03/09 06:58:43 info unpack layer: sha256:80070ed7cf8857a7fa54e7506039f1dc8c03beb2ce337fb45c2c7a963d6c3336 2021/03/09 06:58:43 info unpack layer: sha256:3dda0c19343b691057ef5913c40aa79e2d65e2ffb9cfead972003f055c52854a 2021/03/09 06:58:43 info unpack layer: sha256:c8dedce96c17f919cd38e6d135303d3f2ca29bf0f73245671e1e3693bfa3169f 2021/03/09 06:58:43 info unpack layer: sha256:33199d4ff47fef1ac4cd988b1a9e63341436fdfa00e6de3578d31031555385be 2021/03/09 06:58:52 info unpack layer: sha256:7d44151ac2dae4a5c213f71c964418e5a18472aef650a4e3add71164e1d4ac82 2021/03/09 06:58:53 info unpack layer: sha256:71c13904cc333688f9fa770fd95965f827949ea5c746b4dbb03e546fec3ad006 2021/03/09 06:58:53 info unpack layer: sha256:a03a650d036654b42695ee1f175f5780d39ab41a25caebbd65a999aa946bc4e4 2021/03/09 06:58:54 info unpack layer: sha256:d0e24af2427d84970f842be99c9e7320bebd79c6c408e05fdc8f98f5774cac4f 2021/03/09 06:58:57 info unpack layer: sha256:509c796290f5400effd645bb08a804ec8ce8587687552a105d0a94b0f984208d 2021/03/09 06:59:01 info unpack layer: sha256:fc7b41c3606c7d0cf3e66f4c7211f7ef0613e53fea45b733287465499f0bd216 2021/03/09 06:59:01 info unpack layer: sha256:a0885e753793697a00322473263d6dea5c81d582b626c8cc3e6e34116de37a0b INFO: Creating SIF file... INFO: Converting SIF file to temporary sandbox... INFO: Cleaning up image... Was there something wrong? Thank you for your help.

alexQiSong commented 3 years ago

I had similar issue

rcannood commented 3 years ago

Hello @ch8316f5eyu and @alexQiSong!

I currently have limited accessibility to my computer, but I'll take a look at this issue as soon as I'm back.

Are you both using dyno with singularity?

In the meantime, could you provide me some details on the environment you're trying to run this on? Please run the following in R and show me the output:

library(dyno)
Sys.info()
sessionInfo()
system("singularity --version")
system("docker --version")

Robrecht

Just-Jia commented 3 years ago

Hi, @rcannood , I have the same issue as well. I run the code, also no variable 'model' return: model <- infer_trajectory(dataset, ti_comp1())

message: v0.9.9.01: Pulling from dynverse/ti_comp1 844c33c7e6ea: Pulling fs layer 4f11e4e30170: Pulling fs layer a9724dff2655: Pulling fs layer f5f3a048c9c3: Pulling fs layer a53c4db932de: Pulling fs layer bd5da474b8ba: Pulling fs layer be9b916e18e7: Pulling fs layer b8b469f67972: Pulling fs layer e33132a1a81b: Pulling fs layer 32bd550d2fc1: Pulling fs layer a828ddf00b38: Pulling fs layer d97023e2f782: Pulling fs layer 84d8340a282e: Pulling fs layer bd5da474b8ba: Waiting be9b916e18e7: Waiting b8b469f67972: Waiting d97023e2f782: Waiting 84d8340a282e: Waiting e33132a1a81b: Waiting f5f3a048c9c3: Waiting a828ddf00b38: Waiting 32bd550d2fc1: Waiting a53c4db932de: Waiting 844c33c7e6ea: Verifying Checksum 844c33c7e6ea: Download complete 844c33c7e6ea: Pull complete f5f3a048c9c3: Download complete a53c4db932de: Verifying Checksum a53c4db932de: Download complete bd5da474b8ba: Verifying Checksum bd5da474b8ba: Download complete be9b916e18e7: Download complete a9724dff2655: Verifying Checksum a9724dff2655: Download complete e33132a1a81b: Verifying Checksum e33132a1a81b: Download complete 32bd550d2fc1: Verifying Checksum 32bd550d2fc1: Download complete 4f11e4e30170: Verifying Checksum 4f11e4e30170: Download complete a828ddf00b38: Verifying Checksum a828ddf00b38: Download complete 84d8340a282e: Verifying Checksum 84d8340a282e: Download complete 4f11e4e30170: Pull complete b8b469f67972: Verifying Checksum b8b469f67972: Download complete d97023e2f782: Verifying Checksum d97023e2f782: Download complete a9724dff2655: Pull complete f5f3a048c9c3: Pull complete a53c4db932de: Pull complete bd5da474b8ba: Pull complete be9b916e18e7: Pull complete b8b469f67972: Pull complete e33132a1a81b: Pull complete 32bd550d2fc1: Pull complete a828ddf00b38: Pull complete d97023e2f782: Pull complete 84d8340a282e: Pull complete Digest: sha256:012b3bfef2250767bcd3f3b389ebff82d4a2dc23d39b1bdadf7076e23b833680 Status: Downloaded newer image for dynverse/ti_comp1:v0.9.9.01 docker.io/dynverse/ti_comp1:v0.9.9.01

I use dyno with Docker, the code and output are: `> library(dyno)

Sys.info() sysname release version "Windows" "10 x64" "build 19042" nodename machine login "DESKTOP-H1Q76OC" "x86-64" "just" user effective_user "just" "just" sessionInfo() R version 4.0.2 (2020-06-22) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale: [1] LC_COLLATE=Chinese (Simplified)_China.936 [2] LC_CTYPE=Chinese (Simplified)_China.936
[3] LC_MONETARY=Chinese (Simplified)_China.936 [4] LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.936

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

other attached packages: [1] forcats_0.5.1 stringr_1.4.0
[3] dplyr_1.0.6 purrr_0.3.4
[5] readr_1.4.0 tidyr_1.1.3
[7] tibble_3.1.2 ggplot2_3.3.3
[9] tidyverse_1.3.1 dyno_0.1.2
[11] dynwrap_1.2.2 dynplot_1.0.2.9000
[13] dynmethods_1.0.5 dynguidelines_1.0.1
[15] dynfeature_1.0.0.9000

loaded via a namespace (and not attached): [1] colorspace_2.0-1 ellipsis_0.3.2 rprojroot_2.0.2
[4] dynparam_1.0.2 fs_1.5.0 rstudioapi_0.13
[7] rje_1.10.16 farver_2.1.0 remotes_2.3.0
[10] graphlayouts_0.7.1 dynutils_1.0.6 ggrepel_0.9.1
[13] fansi_0.5.0 lubridate_1.7.10 ranger_0.12.1
[16] xml2_1.3.2 codetools_0.2-16 cachem_1.0.5
[19] knitr_1.33 pkgload_1.2.1 polyclip_1.10-0
[22] jsonlite_1.7.2 broom_0.7.6 dbplyr_2.1.1
[25] ggforce_0.3.3 shiny_1.6.0 compiler_4.0.2
[28] httr_1.4.2 backports_1.2.1 assertthat_0.2.1
[31] Matrix_1.2-18 fastmap_1.1.0 cli_2.5.0
[34] later_1.2.0 tweenr_1.0.2 prettyunits_1.1.1
[37] htmltools_0.5.1.1 tools_4.0.2 igraph_1.2.6
[40] gtable_0.3.0 glue_1.4.2 reshape2_1.4.4
[43] tinytex_0.31 Rcpp_1.0.6 GA_3.2.1
[46] cellranger_1.1.0 vctrs_0.3.8 iterators_1.0.13
[49] ggraph_2.0.5 xfun_0.23 ps_1.6.0
[52] testthat_3.0.2 rvest_1.0.0 mime_0.10
[55] lifecycle_1.0.0 irlba_2.3.3 devtools_2.4.1
[58] MASS_7.3-51.6 scales_1.1.1 tidygraph_1.2.0
[61] babelwhale_1.0.1 hms_1.1.0 promises_1.2.0.1
[64] RColorBrewer_1.1-2 yaml_2.2.1 memoise_2.0.0
[67] gridExtra_2.3 dyndimred_1.0.4 stringi_1.6.2
[70] desc_1.3.0 foreach_1.5.1 pkgbuild_1.2.0
[73] rlang_0.4.11 pkgconfig_2.0.3 lattice_0.20-41
[76] patchwork_1.1.0.9000 cowplot_1.1.1 processx_3.5.2
[79] tidyselect_1.1.1 plyr_1.8.6 magrittr_2.0.1
[82] R6_2.5.0 generics_0.1.0 DBI_1.1.1
[85] pillar_1.6.1 haven_2.4.1 carrier_0.1.0
[88] withr_2.4.2 proxyC_0.2.0 modelr_0.1.8
[91] crayon_1.4.1 lmds_0.1.0 utf8_1.2.1
[94] usethis_2.0.1 viridis_0.6.1 grid_4.0.2
[97] readxl_1.3.1 callr_3.7.0 reprex_2.0.0
[100] digest_0.6.27 xtable_1.8-4 httpuv_1.6.1
[103] RcppParallel_5.1.4 munsell_0.5.0 viridisLite_0.4.0
[106] sessioninfo_1.1.1

system("singularity --version") [1] 127 system("docker --version") Docker version 20.10.6, build 370c289 [1] 0 `

TTsien commented 3 years ago

Hi, I had the same issue on both windows and macOS, using dyno with docker. infer_trajectory() returns no result

output:

Sys.info() sysname "Darwin" release "19.6.0" version "Darwin Kernel Version 19.6.0: Mon Apr 12 20:57:45 PDT 2021; root:xnu-6153.141.28.1~1/RELEASE_X86_64" nodename "qiantianyideMacBook-Pro.local" machine "x86_64" login "root" user "terrytsien" effective_user "terrytsien"

sessionInfo() R version 4.0.2 (2020-06-22) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Catalina 10.15.7

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages: [1] shiny_1.6.0 forcats_0.5.1 stringr_1.4.0 dplyr_1.0.6
[5] purrr_0.3.4 readr_1.4.0 tidyr_1.1.3 tibble_3.1.2
[9] ggplot2_3.3.3 tidyverse_1.3.1 dyno_0.1.2 dynwrap_1.2.2
[13] dynplot_1.0.2.9000 dynmethods_1.0.5 dynguidelines_1.0.1 dynfeature_1.0.0.9000

loaded via a namespace (and not attached): [1] colorspace_2.0-1 ellipsis_0.3.2 rprojroot_2.0.2 dynparam_1.0.2
[5] fs_1.5.0 rstudioapi_0.13 rje_1.10.16 farver_2.1.0
[9] waldo_0.2.5 remotes_2.3.0 graphlayouts_0.7.1 dynutils_1.0.6
[13] ggrepel_0.9.1 lubridate_1.7.10 fansi_0.5.0 xml2_1.3.2
[17] ranger_0.12.1 codetools_0.2-18 cachem_1.0.5 knitr_1.33
[21] polyclip_1.10-0 pkgload_1.2.1 jsonlite_1.7.2 broom_0.7.6
[25] dbplyr_2.1.1 ggforce_0.3.3 compiler_4.0.2 httr_1.4.2
[29] backports_1.2.1 assertthat_0.2.1 Matrix_1.3-3 fastmap_1.1.0
[33] cli_2.5.0 later_1.2.0 tweenr_1.0.2 htmltools_0.5.1.1
[37] prettyunits_1.1.1 tools_4.0.2 igraph_1.2.6 gtable_0.3.0
[41] glue_1.4.2 reshape2_1.4.4 tinytex_0.32 Rcpp_1.0.6
[45] GA_3.2.1 jquerylib_0.1.4 cellranger_1.1.0 vctrs_0.3.8
[49] iterators_1.0.13 ggraph_2.0.5 xfun_0.23 ps_1.6.0
[53] rvest_1.0.0 testthat_3.0.2 akima_0.6-2.1 mime_0.10
[57] lifecycle_1.0.0 irlba_2.3.3 devtools_2.4.1 MASS_7.3-54
[61] scales_1.1.1 tidygraph_1.2.0 babelwhale_1.0.1 hms_1.1.0
[65] promises_1.2.0.1 RColorBrewer_1.1-2 yaml_2.2.1 curl_4.3.1
[69] memoise_2.0.0 gridExtra_2.3 sass_0.4.0 dyndimred_1.0.4
[73] stringi_1.6.2 desc_1.3.0 foreach_1.5.1 pkgbuild_1.2.0
[77] rlang_0.4.11 pkgconfig_2.0.3 lattice_0.20-44 patchwork_1.1.0.9000 [81] cowplot_1.1.1 processx_3.5.2 tidyselect_1.1.1 plyr_1.8.6
[85] magrittr_2.0.1 R6_2.5.0 generics_0.1.0 DBI_1.1.1
[89] pillar_1.6.1 haven_2.4.1 carrier_0.1.0 withr_2.4.2
[93] proxyC_0.2.0 sp_1.4-5 modelr_0.1.8 crayon_1.4.1
[97] shinyWidgets_0.6.0 lmds_0.1.0 utf8_1.2.1 viridis_0.6.1
[101] usethis_2.0.1 readxl_1.3.1 grid_4.0.2 callr_3.7.0
[105] reprex_2.0.0 digest_0.6.27 xtable_1.8-4 httpuv_1.6.1
[109] RcppParallel_5.1.4 munsell_0.5.0 viridisLite_0.4.0 bslib_0.2.5.1
[113] shinyjs_2.0.0 sessioninfo_1.1.1

system("singularity --version") sh: singularity: command not found Warning message: In system("singularity --version") : error in running command system("docker --version") Docker version 20.10.6, build 370c289

KforKuma commented 3 years ago

Hi, I have a similar problem on Ubuntu 20.04, I am using docker and here's my info:

>Sys.info()

                                         sysname 
                                         "Linux" 
                                         release 
                              "5.8.0-53-generic" 
                                         version

"#60~20.04.1-Ubuntu SMP Thu May 6 09:52:46 UTC 2021" machine "x86_64"

> sessionInfo()

R version 4.1.0 (2021-05-18) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.2 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale: [1] LC_CTYPE=zh_CN.UTF-8 LC_NUMERIC=C
[3] LC_TIME=zh_CN.UTF-8 LC_COLLATE=zh_CN.UTF-8
[5] LC_MONETARY=zh_CN.UTF-8 LC_MESSAGES=zh_CN.UTF-8
[7] LC_PAPER=zh_CN.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] forcats_0.5.1 stringr_1.4.0 dplyr_1.0.6
[4] purrr_0.3.4 readr_1.4.0 tidyr_1.1.3
[7] tibble_3.1.2 ggplot2_3.3.3 tidyverse_1.3.1
[10] shiny_1.6.0 SeuratObject_4.0.1 Seurat_4.0.2
[13] Matrix_1.3-4 dyno_0.1.2 dynwrap_1.2.2
[16] dynplot_1.0.2.9000 dynmethods_1.0.5 dynguidelines_1.0.1
[19] dynfeature_1.0.0.9000

loaded via a namespace (and not attached): [1] utf8_1.2.1 reticulate_1.20 tidyselect_1.1.1
[4] htmlwidgets_1.5.3 grid_4.1.0 ranger_0.12.1
[7] Rtsne_0.15 munsell_0.5.0 codetools_0.2-18
[10] ica_1.0-2 future_1.21.0 miniUI_0.1.1.1
[13] withr_2.4.2 colorspace_2.0-1 knitr_1.33
[16] rstudioapi_0.13 ROCR_1.0-11 tensor_1.5
[19] listenv_0.8.0 polyclip_1.10-0 farver_2.1.0
[22] rprojroot_2.0.2 parallelly_1.25.0 vctrs_0.3.8
[25] generics_0.1.0 xfun_0.23 R6_2.5.0
[28] GA_3.2.1 graphlayouts_0.7.1 spatstat.utils_2.1-0 [31] cachem_1.0.5 assertthat_0.2.1 promises_1.2.0.1
[34] scales_1.1.1 ggraph_2.0.5 lmds_0.1.0
[37] gtable_0.3.0 babelwhale_1.0.2 globals_0.14.0
[40] processx_3.5.2 goftest_1.2-2 tidygraph_1.2.0
[43] rlang_0.4.11 akima_0.6-2.1 splines_4.1.0
[46] lazyeval_0.2.2 spatstat.geom_2.1-0 broom_0.7.7
[49] BiocManager_1.30.15 yaml_2.2.1 reshape2_1.4.4
[52] abind_1.4-5 modelr_0.1.8 backports_1.2.1
[55] httpuv_1.6.1 tools_4.1.0 ellipsis_0.3.2
[58] spatstat.core_2.1-2 jquerylib_0.1.4 RColorBrewer_1.1-2
[61] ggridges_0.5.3 Rcpp_1.0.6 plyr_1.8.6
[64] ps_1.6.0 rpart_4.1-15 deldir_0.2-10
[67] pbapply_1.4-3 viridis_0.6.1 cowplot_1.1.1
[70] dynparam_1.0.2 zoo_1.8-9 haven_2.4.1
[73] ggrepel_0.9.1 cluster_2.1.2 fs_1.5.0
[76] magrittr_2.0.1 data.table_1.14.0 scattermore_0.7
[79] carrier_0.1.0 reprex_2.0.0 lmtest_0.9-38
[82] RANN_2.6.1 fitdistrplus_1.1-5 matrixStats_0.59.0
[85] hms_1.1.0 patchwork_1.1.0.9000 shinyjs_2.0.0
[88] mime_0.10 xtable_1.8-4 readxl_1.3.1
[91] gridExtra_2.3 compiler_4.1.0 KernSmooth_2.23-20
[94] crayon_1.4.1 rje_1.10.16 htmltools_0.5.1.1
[97] proxyC_0.2.0 mgcv_1.8-35 later_1.2.0
[100] RcppParallel_5.1.4 lubridate_1.7.10 DBI_1.1.1
[103] tweenr_1.0.2 dbplyr_2.1.1 MASS_7.3-54
[106] cli_2.5.0 parallel_4.1.0 igraph_1.2.6
[109] pkgconfig_2.0.3 sp_1.4-5 plotly_4.9.3
[112] spatstat.sparse_2.0-0 xml2_1.3.2 foreach_1.5.1
[115] bslib_0.2.5.1 dynutils_1.0.6 rvest_1.0.0
[118] digest_0.6.27 dyndimred_1.0.4 sctransform_0.3.2
[121] RcppAnnoy_0.0.18 spatstat.data_2.1-0 cellranger_1.1.0
[124] leiden_0.3.8 uwot_0.1.10 lifecycle_1.0.0
[127] nlme_3.1-152 jsonlite_1.7.2 desc_1.3.0
[130] viridisLite_0.4.0 fansi_0.5.0 pillar_1.6.1
[133] lattice_0.20-44 fastmap_1.1.0 httr_1.4.2
[136] survival_3.2-11 glue_1.4.2 remotes_2.4.0
[139] png_0.1-7 iterators_1.0.13 ggforce_0.3.3
[142] stringi_1.6.2 sass_0.4.0 irlba_2.3.3
[145] future.apply_1.7.0

> system("docker --version")

Docker version 20.10.7, build f0df350

rcannood commented 3 years ago

Hello @ch8316f5eyu @alexQiSong @TTsien @KforKuma,

Sorry for the delayed response. I'm failing to replicate the issue. Can you show me the output of the following code?

library(dyno)
model <- infer_trajectory(example_bifurcating, ti_comp1(), verbose = TRUE)
cat("\nNames: ", paste(names(model), collapse = ", "), "\n", sep = "")

Kind regards, Robrecht

meichendong commented 3 years ago

I had a similar problem that no model variable/object was returned. It seems that installing the package hdf5r solved my problem.

alexQiSong commented 3 years ago

I had a similar problem that no model variable/object was returned. It seems that installing the package hdf5r solved my problem.

Exactly, that works for me as well. My guess is that R does not complain about missing 'hdf5r' package during the installation step so this issue just slipped through the cracks.

pteromysvolans commented 2 years ago

我有一个类似的问题，没有返回模型变量/对象。安装软件包似乎hdf5r解决了我的问题。

谢谢您，问题解决了