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Inferring, interpreting and visualising trajectories using a streamlined set of packages 🦕
https://dynverse.github.io/dyno
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infer_trajectory: Error in readRDS(file) : unknown input format #68

Closed sisterdot closed 4 years ago

sisterdot commented 4 years ago

Dear dyno-team,

while dyno worked for me previously on macosx + docker, i am having trouble getting the package to work on a linux server using singularity

containers are not being pulled, although singularity check is fine:


> dynwrap::test_singularity_installation(detailed = TRUE)
✔ Singularity is installed
✔ Singularity is at correct version (>=3.0): 3.1.0 is installed
INFO:    Converting OCI blobs to SIF format
INFO:    Starting build...
Getting image source signatures
Copying blob sha256:5d20c808ce198565ff70b3ed23a991dd49afac45dece63474b27ce6ed036adc6
 2.01 MiB / 2.01 MiB  0s
Copying config sha256:54c9afe02933973b548088d74fca8dc95f0c3ae0d1bc765efbf2673c31a8e627
 585 B / 585 B  0s
Writing manifest to image destination
Storing signatures
INFO:    Creating SIF file...
INFO:    Build complete: 
INFO:    Image cached as SIF at 
✔ Singularity can pull and run a container from Dockerhub
✔ Singularity can mount temporary volumes
✔ Singularity test successful ------------------------------------------------------------
[1] TRUE

another singularity test

system("singularity exec 'docker://dynverse/ti_slingshot:v0.9.9' echo hi")
INFO:    Converting OCI blobs to SIF format
INFO:    Starting build...
Getting image source signatures
Copying blob sha256:ab1fc7e4bf9195e554669fafa47f69befe22053d7100f5f7002cb9254a36f37c
...

INFO:    Creating SIF file...
INFO:    Build complete: 
...
INFO:    Image cached as SIF at

nevertheless i get an error when trying to use trajectory inference:

dataset <- wrap_expression(
  counts = example_dataset$counts,
  expression = example_dataset$expression
)

model <- infer_trajectory(dataset,c("slingshot"))
Error in readRDS(file) : unknown input format

model <- infer_trajectory(dataset,"slingshot", verbose = TRUE, debug = TRUE)
Error in readRDS(file) : unknown input format

model <- infer_trajectory(dataset, ti_slingshot(), verbose = TRUE)
Error in readRDS(file) : unknown input format

create_ti_method_container()
Error in readRDS(file) : unknown input format

ti_slingshot()
Error in readRDS(file) : unknown input format
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

other attached packages:
[1] dyno_0.1.1            dynwrap_1.1.4.9000    dynplot_1.0.2.9000   
[4] dynmethods_1.0.5      dynguidelines_1.0.0   dynfeature_1.0.0.9000

loaded via a namespace (and not attached):
  [1] fs_1.3.1             usethis_1.5.1        dynutils_1.0.4.9000 
  [4] devtools_2.2.0       RColorBrewer_1.1-2   rprojroot_1.3-2     
  [7] tools_3.5.1          backports_1.1.4      utf8_1.1.4          
 [10] R6_2.4.0             irlba_2.3.3          DT_0.8              
 [13] lazyeval_0.2.2       colorspace_1.4-1     sp_1.3-1            
 [16] withr_2.1.2          tidyselect_0.2.5     carrier_0.1.0       
 [19] gridExtra_2.3        prettyunits_1.0.2    processx_3.4.1      
 [22] proxyC_0.1.5         curl_4.0             compiler_3.5.1      
 [25] cli_1.1.0            desc_1.2.0           scales_1.0.0        
 [28] readr_1.3.1          callr_3.3.1          stringr_1.4.0       
 [31] digest_0.6.20        pkgconfig_2.0.2      htmltools_0.3.6     
 [34] akima_0.6-2          sessioninfo_1.1.1    GA_3.2              
 [37] rje_1.10.10          htmlwidgets_1.3      rlang_0.4.0         
 [40] shiny_1.3.2          farver_1.1.0         dplyr_0.8.3         
 [43] magrittr_1.5         patchwork_0.0.1      Matrix_1.2-14       
 [46] fansi_0.4.0          Rcpp_1.0.2           dyndimred_1.0.2.9000
 [49] munsell_0.5.0        viridis_0.5.1        stringi_1.4.3       
 [52] yaml_2.2.0           ggraph_2.0.0         MASS_7.3-50         
 [55] pkgbuild_1.0.5       plyr_1.8.4           grid_3.5.1          
 [58] promises_1.0.1       ggrepel_0.8.1        crayon_1.3.4        
 [61] lattice_0.20-35      cowplot_1.0.0        graphlayouts_0.5.0  
 [64] hms_0.5.1            knitr_1.24           zeallot_0.1.0       
 [67] ps_1.3.0             pillar_1.4.2         igraph_1.2.4.1      
 [70] ranger_0.11.2        babelwhale_1.0.1     codetools_0.2-15    
 [73] reshape2_1.4.3       pkgload_1.0.2        glue_1.3.1          
 [76] remotes_2.1.0        RcppParallel_4.4.3   foreach_1.4.7       
 [79] vctrs_0.2.0          dynparam_1.0.0.9000  tweenr_1.0.1        
 [82] httpuv_1.5.1         testthat_2.2.1       gtable_0.3.0        
 [85] purrr_0.3.2          polyclip_1.10-0      tidyr_0.8.3         
 [88] assertthat_0.2.1     ggplot2_3.2.1        xfun_0.9            
 [91] ggforce_0.3.1        lmds_0.1.0           mime_0.7            
 [94] xtable_1.8-4         tidygraph_1.1.2      later_0.8.0         
 [97] viridisLite_0.3.0    tibble_2.1.3         iterators_1.0.12    
[100] memoise_1.1.0        ellipsis_0.2.0.1

thankful for any suggestions!

rcannood commented 4 years ago

Hello @sisterdot!

Sorry for the late reply. I think this issue could have been related to a bug in babelwhale -- the package that communicates with Docker and Singularity. Could you run the following code on each host where you are using Singularity?

install.packages("babelwhale") # update to babelwhale 1.0.1
library(babelwhale)
config <- create_singularity_config("absolute_path_to_cache_dir")
set_default_config(config)
get_default_config() # this should work now
dynmethods::ti_slingshot() # this as well, hopefully

Kind regards, Robrecht

sisterdot commented 4 years ago

Thank you Robrecht,

updated babelwhale and it worked out :-)

THANKS A LOT!!!

other attached packages:
[1] dyno_0.1.1            dynwrap_1.1.4.9000    dynplot_1.0.2.9000   
[4] dynmethods_1.0.5      dynguidelines_1.0.0   dynfeature_1.0.0.9000
[7] babelwhale_1.0.1
rcannood commented 4 years ago

:+1: