model.tree.pcreode <- infer_trajectory(dataset, ti_pcreode(n_pca_components = 10, num_runs = 10L), seed = 7, verbose = TRUE)
docker.io/dynverse/ti_pcreode:v0.9.9.01
Executing 'pcreode' on '20190808_144935__data_wrapper__GQCmdkdhU4' With parameters: list(n_pca_components = 10, num_runs = 10L),
inputs: expression, and
priors : 
Input saved to C:\Users\FUCHSD~1\AppData\Local\Temp\Rtmpslaedt\file2eac2c0f391d/ti
Running method using babelwhale
Running "C:\PROGRA~1\Docker\Docker\RESOUR~1\bin\docker.exe" run --name 20190808_154412__container__DJeLusmOdl -e "TMPDIR=/tmp2" \
  --workdir /ti/workspace -v "/c/Users/FUCHSD~1/AppData/Local/Temp/Rtmpslaedt/file2eac2c0f391d/ti:/ti" -v \
  "/c/Users/FUCHSD~1/AppData/Local/Temp/Rtmpslaedt/file2eac1ad32718/tmp:/tmp2" "dynverse/ti_pcreode:v0.9.9.01" --dataset /ti/input.h5 \
  --output /ti/output.h5
Traceback (most recent call last):
  File "/code/run.py", line 34, in <module>
    pca_reduced_data = data_pca.pca_set_components(min(parameters["n_pca_components"],expression.shape[1]))
  File "/pCreode/pcreode/pcreode.py", line 83, in pca_set_components
    return( self.pca[:,:n_components])
TypeError: slice indices must be integers or None or have an __index__ method
Traceback (most recent call last):
  File "/code/run.py", line 34, in <module>
    pca_reduced_data = data_pca.pca_set_components(min(parameters["n_pca_components"],expression.shape[1]))
  File "/pCreode/pcreode/pcreode.py", line 83, in pca_set_components
    return( self.pca[:,:n_components])
TypeError: slice indices must be integers or None or have an __index__ method
Error: Error during trajectory inference, see output above <U+2191><U+2191><U+2191>

> str(dataset)
List of 11
 $ id                  : chr "20190808_144935__data_wrapper__GQCmdkdhU4"
 $ cell_ids            : chr [1:1654] "BM_1_GTATCTTAGGGCTTGA.1" "BM_1_TCATTTGTCTTATCTG.1" "BM_1_GATCGATGTAACGACG.1" "BM_1_ATCCGAACAGTGACAG.1" ...
 $ cell_info           : NULL
 $ counts              :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  .. ..@ i       : int [1:2322752] 12 16 104 114 120 122 130 152 159 171 ...
  .. ..@ p       : int [1:10442] 0 42 45 427 434 601 602 606 653 981 ...
  .. ..@ Dim     : int [1:2] 1654 10441
  .. ..@ Dimnames:List of 2
  .. .. ..$ : chr [1:1654] "BM_1_GTATCTTAGGGCTTGA.1" "BM_1_TCATTTGTCTTATCTG.1" "BM_1_GATCGATGTAACGACG.1" "BM_1_ATCCGAACAGTGACAG.1" ...
  .. .. ..$ : chr [1:10441] "A2M" "A3GALT2" "AAAS" "AACS" ...
  .. ..@ x       : num [1:2322752] 1 1 1 1 1 2 1 2 1 1 ...
  .. ..@ factors : list()
 $ expression          :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  .. ..@ i       : int [1:2322752] 12 16 104 114 120 122 130 152 159 171 ...
  .. ..@ p       : int [1:10442] 0 42 45 427 434 601 602 606 653 981 ...
  .. ..@ Dim     : int [1:2] 1654 10441
  .. ..@ Dimnames:List of 2
  .. .. ..$ : chr [1:1654] "BM_1_GTATCTTAGGGCTTGA.1" "BM_1_TCATTTGTCTTATCTG.1" "BM_1_GATCGATGTAACGACG.1" "BM_1_ATCCGAACAGTGACAG.1" ...
  .. .. ..$ : chr [1:10441] "A2M" "A3GALT2" "AAAS" "AACS" ...
  .. ..@ x       : num [1:2322752] 1 1 1 1 1 2 1 2 1 1 ...
  .. ..@ factors : list()
 $ expression_projected: NULL
 $ feature_info        :Classes ‘tbl_df’, ‘tbl’ and 'data.frame':	10441 obs. of  1 variable:
  ..$ feature_id: chr [1:10441] "A2M" "A3GALT2" "AAAS" "AACS" ...
 $ feature_ids         : chr [1:10441] "A2M" "A3GALT2" "AAAS" "AACS" ...
 $ prior_information   :List of 5
  ..$ start_id : chr [1:100] "BM_1_GTATCTTAGGGCTTGA.1" "BM_1_TCATTTGTCTTATCTG.1" "BM_1_GATCGATGTAACGACG.1" "BM_1_ATCCGAACAGTGACAG.1" ...
  ..$ end_id   : chr [1:500] "PB_TACGGATGTAGAGCTG.1" "PB_ACCCACTTCCGCATCT.1" "BM_1_GACCAATAGCTACCTA.1" "BM_1_GACCAATGTGCAGACA.1" ...
  ..$ groups_id:'data.frame':	1654 obs. of  2 variables:
  .. ..$ cell_id : chr [1:1654] "BM_1_GTATCTTAGGGCTTGA.1" "BM_1_TCATTTGTCTTATCTG.1" "BM_1_GATCGATGTAACGACG.1" "BM_1_ATCCGAACAGTGACAG.1" ...
  .. ..$ group_id: chr [1:1654] "HSC" "HSC" "HSC" "HSC" ...
  ..$ start_n  : num 1
  ..$ end_n    : num 5
 $ group_ids           : chr [1:19] "HSC" "MPP" "BCP" "BC" ...
 $ grouping            : Named chr [1:1654] "HSC" "HSC" "HSC" "HSC" ...
  ..- attr(*, "names")= chr [1:1654] "BM_1_GTATCTTAGGGCTTGA.1" "BM_1_TCATTTGTCTTATCTG.1" "BM_1_GATCGATGTAACGACG.1" "BM_1_ATCCGAACAGTGACAG.1" ... - attr(*, "class")= chr [1:5] "dynwrap::with_grouping" "dynwrap::with_prior" "dynwrap::with_expression" "dynwrap::data_wrapper" ...

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)

Matrix products: default

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 
 
locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] dyno_0.1.1                  dynwrap_1.1.4.9000          dynplot_1.0.2.9000          dynmethods_1.0.5           
 [5] dynguidelines_1.0.0         dynfeature_1.0.0.9000       scran_1.12.1                scater_1.12.2              
 [9] futile.matrix_1.2.7         Matrix_1.2-18               data.table_1.12.2           gplots_3.0.3               
[13] Seurat_3.0.2                forcats_0.4.0               stringr_1.4.0               dplyr_0.8.3                
[17] purrr_0.3.2                 readr_1.3.1                 tidyr_0.8.3                 tibble_2.1.3               
[21] ggplot2_3.2.0               tidyverse_1.2.1             SingleCellExperiment_1.6.0  SummarizedExperiment_1.14.1
[25] DelayedArray_0.10.0         BiocParallel_1.18.0         matrixStats_0.54.0          Biobase_2.44.0             
[29] GenomicRanges_1.36.0        GenomeInfoDb_1.20.0         IRanges_2.18.1              S4Vectors_0.22.0           
[33] BiocGenerics_0.30.0        

loaded via a namespace (and not attached):
  [1] reticulate_1.13          R.utils_2.9.0            tidyselect_0.2.5         htmlwidgets_1.3          grid_3.6.1              
  [6] ranger_0.11.2            Rtsne_0.15               munsell_0.5.0            codetools_0.2-16         ica_1.0-2               
 [11] statmod_1.4.32           future_1.14.0            withr_2.1.2              colorspace_1.4-1         rstudioapi_0.10         
 [16] ROCR_1.0-7               gbRd_0.4-11              listenv_0.7.0            labeling_0.3             Rdpack_0.11-0           
 [21] GenomeInfoDbData_1.2.1   polyclip_1.10-0          bit64_0.9-8              farver_1.1.0             vctrs_0.2.0             
 [26] generics_0.0.2           lambda.r_1.2.3           R6_2.4.0                 GA_3.2                   ggbeeswarm_0.6.0        
 [31] rsvd_1.0.2               locfit_1.5-9.1           hdf5r_1.2.0              bitops_1.0-6             assertthat_0.2.1        
 [36] promises_1.0.1           SDMTools_1.1-221.1       scales_1.0.0             ggraph_1.0.2             beeswarm_0.2.3          
 [41] gtable_0.3.0             babelwhale_1.0.0.9000    npsurv_0.4-0             globals_0.12.4           processx_3.4.1          
 [46] tidygraph_1.1.2          rlang_0.4.0              zeallot_0.1.0            scatterplot3d_0.3-41     splines_3.6.1           
 [51] lazyeval_0.2.2           broom_0.5.2              yaml_2.2.0               reshape2_1.4.3           modelr_0.1.4            
 [56] backports_1.1.4          httpuv_1.5.1             tools_3.6.1              RColorBrewer_1.1-2       dynamicTreeCut_1.63-1   
 [61] ggridges_0.5.1           Rcpp_1.0.2               plyr_1.8.4               lambda.tools_1.0.9       zlibbioc_1.30.0         
 [66] RCurl_1.95-4.12          ps_1.3.0                 pbapply_1.4-1            viridis_0.5.1            cowplot_1.0.0           
 [71] dynparam_1.0.0.9000      zoo_1.8-6                haven_2.1.1              ggrepel_0.8.1            cluster_2.1.0           
 [76] magrittr_1.5             futile.options_1.0.1     carrier_0.1.0            lmtest_0.9-37            RANN_2.6.1              
 [81] fitdistrplus_1.0-14      patchwork_0.0.1          hms_0.5.0                lsei_1.2-0               mime_0.7.1              
 [86] xtable_1.8-4             RMTstat_0.3              readxl_1.3.1             gridExtra_2.3            testthat_2.2.1          
 [91] compiler_3.6.1           KernSmooth_2.23-15       crayon_1.3.4             rje_1.9                  R.oo_1.22.0             
 [96] htmltools_0.3.6          proxyC_0.1.5             later_0.8.0              RcppParallel_4.4.3       lubridate_1.7.4         
[101] diffusionMap_1.1-0.1     tweenr_1.0.1             formatR_1.7.1            MASS_7.3-51.4            cli_1.1.0               
[106] R.methodsS3_1.7.1        gdata_2.18.0             metap_1.1                igraph_1.2.4.1           pkgconfig_2.0.2         
[111] plotly_4.9.0             foreach_1.5.1            xml2_1.2.1               vipor_0.4.5              dqrng_0.2.1             
[116] dynutils_1.0.4.9000      XVector_0.24.0           bibtex_0.4.2             rvest_0.3.4              dyndimred_1.0.2.9000    
[121] digest_0.6.20            sctransform_0.2.0        tsne_0.1-3               cellranger_1.1.0         edgeR_3.26.6            
[126] DelayedMatrixStats_1.6.0 shiny_1.3.2              gtools_3.8.1             nlme_3.1-141             jsonlite_1.6            
[131] BiocNeighbors_1.2.0      futile.logger_1.4.3      viridisLite_0.3.0        limma_3.40.6             pillar_1.4.2            
[136] lattice_0.20-38          httr_1.4.1               survival_2.44-1.1        glue_1.3.1               remotes_2.1.0           
[141] iterators_1.0.12         png_0.1-7                bit_1.1-14               ggforce_0.2.2            stringi_1.4.3           
[146] BiocSingular_1.0.0       caTools_1.17.1.2         irlba_2.3.3              future.apply_1.3.0       ape_5.3

dynwrap::test_docker_installation(detailed = TRUE)
✔ Docker is installed
✔ Docker daemon is running
✔ Docker is at correct version (>1.0): 1.39
✔ Docker is in linux mode
✔ Docker can pull images
✔ Docker can run image
✔ Docker can mount temporary volumes
✔ Docker test successful -----------------------------------------------------------------

dataset <- wrap_expression(expression = example_dataset$expression,
                            counts = example_dataset$counts)
dataset <- add_prior_information(dataset,start_id = "Cell1")

answers <- dynguidelines::answer_questions(
  multiple_disconnected = TRUE, 
  expect_topology = NULL, 
  expected_topology = NULL, 
  n_cells = 1000, 
  n_features = 3, 
  memory = "30GB", 
  prior_information = "start_id", 
  docker = TRUE
)
guidelines <- dynguidelines::guidelines(answers = answers) 

model <- infer_trajectory(dataset,"paga")

/usr/local/lib/python3.7/site-packages/scanpy/preprocessing/_deprecated/highly_variable_genes.py:168: RuntimeWarning: invalid value encountered in true_divide
  / disp_mad_bin[df['mean_bin'].values].values
Traceback (most recent call last):
  File "/code/run.py", line 60, in <module>
    sc.pp.recipe_zheng17(adata, n_top_genes=n_top_genes)
  File "/usr/local/lib/python3.7/site-packages/scanpy/preprocessing/_recipes.py", line 108, in recipe_zheng17
    adata.X, flavor='cell_ranger', n_top_genes=n_top_genes, log=False)
  File "/usr/local/lib/python3.7/site-packages/scanpy/preprocessing/_deprecated/highly_variable_genes.py", line 175, in filter_genes_dispersion
    disp_cut_off = dispersion_norm[n_top_genes-1]
IndexError: index 2 is out of bounds for axis 0 with size 0

filter, lag

intersect, setdiff, setequal, union

flatten

dat <- add_prior_information(
  dataset = dat
  start_id = c("A1, "A2", "A3"),
  end_id = c("C1", "C2", "C3"),
  groups_id = data.frame(cell_id = c("A1, "A2", "A3", "B1", "B2", "B3", "C1", "C2", "C3"),
                         group_id = c("A", "A", "A", "B", "B", "B", "C", "C", "C"),
  groups_network = data.frame(from = c("A", "B"), to = c("B", "C"))
  start_n = 1,
  end_n = 1
)

mod <- infer_trajectory(dat, "slingshot", give_priors = c("start_id", "end_id", "groups_id", "groups_network", "start_n", "end_n"), seed = 1701)

1. dynwrap::infer_trajectory(dataset, method = ti_monocle_ddrtree(reduction_method = "DDRTree", 
 .     max_components = 5, norm_method = "log", filter_features_mean_expression = 0.1), 
 .     verbose = TRUE)
2. stop("Error during trajectory inference \n", crayon::bold(error), 
 .     call. = FALSE)

$ singularity exec 'docker://dynverse/ti_slingshot:v1.0.3' echo hi
FATAL:   Unable to handle docker://dynverse/ti_slingshot:v1.0.3 uri: failed to get SHA of 
docker://dynverse/ti_slingshot:v1.0.3: error getting username and password: error reading 
JSON file "/run/user/68333/containers/auth.json": error unmarshaling JSON at "/run/user
/68333/containers/auth.json": unexpected end of JSON input

models <- dynwrap::infer_trajectories(
  dataset, 
  method = list(ti_slingshot(), ti_mst(), ti_slice(), ti_pcreode())
)

STDOUT
Running singularity exec 'docker://dynverse/ti_slingshot:v1.0.3' echo hi

STDERR
Error in processx::run("singularity", c("exec", paste0("docker://", container_id),  : 
  System command error
Calls: <Anonymous> ... create_ti_method_container -> <Anonymous> -> <Anonymous>
Execution halted

$ singularity --version
singularity version 3.3.0-1.el7

Executing 'projected_paga' on '20190409_063127__data_wrapper__ygGdphzfxh'
With parameters: list(n_neighbors = 15L, n_comps = 50L, n_dcs = 15L, resolution = 1L,     embedding_type = "fa", connectivity_cutoff = 0.05),
inputs: counts, and
priors : 
Input saved to /tmp/RtmpuyJ9Xp/file2a3f56e8a7d33/ti
Running /opt/software/singularity-3.1/bin/singularity run --pwd /ti/workspace \
  -B \
  '/tmp/RtmpuyJ9Xp/file2a3f56e8a7d33/ti:/ti,/tmp/RtmpuyJ9Xp/file2a3f514c36879/tmp:/tmp2' \
  'docker://dynverse/ti_projected_paga:v0.9.9.01' --dataset /ti/input.h5 \
  --output /ti/output.h5
WARNING: Could not set container working directory /ti/workspace: chdir /ti/workspace: no such file or directory
Traceback (most recent call last):
  File "/code/run.py", line 3, in <module>
    import dynclipy
  File "/usr/local/lib/python3.7/site-packages/dynclipy/__init__.py", line 3, in <module>
    from rpy2.robjects import pandas2ri
  File "/usr/local/lib/python3.7/site-packages/rpy2/robjects/pandas2ri.py", line 13, in <module>
    from pandas.core.frame import DataFrame as PandasDataFrame
  File "/home/wueflo00/.local/lib/python3.7/site-packages/pandas/__init__.py", line 19, in <module>
    "Missing required dependencies {0}".format(missing_dependencies))
ImportError: Missing required dependencies ['numpy']
Error: Error during trajectory inference 
WARNING: Could not set container working directory /ti/workspace: chdir /ti/workspace: no such file or directory
Traceback (most recent call last):
  File "/code/run.py", line 3, in <module>
    import dynclipy
  File "/usr/local/lib/python3.7/site-packages/dynclipy/__init__.py", line 3, in <module>
    from rpy2.robjects import pandas2ri
  File "/usr/local/lib/python3.7/site-packages/rpy2/robjects/pandas2ri.py", line 13, in <module>
    from pandas.core.frame import DataFrame as PandasDataFrame
  File "/home/wueflo00/.local/lib/python3.7/site-packages/pandas/__init__.py", line 19, in <module>
    "Missing required dependencies {0}".format(missing_dependencies))
ImportError: Missing required dependencies ['numpy']

> library(dynwrap)
> assayNames(sce)
[1] "counts"    "logcounts"
> dataset <- wrap_expression(counts = counts(sce),
                             +   expression =logcounts(sce)
                             + )
> model <- infer_trajectory(dataset,"slingshot")
Loading required namespace: dynmethods
Using default tag: latest
latest: Pulling from dynverse/ti_slingshot
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Digest: sha256:9408fbc09ce683f658344fcda7c2590928f4ff577098123d883c7039f324e5c5
Status: Downloaded newer image for dynverse/ti_slingshot:latest
Error traceback:
  1: 
  Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:
  
  filter, lag

The following objects are masked from ‘package:base’:
  
  intersect, setdiff, setequal, union


Attaching package: ‘purrr’

The following object is masked from ‘package:jsonlite’:
  
  flatten

Warning messages:
  1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE 
Killed

Error: $ operator is invalid for atomic vectors
In addition: Warning message:
  In babelwhale::get_label(container_id, "version") : 
  
  Error: No such image: dynverse/ti_slingshot

library(Seurat)
library(dyno)
library(Matrix)
library(dplyr)

seu.data <- Read10X(data.dir = path)
seu<-CreateSeuratObject(seu.data, min.cells = 2,min.features = 200)
seuNorm <- NormalizeData(object = seu, normalization.method = "LogNormalize", scale.factor = 10000)

dataset <-wrap_expression(id         = "MyData",
                          expression = t(seuNorm@assays[[1]]@data),
                          counts     = t(seuNorm@assays[[1]]@counts) )

guidelines <- guidelines_shiny(dataset)
methods_selected <- guidelines$methods_selected[1] 

dataset <- add_prior_information(
  dataset,
  start_id = "AAACCTGAGAGGTTAT" 
)

model <- infer_trajectory(dataset, methods_selected,  verbose = TRUE)

v0.9.9.04: Pulling from dynverse/ti_paga_tree
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Digest: sha256:18b8a4745e2f1d1e655a021f5949441b46dcaf32d8edbcb149650b5137ebc250
Status: Downloaded newer image for dynverse/ti_paga_tree:v0.9.9.04
Executing 'paga_tree' on 'MyData'
With parameters: list(n_neighbors = 15L, n_comps = 50L, n_dcs = 15L, resolution = 1L,     embedding_type = "fa"),
inputs: counts, and
priors : start_id
Loading required namespace: hdf5r
Input saved to D:\Users\sandra.wiedenmann\AppData\Local\Temp\Rtmp6hdAbw\file3f782c6a2b54/ti
Running method using babelwhale
Running "C:\PROGRA~1\Docker\Docker\RESOUR~1\bin\docker.exe" run --name 20190812_125834__container__jby8fcpVMu -e \
  "TMPDIR=/tmp2" --workdir /ti/workspace -v \
  "/d/Users/sandra.wiedenmann/AppData/Local/Temp/Rtmp6hdAbw/file3f782c6a2b54/ti:/ti" -v \
  "/d/Users/sandra.wiedenmann/AppData/Local/Temp/Rtmp6hdAbw/file3f78189f64f5/tmp:/tmp2" \
  "dynverse/ti_paga_tree:v0.9.9.04" --dataset /ti/input.h5 --output /ti/output.h5 --use_priors all
|

R version 3.6.0 (2019-04-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252    LC_MONETARY=German_Germany.1252
[4] LC_NUMERIC=C                    LC_TIME=German_Germany.1252    

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

other attached packages:
 [1] shiny_1.3.2           dplyr_0.8.3           Matrix_1.2-17         dyno_0.1.1            dynwrap_1.1.3        
 [6] dynplot_1.0.1         dynmethods_1.0.2      dynguidelines_1.0.0   dynfeature_1.0.0.9000 Seurat_3.0.1         

loaded via a namespace (and not attached):
  [1] backports_1.1.4     Hmisc_4.2-0         dyndimred_1.0.1     babelwhale_1.0.0    plyr_1.8.4         
  [6] igraph_1.2.4.1      lazyeval_0.2.2      sp_1.3-1            proxyC_0.1.5        splines_3.6.0      
 [11] listenv_0.7.0       ggplot2_3.2.0       digest_0.6.20       foreach_1.4.7       htmltools_0.3.6    
 [16] viridis_0.5.1       gdata_2.18.0        magrittr_1.5        checkmate_1.9.4     carrier_0.1.0      
 [21] cluster_2.0.8       ROCR_1.0-7          remotes_2.1.0       globals_0.12.4      readr_1.3.1        
 [26] RcppParallel_4.4.3  R.utils_2.9.0       dynutils_1.0.3      pdist_1.2           colorspace_1.4-1   
 [31] ggrepel_0.8.1       xfun_0.8            crayon_1.3.4        jsonlite_1.6        zeallot_0.1.0      
 [36] iterators_1.0.12    survival_2.44-1.1   zoo_1.8-6           ape_5.3             glue_1.3.1         
 [41] polyclip_1.10-0     gtable_0.3.0        future.apply_1.3.0  dynparam_1.0.0      scales_1.0.0       
 [46] bibtex_0.4.2        Rcpp_1.0.2          metap_1.1           viridisLite_0.3.0   xtable_1.8-4       
 [51] htmlTable_1.13.1    reticulate_1.13     bit_1.1-14          foreign_0.8-71      rsvd_1.0.2         
 [56] akima_0.6-2         SDMTools_1.1-221.1  Formula_1.2-3       tsne_0.1-3          htmlwidgets_1.3    
 [61] httr_1.4.1          FNN_1.1.3           gplots_3.0.1.1      RColorBrewer_1.1-2  acepack_1.4.1      
 [66] ica_1.0-2           pkgconfig_2.0.2     R.methodsS3_1.7.1   farver_1.1.0        nnet_7.3-12        
 [71] tidyselect_0.2.5    rlang_0.4.0         reshape2_1.4.3      later_0.8.0         munsell_0.5.0      
 [76] tools_3.6.0         cli_1.1.0           ranger_0.11.2       ggridges_0.5.1      stringr_1.4.0      
 [81] yaml_2.2.0          npsurv_0.4-0        bit64_0.9-7         processx_3.4.1      knitr_1.24         
 [86] fitdistrplus_1.0-14 tidygraph_1.1.2     caTools_1.17.1.2    purrr_0.3.2         RANN_2.6.1         
 [91] ggraph_1.0.2        pbapply_1.4-1       future_1.14.0       nlme_3.1-139        mime_0.7           
 [96] GA_3.2              R.oo_1.22.0         hdf5r_1.2.0         compiler_3.6.0      rstudioapi_0.10    
[101] plotly_4.9.0        png_0.1-7           testthat_2.2.1      lsei_1.2-0          tibble_2.1.3       
[106] tweenr_1.0.1        stringi_1.4.3       ps_1.3.0            lattice_0.20-38     shinyjs_1.0        
[111] vctrs_0.2.0         pillar_1.4.2        Rdpack_0.11-0       lmtest_0.9-37       data.table_1.12.2  
[116] cowplot_1.0.0       bitops_1.0-6        irlba_2.3.3         gbRd_0.4-11         patchwork_0.0.1    
[121] httpuv_1.5.1        R6_2.4.0            latticeExtra_0.6-28 promises_1.0.1      KernSmooth_2.23-15 
[126] gridExtra_2.3       codetools_0.2-16    MASS_7.3-51.4       gtools_3.8.1        assertthat_0.2.1   
[131] rje_1.9             shinyWidgets_0.4.8  sctransform_0.2.0   parallel_3.6.0      hms_0.5.0          
[136] grid_3.6.0          rpart_4.1-15        tidyr_0.8.3         Rtsne_0.15          ggforce_0.2.2      
[141] base64enc_0.1-3    

RawCount <- t(assay(sce, "logcounts"))
NormExprs <-  t(assay(sce, "norm_exprs"))

dataset <- wrap_expression(
  counts = RawCount,
  expression = NormExprs)

##Specify where to place singularity containers
singularity_config <- dynwrap::set_default_config(dynwrap::create_singularity_config(cache_dir = "/hpc/users/cohenp05/Comp1_Container/"))
babelwhale::set_default_config(singularity_config)

FATAL:   Unable to handle docker://alpine:3.7 uri: failed to get SHA of docker://alpine:3.7: pinging docker registry returned: Get https://registry-1.docker.io/v2/: dial tcp 52.22.67.152:443: connect: network is unreachable

R version 3.5.3 (2019-03-11)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /hpc/packages/minerva-centos7/intel/parallel_studio_xe_2019/compilers_and_libraries_2019.0.117/linux/mkl/lib/intel64_lin/libmkl_gf_lp64.so

locale:
[1] C

attached base packages:
 [1] splines   stats4    parallel  stats     graphics  grDevices utils    
 [8] datasets  methods   base     

other attached packages:
 [1] rlist_0.4.6.1       forcats_0.4.0       stringr_1.4.0      
 [4] purrr_0.3.2         readr_1.3.1         tidyr_0.8.3        
 [7] tibble_2.1.1        tidyverse_1.2.1     dyno_0.1.1         
[10] dynwrap_1.1.3       dynplot_1.0.1       dynmethods_1.0.4   
[13] dynguidelines_1.0.0 dynfeature_1.0.0    RColorBrewer_1.1-2 
[16] data.table_1.12.2   monocle_2.10.1      DDRTree_0.1.5      
[19] irlba_2.3.3         VGAM_1.1-1          Biobase_2.42.0     
[22] BiocGenerics_0.28.0 Matrix_1.2-15       gridExtra_2.3      
[25] Seurat_3.0.2        dplyr_0.8.1         plyr_1.8.4         
[28] cowplot_0.9.4       ggplot2_3.1.1      

loaded via a namespace (and not attached):
  [1] reticulate_1.12       R.utils_2.8.0         tidyselect_0.2.5     
  [4] htmlwidgets_1.3       grid_3.5.3            combinat_0.0-8       
  [7] ranger_0.11.2         docopt_0.6.1          Rtsne_0.15           
 [10] munsell_0.5.0         codetools_0.2-16      ica_1.0-2            
 [13] future_1.13.0         withr_2.1.2           colorspace_1.4-1     
 [16] fastICA_1.2-1         knitr_1.23            rstudioapi_0.10      
 [19] ROCR_1.0-7            gbRd_0.4-11           listenv_0.7.0        
 [22] Rdpack_0.11-0         slam_0.1-45           polyclip_1.10-0      
 [25] farver_1.1.0          pheatmap_1.0.12       generics_0.0.2       
 [28] xfun_0.7              R6_2.4.0              GA_3.2               
 [31] rsvd_1.0.0            pdist_1.2             bitops_1.0-6         
 [34] assertthat_0.2.1      promises_1.0.1        SDMTools_1.1-221.1   
 [37] scales_1.0.0          ggraph_1.0.2          nnet_7.3-12          
 [40] gtable_0.3.0          babelwhale_0.0.0.9000 npsurv_0.4-0         
 [43] globals_0.12.4        processx_3.3.1        tidygraph_1.1.2      
 [46] rlang_0.3.4           lazyeval_0.2.2        acepack_1.4.1        
 [49] broom_0.5.2           checkmate_1.9.3       yaml_2.2.0           
 [52] reshape2_1.4.3        modelr_0.1.4          backports_1.1.4      
 [55] httpuv_1.5.1          Hmisc_4.2-0           tools_3.5.3          
 [58] gplots_3.0.1.1        ggridges_0.5.1        Rcpp_1.0.1           
 [61] base64enc_0.1-3       densityClust_0.3      ps_1.3.0             
 [64] rpart_4.1-15          pbapply_1.4-0         viridis_0.5.1        
 [67] dynparam_1.0.0        zoo_1.8-5             haven_2.1.0          
 [70] ggrepel_0.8.1         cluster_2.0.7-1       magrittr_1.5         
 [73] carrier_0.1.0         lmtest_0.9-37         RANN_2.6.1           
 [76] fitdistrplus_1.0-14   matrixStats_0.54.0    hms_0.4.2            
 [79] patchwork_0.0.1       lsei_1.2-0            mime_0.6             
 [82] xtable_1.8-4          readxl_1.3.1          sparsesvd_0.1-4      
 [85] HSMMSingleCell_1.2.0  testthat_2.1.1        compiler_3.5.3       
 [88] KernSmooth_2.23-15    crayon_1.3.4          rje_1.9              
 [91] R.oo_1.22.0           htmltools_0.3.6       proxyC_0.1.4         
 [94] later_0.8.0           Formula_1.2-3         RcppParallel_4.4.2   
 [97] lubridate_1.7.4       tweenr_1.0.1          MASS_7.3-51.1        
[100] cli_1.1.0             R.methodsS3_1.7.1     gdata_2.18.0         
[103] metap_1.1             igraph_1.2.4.1        pkgconfig_2.0.2      
[106] foreign_0.8-71        plotly_4.9.0          xml2_1.2.0           
[109] foreach_1.4.4         dynutils_1.0.3        rvest_0.3.4          
[112] bibtex_0.4.2          digest_0.6.19         dyndimred_1.0.1      
[115] sctransform_0.2.0     tsne_0.1-3            cellranger_1.1.0     
[118] htmlTable_1.13.1      shiny_1.3.2           gtools_3.8.1         
[121] nlme_3.1-137          jsonlite_1.6          viridisLite_0.3.0    
[124] limma_3.38.3          pillar_1.4.0          lattice_0.20-38      
[127] httr_1.4.0            survival_2.44-1.1     glue_1.3.1           
[130] remotes_2.0.4         qlcMatrix_0.9.7       FNN_1.1.3            
[133] png_0.1-7             iterators_1.0.10      ggforce_0.2.2        
[136] stringi_1.4.3         latticeExtra_0.6-28   caTools_1.17.1.2     
[139] future.apply_1.2.0    ape_5.3

Error: --dataset should contain a pathname of a .loom or .h5 file. Add a '-h' flag for help.
Execution halted

...
Downloading GitHub repo dynverse/dyneval@master
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
* installing *source* package ‘dyneval’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded
* DONE (dyneval)
Downloading GitHub repo dynverse/dynwrap@devel
Skipping dynwrap, it is already being installed
Error in vapply(remotes, install_remote, ..., FUN.VALUE = character(1)) :
  values must be type 'character',
 but FUN(X[[2]]) result is type 'logical'
Calls: <Anonymous> ... update -> update.package_deps -> install_remotes -> vapply
Execution halted
...

✔ Singularity is installed
✔ Singularity is at correct version (>=3.0): 3.3.0-1 is installed
✔ Singularity can pull and run a container from Dockerhub
✔ Singularity can mount temporary volumes
✔ Singularity test successful ------------------------------------------------------------
[1] TRUE

Got permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Get http://%2Fvar%2Frun%2Fdocker.sock/v1.40/version: dial unix /var/run/docker.sock: connect: permission denied
Error in processx::run("docker", c("images", paste0("--format=", format),  : 
  System command error

dataset_file <- c("real/gold/stimulated-dendritic-cells-LPS_shalek/dataset.rds")

## Import data
dataset <- read_rds(derived_file(dataset_file, "01-datasets"))

#c("slingshot", "monocle_ddrtree", "comp1", "paga_tree")
## Select Method
methods_selected <- "monocle_ddrtree" ## "paga_tree"
#methods_selected <- ti_monocle_ddrtree() ##  ti_paga_tree()

## Infer trajectory
trajectory <- infer_trajectory(dataset, methods_selected, verbose = TRUE)

Executing 'monocle_ddrtree' on 'real/gold/stimulated-dendritic-cells-LPS_shalek'
With parameters: list(reduction_method = "ICA", max_components = 2L, norm_method = "log",     auto_param_selection = TRUE, filter_features = TRUE, filter_features_mean_expression = 0.1),
inputs: counts, and
priors : 
Input saved to /tmp/RtmpCyjjsc/file88774270f8b5/ti
Running /usr/bin/docker run -e 'TMPDIR=/tmp2' --workdir /ti/workspace -v '/tmp/RtmpCyjjsc/file88774270f8b5/ti:/ti' -v \
  '/tmp/RtmpCyjjsc/file88772160a383/tmp:/tmp2' 'dynverse/ti_monocle_ddrtree:v0.9.9.01' --dataset /ti/input.h5 --output /ti/output.h5
Error in normalise(counts) : 
  trying to get slot "x" from an object of a basic class ("matrix") with no slots
Calls: <Anonymous> -> parse_dataset -> normalise
Execution halted
Error: Error during trajectory inference 
Error in normalise(counts) : 
  trying to get slot "x" from an object of a basic class ("matrix") with no slots
Calls: <Anonymous> -> parse_dataset -> normalise
Execution halted

Executing 'paga_tree' on 'real/gold/stimulated-dendritic-cells-LPS_shalek'
With parameters: list(n_neighbors = 15L, n_comps = 50L, n_dcs = 15L, resolution = 1L,     embedding_type = "fa"),
inputs: counts, and
priors : start_id
Input saved to /tmp/RtmpCyjjsc/file887759e3f4e5/ti
Running /usr/bin/docker run -e 'TMPDIR=/tmp2' --workdir /ti/workspace -v '/tmp/RtmpCyjjsc/file887759e3f4e5/ti:/ti' -v \
  '/tmp/RtmpCyjjsc/file88773e675320/tmp:/tmp2' 'dynverse/ti_paga_tree:v0.9.9.01' --dataset /ti/input.h5 --output /ti/output.h5
R[write to console]: Error in normalise(counts) : 
  trying to get slot "x" from an object of a basic class ("matrix") with no slots
Calls: <Anonymous> ... <Anonymous> -> <Anonymous> -> parse_dataset -> normalise

Traceback (most recent call last):
  File "/code/run.py", line 22, in <module>
    task = dynclipy.main()
  File "/usr/local/lib/python3.7/site-packages/dynclipy/read.py", line 123, in main
    """)
  File "/usr/local/lib/python3.7/site-packages/rpy2/robjects/__init__.py", line 389, in __call__
    res = self.eval(p)
  File "/usr/local/lib/python3.7/site-packages/rpy2/robjects/functions.py", line 192, in __call__
    .__call__(*args, **kwargs))
  File "/usr/local/lib/python3.7/site-packages/rpy2/robjects/functions.py", line 121, in __call__
    res = super(Function, self).__call__(*new_args, **new_kwargs)
  File "/usr/local/lib/python3.7/site-packages/rpy2/rinterface_lib/conversion.py", line 28, in _
    cdata = function(*args, **kwargs)
  File "/usr/local/lib/python3.7/site-packages/rpy2/rinterface.py", line 773, in __call__
    raise embedded.RRuntimeError(_rinterface._geterrmessage())
rpy2.rinterface_lib.embedded.RRuntimeError: Error in normalise(counts) : 
  trying to get slot "x" from an object of a basic class ("matrix") with no slots
Calls: <Anonymous> ... <Anonymous> -> <Anonymous> -> parse_dataset -> normalise

Error: Error during trajectory inference 
R[write to console]: Error in normalise(counts) : 
  trying to get slot "x" from an object of a basic class ("matrix") with no slots
Calls: <Anonymous> ... <Anonymous> -> <Anonymous> -> parse_dataset -> normalise

Traceback (most recent call last):
  File "/code/run.py", line 22, in <module>
    task = dynclipy.main()
  File "/usr/local/lib/python3.7/site-packages/dynclipy/read.py", line 123, in main
    """)
  File "/usr/local/lib/python3.7/site-packages/rpy2/robjects/__init__.py", line 389, in __call__
    res = self.eval(p)
  File "/usr/local/lib/python3.7/site-packages/rpy2/robjects/functions.py", line 192, in __call__
    .__call__(*args, **kwargs))
  File "/usr/local/lib/python3.7/site-packages/rpy2/robjects/functions.py", line 121, in __call__
    res = super(Function, self).__call__(*new_args, **new_kwargs)
  File "/usr/local/lib/python3.7/site-packages/rpy2/rinterface_lib/conversion.py", line 28, in _
    cdata = function(*args, *

Error in normalise(counts) : 
  trying to get slot "x" from an object of a basic class ("matrix") with no slots
Calls: <Anonymous> ... <Anonymous> -> <Anonymous> -> parse_dataset -> normalise

> library(dyno)
> model <- infer_trajectory(example_dataset, ti_comp1(), verbose = T)
Executing 'comp1' on 'example'
With parameters: list(dimred = "pca", ndim = 2L, component = 1L),
inputs: expression, and
priors : 
Input saved to C:\Users\reismab\AppData\Local\Temp\RtmpOK0ZZ0\file19089056d27/ti
Running "C:\PROGRA~1\Docker\Docker\RESOUR~1\bin\docker.exe" run -e "TMPDIR=/tmp2" --workdir /ti/workspace -v \
  "/c/Users/reismab/AppData/Local/Temp/RtmpOK0ZZ0/file19089056d27/ti:/ti" -v \
  "/c/Users/reismab/AppData/Local/Temp/RtmpOK0ZZ0/file19083e865acc/tmp:/tmp2" "dynverse/ti_comp1:v0.9.9" --dataset \
  /ti/input.h5 --output /ti/output.h5
Loading required package: dynutils
Error: Error during trajectory inference 
HDF5-API Errors:
    error #000: C:\pkg\hdf5-1.8.14\src\H5Tnative.c in H5Tget_native_type(): line 119: cannot retrieve native type
        class: HDF5
        major: Invalid arguments to routine
        minor: Inappropriate type

    error #001: C:\pkg\hdf5-1.8.14\src\H5Tnative.c in H5T_get_native_type(): line 400: cannot get member value
        class: HDF5
        major: Invalid arguments to routine
        minor: Inappropriate type

    error #002: C:\pkg\hdf5-1.8.14\src\H5T.c in H5T_convert(): line 4816: data type conversion failed
        class: HDF5
        major: Attribute
        minor: Unable to encode value

    error #003: C:\pkg\hdf5-1.8.14\src\H5Tconv.c in H5T__conv_i_i(): line 3639: can't find property list for ID
        class: HDF5
        major: Object atom
        minor: Unable to find atom information (already closed?)

    error #004: C:\pkg\hdf5-1.8.14\src\H5Pint.c in H5P_object_verify(): line 3381: property list is no

> sessionInfo()
R version 3.5.3 (2019-03-11)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
[1] shiny_1.2.0         dyno_0.9.9          dynwrap_1.0.0       dynplot_1.0.0       dynmethods_1.0.0    dynguidelines_1.0.0
[7] dynfeature_1.0.0   

loaded via a namespace (and not attached):
  [1] colorspace_1.4-1      rprojroot_1.3-2       dynparam_1.0.0        htmlTable_1.13.1      base64enc_0.1-3      
  [6] fs_1.2.7              rstudioapi_0.10       rje_1.9               farver_1.1.0          remotes_2.0.2        
 [11] dynutils_1.0.2        bit64_0.9-7           ggrepel_0.8.0         ranger_0.11.2         codetools_0.2-16     
 [16] splines_3.5.3         knitr_1.22            polyclip_1.10-0       pkgload_1.0.2         Formula_1.2-3        
 [21] jsonlite_1.6          cluster_2.0.7-1       ggforce_0.2.1         readr_1.3.1           compiler_3.5.3       
 [26] backports_1.1.3       assertthat_0.2.1      Matrix_1.2-15         lazyeval_0.2.2        cli_1.1.0            
 [31] later_0.8.0           tweenr_1.0.1          acepack_1.4.1         htmltools_0.3.6       prettyunits_1.0.2    
 [36] tools_3.5.3           igraph_1.2.4          gtable_0.3.0          glue_1.3.1            reshape2_1.4.3       
 [41] dplyr_0.8.0.1         Rcpp_1.0.1            GA_3.2                iterators_1.0.10      ggraph_1.0.2         
 [46] xfun_0.6              stringr_1.4.0         ps_1.3.0              testthat_2.0.1        akima_0.6-2          
 [51] mime_0.6              devtools_2.0.1        MASS_7.3-51.1         scales_1.0.0          tidygraph_1.1.2      
 [56] babelwhale_0.0.0.9000 hms_0.4.2             promises_1.0.1        RColorBrewer_1.1-2    yaml_2.2.0           
 [61] curl_3.3              memoise_1.1.0         gridExtra_2.3         ggplot2_3.1.0         dyndimred_1.0.0      
 [66] rpart_4.1-13          latticeExtra_0.6-28   stringi_1.4.3         desc_1.2.0            foreach_1.4.4        
 [71] checkmate_1.9.1       shades_1.3.1          pkgbuild_1.0.3        rlang_0.3.3           pkgconfig_2.0.2      
 [76] lattice_0.20-38       purrr_0.3.2           patchwork_0.0.1       htmlwidgets_1.3       bit_1.1-14           
 [81] cowplot_0.9.4         pdist_1.2             processx_3.3.0        tidyselect_0.2.5      plyr_1.8.4           
 [86] magrittr_1.5          R6_2.4.0              Hmisc_4.2-0           pillar_1.3.1          foreign_0.8-71       
 [91] carrier_0.1.0         withr_2.1.2           sp_1.3-1              survival_2.43-3       nnet_7.3-12          
 [96] tibble_2.1.1          crayon_1.3.4          hdf5r_1.1.1           shinyWidgets_0.4.8    viridis_0.5.1        
[101] usethis_1.4.0         grid_3.5.3            data.table_1.12.0     callr_3.2.0           digest_0.6.18        
[106] xtable_1.8-3          tidyr_0.8.3           httpuv_1.5.0          munsell_0.5.0         viridisLite_0.3.0    
[111] shinyjs_1.0           sessioninfo_1.1.1  

> dynwrap::test_docker_installation(detailed = TRUE)
<U+2714> Docker is installed
<U+2714> Docker daemon is running
<U+2714> Docker is at correct version (>1.0): 1.39
<U+2714> Docker is in linux mode
<U+2714> Docker can pull images
<U+2714> Docker can run image
<U+2714> Docker can mount temporary volumes
<U+2714> Docker test successful -----------------------------------------------------------------
[1] TRUE

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> devtools::install_github('dynverse/dyno')
Error: HTTP error 403.
  API rate limit exceeded for 35.195.YY.XX. (But here's the good news: Authenticated requests get a higher rate lim
it. Check out the documentation for more details.)
  Rate limit remaining: 0/60
  Rate limit reset at: 2018-12-16 13:41:48 UTC
  To increase your GitHub API rate limit
  - Use `usethis::browse_github_pat()` to create a Personal Access Token.
  - Use `usethis::edit_r_environ()` and add the token as `GITHUB_PAT`.
> traceback()
8: stop(github_error(res))
7: github_DESCRIPTION(username = remote$username, repo = remote$repo, 
       subdir = remote$subdir, host = remote$host, ref = remote$ref, 
       pat = remote$auth_token %||% github_pat(), use_curl = use_curl)
6: remote_package_name.github_remote(remote)
5: remote_package_name(remote)
4: FUN(X[[i]], ...)
3: vapply(remotes, install_remote, ..., FUN.VALUE = character(1))
2: install_remotes(remotes, auth_token = auth_token, host = host, 
       dependencies = dependencies, upgrade = upgrade, force = force, 
       quiet = quiet, build = build, build_opts = build_opts, repos = repos, 
       type = type, ...)
1: devtools::install_github("dynverse/dyno")

#Annotate starting cells
start_cells = as.vector([email protected])
#Add prior information to dataset
add_prior_information(dataset = dataset_object, start_id = start_cells)
#Run model
model_PAGA <- infer_trajectory(dataset = dataset_object, method = methods_selected[2], verbose = T, give_priors = "start_id")

> 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

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 

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