Stuck when loading slingshot

[joschif]

Hi all,

I installed slingshot using the command BiocManager::install("slingshot") with
Bioconductor version 3.8 (BiocManager 1.30.4) and R 3.5.1 (2018-07-02). This seemed to work without issues. However, when loading slingshot with library(slingshot) nothing happens and R gets stuck without error messages or any chance to cancel the process without force quitting R. Any ideas?

Cheers,
Jonas

R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS  10.14.1

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/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  
[7] base     

loaded via a namespace (and not attached):
[1] compiler_3.5.1 tools_3.5.1    yaml_2.2.0 ```

[kstreet13]

Hi @AsTair ,

Thank you for the detailed report. Unfortunately, I am not able to replicate your issue, under nearly identical settings. It does take a couple seconds for the package to load and I get the following messages:

Loading required package: princurve
Warning message:
replacing previous import ‘SingleCellExperiment::weights’ by ‘stats::weights’ when loading ‘slingshot’ 

but it doesn't freeze up. I am also on Bioconductor version 3.8 and R 3.5.1. The only difference I see between our settings is that I am running a slightly older version of macOS (10.13.6). I will continue to look into this and thank you again for the report.

R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/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] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] slingshot_1.0.0      bigmemory_4.5.33     Biobase_2.42.0       BiocGenerics_0.28.0 
[5] princurve_2.1.3      BiocInstaller_1.32.1 scales_1.0.0         RColorBrewer_1.1-2  

loaded via a namespace (and not attached):
  [1] uuid_0.1-2                  copula_0.999-18             NMF_0.21.0                 
  [4] plyr_1.8.4                  igraph_1.2.2                lazyeval_0.2.1             
  ...
[139] class_7.3-14                shiny_1.2.0                 numDeriv_2016.8-1          
[142] clusterExperiment_2.2.0  

[joschif]

Hi @kstreet13,

thanks for looking into it. I haven't solved it yet, but when trying to install the package from source, I experience the same issue already during installation. In that case I get the following messages before R freezes:

Skipping 18 packages ahead of CRAN: Biobase, BiocGenerics, BiocParallel, clusterExperiment, DelayedArray, GenomeInfoDb, GenomeInfoDbData, GenomicRanges, HDF5Array, IRanges, limma, rhdf5, Rhdf5lib, S4Vectors, SingleCellExperiment, SummarizedExperiment, XVector, zlibbioc
✔  checking for file ‘/private/var/folders/fc/t6k_jht14qn_mb3cm73y_1j40000gn/T/Rtmp3aO4Fq/remotes1a3c47a864a8/kstreet13-slingshot-d57cbab/DESCRIPTION’ ...
─  preparing ‘slingshot’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  looking to see if a ‘data/datalist’ file should be added
─  building ‘slingshot_1.1.0.tar.gz’
   
* installing *source* package ‘slingshot’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘SingleCellExperiment::weights’ by ‘stats::weights’ when loading ‘slingshot’

[kstreet13]

Hey @AsTair ,

Ok, it looks like you're using the devel version of slingshot (v 1.1.0), which I've recently discovered has some issues. Have you tried the same thing with the release version (v 1.0.0, available here)?

[joschif]

Hi @kstreet13,

thanks for the hint, but installing v 1.0.0 from source causes the same issue.

[kstreet13]

Hey @AsTair ,

I recently changed things (in the latest version on Github) so that only the necessary functions from SingleCellExperiment are imported, rather than everything. This seems to have removed the warning you were getting about weights, so you may have more luck now.