Comments (5)
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
from slingshot.
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’
from slingshot.
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)?
from slingshot.
Hi @kstreet13,
thanks for the hint, but installing v 1.0.0 from source causes the same issue.
from slingshot.
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.
from slingshot.
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