Comments (5)
LuckyMD
commented on July 21, 2024
In case this helps... this was the sessionInfo() of my latest attempt:
R version 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin13.4.0 (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: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.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 stats4 tools stats graphics grDevices utils
[8] datasets methods base
other attached packages:
[1] RColorBrewer_1.1-2 slingshot_0.99.12
[3] princurve_2.0.4 scran_1.6.9
[5] SingleCellExperiment_1.0.0 SummarizedExperiment_1.8.1
[7] DelayedArray_0.4.1 matrixStats_0.54.0
[9] Biobase_2.38.0 GenomicRanges_1.30.3
[11] GenomeInfoDb_1.14.0 IRanges_2.12.0
[13] S4Vectors_0.16.0 BiocGenerics_0.24.0
[15] BiocParallel_1.12.0
loaded via a namespace (and not attached):
[1] uuid_0.1-2 NMF_0.21.0 plyr_1.8.4
[4] igraph_1.2.2 lazyeval_0.2.1 shinydashboard_0.7.1
[7] splines_3.4.3 crosstalk_1.0.0 rncl_0.8.3
[10] ggplot2_3.1.0 gridBase_0.4-7 scater_1.6.3
[13] digest_0.6.18 foreach_1.4.4 htmltools_0.3.6
[16] viridis_0.5.1 magrittr_1.5 memoise_1.1.0
[19] cluster_2.0.7-1 doParallel_1.0.14 limma_3.34.9
[22] prettyunits_1.0.2 colorspace_1.3-2 blob_1.1.1
[25] dplyr_0.7.7 jsonlite_1.5 crayon_1.3.4
[28] RCurl_1.95-4.11 tximport_1.6.0 bindr_0.1.1
[31] phylobase_0.8.4 zoo_1.8-4 iterators_1.0.10
[34] ape_5.2 glue_1.3.0 registry_0.5
[37] gtable_0.2.0 zlibbioc_1.24.0 XVector_0.18.0
[40] webshot_0.5.1 kernlab_0.9-27 prabclus_2.2-6
[43] DEoptimR_1.0-8 scales_1.0.0 mvtnorm_1.0-8
[46] DBI_1.0.0 edgeR_3.20.9 rngtools_1.3.1
[49] bibtex_0.4.2 miniUI_0.1.1.1 Rcpp_0.12.19
[52] viridisLite_0.3.0 xtable_1.8-3 progress_1.2.0
[55] bit_1.1-14 mclust_5.4.1 DT_0.4
[58] htmlwidgets_1.3 httr_1.3.1 FNN_1.1.2.1
[61] fpc_2.1-11.1 modeltools_0.2-22 pkgconfig_2.0.2
[64] XML_3.98-1.16 flexmix_2.3-14 nnet_7.3-12
[67] locfit_1.5-9.1 dynamicTreeCut_1.63-1 manipulateWidget_0.10.0
[70] howmany_0.3-1 tidyselect_0.2.5 rlang_0.3.0.1
[73] reshape2_1.4.3 later_0.7.5 AnnotationDbi_1.40.0
[76] munsell_0.5.0 RSQLite_2.1.1 ade4_1.7-13
[79] stringr_1.3.1 knitr_1.20 bit64_0.9-7
[82] robustbase_0.93-3 rgl_0.99.16 purrr_0.2.5
[85] dendextend_1.9.0 bindrcpp_0.2.2 nlme_3.1-137
[88] whisker_0.3-2 mime_0.6 xml2_1.2.0
[91] biomaRt_2.34.2 compiler_3.4.3 beeswarm_0.2.3
[94] tibble_1.4.2 statmod_1.4.30 RNeXML_2.2.0
[97] stringi_1.2.4 RSpectra_0.13-1 lattice_0.20-38
[100] trimcluster_0.1-2.1 Matrix_1.2-15 pillar_1.3.0
[103] data.table_1.11.8 bitops_1.0-6 httpuv_1.4.5
[106] R6_2.3.0 promises_1.0.1 gridExtra_2.3
[109] vipor_0.4.5 codetools_0.2-15 MASS_7.3-51.1
[112] assertthat_0.2.0 rhdf5_2.22.0 pkgmaker_0.27
[115] rjson_0.2.20 withr_2.1.2 GenomeInfoDbData_1.0.0
[118] locfdr_1.1-8 diptest_0.75-7 hms_0.4.2
[121] grid_3.4.3 tidyr_0.8.2 class_7.3-14
[124] clusterExperiment_1.4.0 shiny_1.2.0 ggbeeswarm_0.6.0
I am still running R 3.4.3 due to some other dependencies and changed the DESCRIPTION file to make this work.
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kstreet13
commented on July 21, 2024
Hi @LuckyMD ,
Thank you for the informative report! Unfortunately, I'm not sure what's going on here and I am unable to reproduce the error with the latest versions of slingshot (0.99.12) and princurve (2.1.3).
When I reverted to slingshot-0.99.8, I did get the same error message as you, but that line of code doesn't exist in the the latest version (it seems to have been changed in version 0.99.11 to reflect changes to the princurve package), so I'm not sure why it would show up in an error message. I wouldn't think that the older version of R would have any effect, though, as nothing in slingshot is specific to 3.5.
If it's not too much trouble, could you try re-installing slingshot-0.99.12 and let me know if the error persists?
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LuckyMD
commented on July 21, 2024
Hi,
Thanks for the quick response. I will reinstall the latest slingshot from github and reinstall princurve 2.1.3 to see if the error persists.
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LuckyMD
commented on July 21, 2024
Reinstalling seems to have fixed everything. Sorry I bothered you with this. It may have been a simple case of restarting the jupyter kernel (although the correct package versions were loaded...).
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kstreet13
commented on July 21, 2024
No worries! I agree that this was very strange, since the session info listed the latest version. I'll be keeping an eye out for what may have caused that.
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