Unable to load example .crb files in v1.3
Closed this issue · 2 comments
I am attempting to load the example .crb files provided in the Cerebro repo and getting an error
2020-10-26 16:24:15] Active tab: loadData
[2020-10-26 16:24:24] File to load: /var/folders/f4/g3fts2nd6dngs42nn5b00ppc0000gn/T//RtmpI20lgG/6780fae42d6f64fe913255e4/0.crb
Warning: Error in message: attempt to apply non-function
[No stack trace available]
Warning: Error in message: attempt to apply non-function
74: <Anonymous>
Warning: Error in message: attempt to apply non-function
108: <Anonymous>
Warning: Error in message: attempt to apply non-function
74: <Anonymous>
Warning: Error in message: attempt to apply non-function
104: <Anonymous>
Warning: Error in message: attempt to apply non-function
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Warning: Error in message: attempt to apply non-function
104: <Anonymous>
Warning: Error in message: attempt to apply non-function
104: <Anonymous>
Warning: Error in message: attempt to apply non-function
113: <Anonymous>
Warning: Error in message: attempt to apply non-function
113: <Anonymous>
Warning: Error in message: attempt to apply non-function
112: <Anonymous>
Warning: Error in message: attempt to apply non-function
113: <Anonymous>
Warning: Error in message: attempt to apply non-function
113: <Anonymous>
Warning: Error in message: attempt to apply non-function
113: <Anonymous>
This works however if I used v1.2
My session info:
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.5
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
Random number generation:
RNG: Mersenne-Twister
Normal: Inversion
Sample: Rounding
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 base
other attached packages:
[1] shiny_1.5.0 cerebroApp_1.3.0 BiocManager_1.30.10
loaded via a namespace (and not attached):
[1] backports_1.1.10 BiocFileCache_1.10.2 plyr_1.8.6 igraph_1.2.6 lazyeval_0.2.2
[6] GSEABase_1.48.0 shinydashboard_0.7.1 splines_3.6.1 crosstalk_1.1.0.1 listenv_0.8.0
[11] ggplot2_3.3.2 digest_0.6.27 htmltools_0.5.0 formattable_0.2.0.1 viridis_0.5.1
[16] fansi_0.4.1 magrittr_1.5 memoise_1.1.0 tensor_1.5 cluster_2.1.0
[21] ROCR_1.0-11 remotes_2.2.0 shinyFiles_0.8.0 globals_0.13.1 readr_1.4.0
[26] annotate_1.64.0 matrixStats_0.57.0 askpass_1.1 prettyunits_1.1.1 colorspace_1.4-1
[31] blob_1.2.1 rappdirs_0.3.1 ggrepel_0.8.2 xfun_0.18 dplyr_1.0.2
[36] callr_3.5.1 crayon_1.3.4 RCurl_1.98-1.2 jsonlite_1.7.1 graph_1.64.0
[41] spatstat.data_1.4-3 spatstat_1.64-1 zoo_1.8-8 survival_3.2-7 ape_5.4-1
[46] glue_1.4.2 polyclip_1.10-0 gtable_0.3.0 leiden_0.3.3 pkgbuild_1.1.0
[51] future.apply_1.6.0 BiocGenerics_0.32.0 abind_1.4-5 scales_1.1.1 msigdbr_7.2.1
[56] DBI_1.1.0 miniUI_0.1.1.1 Rcpp_1.0.5 viridisLite_0.3.0 xtable_1.8-4
[61] progress_1.2.2 tidytree_0.3.3 reticulate_1.18 rsvd_1.0.3 bit_4.0.4
[66] stats4_3.6.1 GSVA_1.34.0 DT_0.16 htmlwidgets_1.5.2 httr_1.4.2
[71] RColorBrewer_1.1-2 ellipsis_0.3.1 Seurat_3.2.2 ica_1.0-2 farver_2.0.3
[76] pkgconfig_2.0.3 XML_3.99-0.3 uwot_0.1.8 deldir_0.1-29 dbplyr_1.4.4
[81] labeling_0.4.2 tidyselect_1.1.0 rlang_0.4.8 reshape2_1.4.4 later_1.1.0.1
[86] AnnotationDbi_1.48.0 munsell_0.5.0 tools_3.6.1 cli_2.1.0 generics_0.0.2
[91] RSQLite_2.2.1 ggridges_0.5.2 evaluate_0.14 stringr_1.4.0 fastmap_1.0.1
[96] goftest_1.2-2 yaml_2.2.1 ggtree_2.0.4 knitr_1.30 processx_3.4.4
[101] bit64_4.0.5 fs_1.5.0 fitdistrplus_1.1-1 shinycssloaders_1.0.0 purrr_0.3.4
[106] RANN_2.6.1 pbapply_1.4-3 future_1.19.1 nlme_3.1-150 mime_0.9
[111] biomaRt_2.42.1 compiler_3.6.1 shinythemes_1.1.2 rstudioapi_0.11 png_0.1-7
[116] plotly_4.9.2.1 curl_4.3 spatstat.utils_1.17-0 treeio_1.10.0 tibble_3.0.4
[121] geneplotter_1.64.0 stringi_1.5.3 ps_1.4.0 lattice_0.20-41 Matrix_1.2-18
[126] shinyjs_2.0.0 vctrs_0.3.4 pillar_1.4.6 lifecycle_0.2.0 lmtest_0.9-38
[131] RcppAnnoy_0.0.16 data.table_1.13.2 cowplot_1.1.0 bitops_1.0-6 irlba_2.3.3
[136] patchwork_1.0.1 httpuv_1.5.4 qvalue_2.18.0 R6_2.4.1 promises_1.1.1
[141] KernSmooth_2.23-17 gridExtra_2.3 IRanges_2.20.2 codetools_0.2-16 colourpicker_1.1.0
[146] MASS_7.3-53 assertthat_0.2.1 openssl_1.4.3 rprojroot_1.3-2 shinyWidgets_0.5.4
[151] withr_2.3.0 sctransform_0.3.1 S4Vectors_0.24.4 mgcv_1.8-33 parallel_3.6.1
[156] hms_0.5.3 rpart_4.1-15 grid_3.6.1 tidyr_1.1.2 rmarkdown_2.5
[161] rvcheck_0.1.8 Rtsne_0.15 Biobase_2.46.0
Additionally, I'm wondering if I should be able to load an object directly after processing with Seurat, or if I need to pre-process into a cerebro object
Thank you!
Hi @alexjacobsCDS!
Unfortunately, I haven't found time yet to process the example data sets in the Cerebro repository with cerebroApp v1.3. Therefore, it is expected that they don't work with Cerebro v1.3. Moreover, due to reasons explained in the release notes of v1.3, I currently can't produce a standalone version of Cerebro v1.3.
Regarding your second question: Data must be exported with cerebroApp functions before loading it into Cerebro. This can be done either from a Seurat file or a SingleCellExperiment file, as explained in the vignettes on the cerebroApp website.
Best,
Roman
@romanhaa Thank you for your response! Closing this issue