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aertslab / RcisTarget

RcisTarget: Transcription factor binding motif enrichment
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R is down when I run "importRankings" function #11

Closed yishuiaoi closed 5 years ago

yishuiaoi commented 5 years ago

Hello. I am trying to go through the SCENIC tutorial process. I found that R is shutdown when I run "importRankings" function. I tested in the following code: just loading the RcisTarget package, and R was shutdown after I ran this function. Any suggestions on this? Thank you very much.

Here is my code:

library(RcisTarget) getwd() dbFile <- file.path(getwd(), "data", "RcisTarget", "mm9-500bp-upstream-7species.mc9nr.feather" ) importRankings(dbFile) sessionInfo()

Here is my session information:

R version 3.6.0 (2019-04-26) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 17763)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

other attached packages: [1] RcisTarget_1.4.0

loaded via a namespace (and not attached): [1] Rcpp_1.0.1 XVector_0.24.0
[3] GenomeInfoDb_1.20.0 compiler_3.6.0
[5] pillar_1.3.1 later_0.8.0
[7] zlibbioc_1.30.0 R.methodsS3_1.7.1
[9] R.utils_2.8.0 bitops_1.0-6
[11] tools_3.6.0 digest_0.6.18
[13] bit_1.1-14 lattice_0.20-38
[15] annotate_1.62.0 RSQLite_2.1.1
[17] memoise_1.1.0 tibble_2.1.1
[19] pkgconfig_2.0.2 rlang_0.3.4
[21] Matrix_1.2-17 graph_1.62.0
[23] DelayedArray_0.10.0 shiny_1.3.2
[25] DBI_1.0.0 rstudioapi_0.10
[27] parallel_3.6.0 AUCell_1.6.0
[29] GenomeInfoDbData_1.2.1 S4Vectors_0.22.0
[31] IRanges_2.18.0 hms_0.4.2
[33] grid_3.6.0 stats4_3.6.0
[35] bit64_0.9-7 GSEABase_1.46.0
[37] data.table_1.12.2 Biobase_2.44.0
[39] R6_2.4.0 AnnotationDbi_1.46.0
[41] BiocParallel_1.17.18 XML_3.98-1.19
[43] blob_1.1.1 feather_0.3.3
[45] magrittr_1.5 matrixStats_0.54.0
[47] GenomicRanges_1.36.0 promises_1.0.1
[49] htmltools_0.3.6 BiocGenerics_0.30.0
[51] SummarizedExperiment_1.14.0 mime_0.6
[53] xtable_1.8-4 httpuv_1.5.1
[55] RCurl_1.95-4.12 crayon_1.3.4
[57] R.oo_1.22.0

s-aibar commented 5 years ago

Dear @yishuiaoi ,

That error usually happens when the databases are incomplete/corrupt (e.g. by a failed download).

We recommended to download the databases is using zsync_curl (https://resources.aertslab.org/cistarget/help.html). Once you have the files, make sure the sha256sum match the reported ones (https://resources.aertslab.org/cistarget/databases/sha256sum.txt).

Please, let me know whether this helps!

yishuiaoi commented 5 years ago

Thank you! You are right. I changed a data set and it is good now. Thank you very much!