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ge11232002 / TFBSTools

Software Package for Transcription Factor Binding Site (TFBS) Analysis
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Error in .validate_Vector_vertical_slots(x) #26

Closed Zepeng-Mu closed 3 years ago

Zepeng-Mu commented 3 years ago

Hi, I am encountering this error message with R4.0 (no error in R3.6):

library(JASPAR2016)
library(TFBSTools)
opts <- list("species" = 9606, "all_versions" = F, "matrixtype" = "PFM")
motif2016 <- getMatrixSet(JASPAR2016, opts)

gives me:

Error in .validate_Vector_vertical_slots(x) : 
  could not find function ".validate_Vector_vertical_slots"

Session info:

R version 4.0.0 (2020-04-24)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)

Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] TFBSTools_1.28.0     JASPAR2016_1.18.0    ComplexHeatmap_2.7.3 edgeR_3.32.0        
 [5] limma_3.46.0         ggrepel_0.8.2        data.table_1.13.4    forcats_0.5.0       
 [9] stringr_1.4.0        dplyr_1.0.2          purrr_0.3.4          readr_1.3.1         
[13] tidyr_1.0.3          tibble_3.0.1         ggplot2_3.3.1        tidyverse_1.3.0     

loaded via a namespace (and not attached):
  [1] colorspace_2.0-0            rjson_0.2.20                ellipsis_0.3.1             
  [4] circlize_0.4.11             XVector_0.30.0              GenomicRanges_1.42.0       
  [7] GlobalOptions_0.1.2         fs_1.5.0                    clue_0.3-58                
 [10] rstudioapi_0.13             farver_2.0.3                bit64_0.9-7                
 [13] AnnotationDbi_1.51.0        fansi_0.4.1                 lubridate_1.7.8            
 [16] xml2_1.3.2                  R.methodsS3_1.8.1           jsonlite_1.7.2             
 [19] Rsamtools_2.5.0             Cairo_1.5-12.2              seqLogo_1.56.0             
 [22] annotate_1.67.0             broom_0.5.6                 GO.db_3.11.4               
 [25] cluster_2.1.0               dbplyr_1.4.3                png_0.1-7                  
 [28] R.oo_1.23.0                 BiocManager_1.30.10         compiler_4.0.0             
 [31] httr_1.4.2                  backports_1.2.1             assertthat_0.2.1           
 [34] Matrix_1.3-0                cli_2.0.2                   tools_4.0.0                
 [37] gtable_0.3.0                glue_1.4.2                  TFMPvalue_0.0.8            
 [40] GenomeInfoDbData_1.2.4      reshape2_1.4.4              tinytex_0.22               
 [43] Rcpp_1.0.5                  Biobase_2.50.0              cellranger_1.1.0           
 [46] vctrs_0.3.5                 Biostrings_2.58.0           nlme_3.1-151               
 [49] rtracklayer_1.50.0          xfun_0.19                   CNEr_1.26.0                
 [52] rvest_0.3.5                 lifecycle_0.2.0             poweRlaw_0.70.6            
 [55] gtools_3.8.2                XML_3.99-0.3                zlibbioc_1.35.0            
 [58] scales_1.1.1                BSgenome_1.57.0             hms_0.5.3                  
 [61] MatrixGenerics_1.2.0        parallel_4.0.0              SummarizedExperiment_1.20.0
 [64] RColorBrewer_1.1-2          memoise_1.1.0               stringi_1.5.3              
 [67] RSQLite_2.2.0               S4Vectors_0.28.1            caTools_1.18.0             
 [70] BiocGenerics_0.36.0         BiocParallel_1.24.1         shape_1.4.5                
 [73] GenomeInfoDb_1.25.0         rlang_0.4.9                 pkgconfig_2.0.3            
 [76] matrixStats_0.57.0          bitops_1.0-6                pracma_2.2.9               
 [79] lattice_0.20-41             GenomicAlignments_1.25.0    labeling_0.4.2             
 [82] bit_4.0.4                   tidyselect_1.1.0            plyr_1.8.6                 
 [85] magrittr_2.0.1              R6_2.5.0                    IRanges_2.24.1             
 [88] generics_0.1.0              DelayedArray_0.16.0         DBI_1.1.0                  
 [91] pillar_1.4.4                haven_2.2.0                 withr_2.3.0                
 [94] KEGGREST_1.30.1             RCurl_1.98-1.2              modelr_0.1.7               
 [97] crayon_1.3.4                GetoptLong_1.0.5            locfit_1.5-9.4             
[100] readxl_1.3.1                blob_1.2.1                  reprex_0.3.0               
[103] digest_0.6.27               xtable_1.8-4                R.utils_2.9.2              
[106] stats4_4.0.0                munsell_0.5.0               DirichletMultinomial_1.32.0
ge11232002 commented 3 years ago

I cannot reproduce your error. I think it's something specific to your machine. Those exampels are checked by Bioconductor's build system and the pakcage passes without any error. Perhaps try R 4.0.3.

Zepeng-Mu commented 3 years ago

It works in R 4.0.3, thanks!