restarting interrupted promise evaluation error

[rfarouni]

Hi,

I keep getting this error when I try to read an csv file using the read_csv() function called within a R package that I am making. The same code runs fine when I run it as a script outside the package. Also when I use the read.csv() instead, I get no such error. When I debugged the function, it seems to me that the problem might be connected to some kind of "promise already under evaluation error". This discussion seems to hint at the solution but I am not sure how to go about solving it

The code

  csv2 <- "/home/rick/Documents/AltreDataRepo/DNaseEncode.csv"
  csvfile <- read_csv(
    csv2,
    col_types = cols_only(
      datapath  = col_character(),
      bamfiles  = col_character(),
      peakfiles = col_character(),
      sample    = col_character(),
      replicate = col_character()
    )
  )

The error

Error in date_names_lang(date_names) : 
  cannot open file '~/R/x86_64-pc-linux-gnu-library/3.3/readr/R/sysdata.rdb': No such file or directory
In addition: Warning message:
In date_names_lang(date_names) : restarting interrupted promise evaluation

Stack trace (innermost first):
    87: date_names_lang
    86: locale
    85: default_locale
    84: guess_header_
    83: guess_header
    82: col_spec_standardise
    81: read_delimited
    80: read_csv

Session info

R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 15.10

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

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] readr_0.2.2          shinyFiles_0.6.0     rmarkdown_0.9.6      shinydashboard_0.5.1 shiny_0.13.2         ALTRE_0.99.0         GenomicRanges_1.24.1
 [8] GenomeInfoDb_1.8.1   IRanges_2.6.0        S4Vectors_0.10.1     BiocGenerics_0.18.0 

loaded via a namespace (and not attached):
 [1] Biobase_2.32.0                httr_1.1.0                    tidyr_0.4.1                   jsonlite_0.9.21               viridisLite_0.1.3            
 [6] AnnotationHub_2.4.2           splines_3.3.0                 Formula_1.2-1                 assertthat_0.1                interactiveDisplayBase_1.10.3
[11] TTR_0.23-1                    latticeExtra_0.6-28           BSgenome_1.40.0               Rsamtools_1.24.0              yaml_2.1.13                  
[16] RSQLite_1.0.0                 lattice_0.20-33               biovizBase_1.20.0             rlist_0.4.6.1                 chron_2.3-47                 
[21] digest_0.6.9                  RColorBrewer_1.1-2            XVector_0.12.0                colorspace_1.2-6              htmltools_0.3.5              
[26] httpuv_1.3.3                  Matrix_1.2-6                  plyr_1.8.4                    XML_3.98-1.4                  biomaRt_2.28.0               
[31] zlibbioc_1.18.0               purrr_0.2.1                   xtable_1.8-2                  d3vennR_0.1                   scales_0.4.0                 
[36] BiocParallel_1.6.2            EnsDb.Hsapiens.v75_0.99.12    ggplot2_2.1.0                 SummarizedExperiment_1.2.2    GenomicFeatures_1.24.2       
[41] nnet_7.3-12                   Gviz_1.16.1                   quantmod_0.4-5                RJSONIO_1.3-0                 survival_2.39-4              
[46] magrittr_1.5                  mime_0.4                      xts_0.9-7                     foreign_0.8-66                BiocInstaller_1.22.2         
[51] rsconnect_0.4.3               tools_3.3.0                   data.table_1.9.6              highcharter_0.3.0             matrixStats_0.50.2           
[56] stringr_1.0.0                 munsell_0.4.3                 cluster_2.0.4                 AnnotationDbi_1.34.3          ensembldb_1.4.6              
[61] Biostrings_2.40.2             grid_3.3.0                    RCurl_1.95-4.8                dichromat_2.0-0               VariantAnnotation_1.18.1     
[66] htmlwidgets_0.6               igraph_1.0.1                  bitops_1.0-6                  gtable_0.2.0                  DBI_0.4-1                    
[71] markdown_0.7.7                R6_2.1.2                      gridExtra_2.2.1               GenomicAlignments_1.8.1       zoo_1.7-13                   
[76] dplyr_0.4.3                   rtracklayer_1.32.0            Hmisc_3.17-4                  stringi_1.1.1                 Rcpp_0.12.5                  
[81] rpart_4.1-10                  acepack_1.3-3.3    

[hadley]

Can you please provide a reproducible example?

[hadley]

We've got no idea what might cause this. I'd recommend restarting R and reinstalling readr.

[rfarouni]

The error disappeared when I required functions from other packages to be loaded using the double colon. I think the error could also be the result of having the embedded Shiny app in my package load/attach certain package into the Shiny global namespace, which could have somehow interacted with other packages loaded by my package. Thanks

[fang19911030]

When i try to use TCGAbiolinks, i have the same problem about this package.

[chenyuqing]

@fang19911030 me too, how do you deal with it ???

[fang19911030]

Don‘t use TCGAbiolinks in Rstudio，the error will not happen. But i don't know the reason for that’