[R] Cacheing of functions from libraries other than the base in Rmarkdown

Chris Evans chr|@ho|d @end|ng |rom p@yctc@org
Sat Sep 18 21:26:08 CEST 2021

This question may belong somewhere else, if so, please signpost me and accept apologies.

What is happening is that I have a large (for me, > 3k lines) Rmarkdown file with many R code blocks (no other code or 
engine is used) working on some large datasets.  I have some inline r like 

   There are `r n_distinct(tibDat$ID)` participants and `r nrow(tibDat)` rows of data.

What I am finding is that even if one knit has worked fine and I change something somewhere and knit again, the second
knit is often failing with an error like

   n_distinct(tibDat$ID) : could not find function "n_distinct"

This is not happening for functions like nrow() from base R and it mostly seems to happen to functions from the tidyverse.

I think what is happening is some sort of cache corruption presumably caused by the memory demands.  I am pretty sure I've
seen this before but a long time ago and dealt with it by deleting the files and cache folders created by the knit.  That
works now too but as knitting the whole file now takes over 20 minutes, I really don't want to have to do that.

I have found that replacing things with base functions fixes the problem every time, e.g. replacing `r n_distinct(tibDat$ID)`
with `r length(unique(tibDat$ID))` works fine.  The other workaround is to compute what you need for the inline 
computation at the end of the preceding code block, trivial e.g. at the end of the preceding code block:

n_distinct(tibDat$ID) -> tmpN

and then

  `r tmpN` 

that works fine so I have my workarounds but I guess I have three questions:

1) do others see this?
2) is there some setting that might, assuming my guess about the cause is correct, increase some storage somewhere and avert this?
3) if it is a bug, where should I report it (as I'm not sure what is causing it!)?

Thanks in advance,


> sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3

 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8     LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8    LC_PAPER=en_GB.UTF-8       LC_NAME=C                 

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

other attached packages:
 [1] boot_1.3-28         CECPfuns_0.0.0.9041 janitor_2.1.0       lubridate_1.7.10    forcats_0.5.1       stringr_1.4.0       dplyr_1.0.7         purrr_0.3.4         readr_2.0.1         tidyr_1.1.3         tibble_3.1.4       
[12] ggplot2_3.3.5       tidyverse_1.3.1     english_1.2-6       pander_0.6.4       

loaded via a namespace (and not attached):
 [1] fs_1.5.0            bit64_4.0.5         RColorBrewer_1.1-2  httr_1.4.2          tools_4.1.1         backports_1.2.1     utf8_1.2.2          R6_2.5.1            rpart_4.1-15        Hmisc_4.5-0         DBI_1.1.1          
[12] colorspace_2.0-2    nnet_7.3-16         withr_2.4.2         tidyselect_1.1.1    gridExtra_2.3       bit_4.0.4           compiler_4.1.1      cli_3.0.1           rvest_1.0.1         htmlTable_2.2.1     xml2_1.3.2         
[23] labeling_0.4.2      scales_1.1.1        checkmate_2.0.0     corrr_0.4.3         odbc_1.3.2          digest_0.6.27       readODS_1.7.0       foreign_0.8-81      rmarkdown_2.11      base64enc_0.1-3     jpeg_0.1-9         
[34] pkgconfig_2.0.3     htmltools_0.5.2     dbplyr_2.1.1        fastmap_1.1.0       RJDBC_0.2-8         htmlwidgets_1.5.4   rlang_0.4.11        readxl_1.3.1        rstudioapi_0.13     farver_2.1.0        generics_0.1.0     
[45] jsonlite_1.7.2      magrittr_2.0.1      Formula_1.2-4       Matrix_1.3-4        Rcpp_1.0.7          munsell_0.5.0       fansi_0.5.0         lifecycle_1.0.0     stringi_1.7.4       yaml_2.2.1          snakecase_0.11.0   
[56] grid_4.1.1          blob_1.2.2          crayon_1.4.1        lattice_0.20-44     haven_2.4.3         splines_4.1.1       hms_1.1.0           knitr_1.34          pillar_1.6.2        reprex_2.0.1        glue_1.4.2         
[67] evaluate_0.14       latticeExtra_0.6-29 data.table_1.14.0   modelr_0.1.8        png_0.1-7           vctrs_0.3.8         tzdb_0.1.2          psy_1.1             cellranger_1.1.0    gtable_0.3.0        assertthat_0.2.1   
[78] xfun_0.26           broom_0.7.9         rsconnect_0.8.24    viridisLite_0.4.0   survival_3.2-13     rJava_1.0-4         cluster_2.1.2       ellipsis_0.3.2    

Chris Evans (he/him) <chris using psyctc.org> Visiting Professor, University of Sheffield and UDLA, Quito, Ecuador
I do some consultation work for the University of Roehampton <chris.evans using roehampton.ac.uk> and other places
but <chris using psyctc.org> remains my main Email address.  I have a work web site at:
and a site I manage for CORE and CORE system trust at:
I have "semigrated" to France, see: 

If you want an Emeeting, I am trying to keep them to Thursdays and my diary is at:
Beware: French time, generally an hour ahead of UK.

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