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,
Chris
> 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
locale:
[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
[9] LC_ADDRESS=C LC_TELEPHONE=C
LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=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) <[email protected]> Visiting Professor, University of
Sheffield and UDLA, Quito, Ecuador
I do some consultation work for the University of Roehampton
<[email protected]> and other places
but <[email protected]> remains my main Email address. I have a work web site
at:
https://www.psyctc.org/psyctc/
and a site I manage for CORE and CORE system trust at:
http://www.coresystemtrust.org.uk/
I have "semigrated" to France, see:
https://www.psyctc.org/pelerinage2016/semigrating-to-france/
https://www.psyctc.org/pelerinage2016/register-to-get-updates-from-pelerinage2016/
If you want an Emeeting, I am trying to keep them to Thursdays and my diary is
at:
https://www.psyctc.org/pelerinage2016/ceworkdiary/
Beware: French time, generally an hour ahead of UK.
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