Ah, I completely agree, I should have said! Definitely interested to hear from others here though.
I cannot say how much I have learned here over a now rather frightening length of time: hm, at least 16 years to judge from the oldest Email I've kept! Ouch, getting old. I've put a plea about polymode and Rmd to the ESS help list as equipping my Emacs/ESS to knit whole Rmd files may give me an alternative and a bit more information. Thanks Bert (and all for > 16 years of knowledge and occasional high drama here!) Chris ----- Original Message ----- > From: "Bert Gunter" <bgunter.4...@gmail.com> > To: "Chris Evans" <chrish...@psyctc.org> > Cc: "R-help" <R-help@r-project.org> > Sent: Saturday, 18 September, 2021 22:01:25 > Subject: Re: [R] Cacheing of functions from libraries other than the base in > Rmarkdown > I think you should post on the RStudio help forums. They have specific areas > to > ask for help on their stuff, at least for some of it. You may wish to wait a > bit before doing so, though, just to see if someone here responds. > Bert > On Sat, Sep 18, 2021, 12:26 PM Chris Evans < [ mailto:chrish...@psyctc.org | > chrish...@psyctc.org ] > wrote: >> 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) < [ mailto:ch...@psyctc.org | ch...@psyctc.org ] > >> Visiting >> Professor, University of Sheffield and UDLA, Quito, Ecuador >> I do some consultation work for the University of Roehampton < [ >> mailto:chris.ev...@roehampton.ac.uk | chris.ev...@roehampton.ac.uk ] > and >> other places >> but < [ mailto:ch...@psyctc.org | ch...@psyctc.org ] > remains my main Email >> address. I have a work web site at: >> [ https://www.psyctc.org/psyctc/ | https://www.psyctc.org/psyctc/ ] >> and a site I manage for CORE and CORE system trust at: >> [ http://www.coresystemtrust.org.uk/ | http://www.coresystemtrust.org.uk/ ] >> I have "semigrated" to France, see: >> [ https://www.psyctc.org/pelerinage2016/semigrating-to-france/ | >> https://www.psyctc.org/pelerinage2016/semigrating-to-france/ ] >> [ >> https://www.psyctc.org/pelerinage2016/register-to-get-updates-from-pelerinage2016/ >> | >> 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/ | >> https://www.psyctc.org/pelerinage2016/ceworkdiary/ ] >> Beware: French time, generally an hour ahead of UK. >> ______________________________________________ >> [ mailto:R-help@r-project.org | R-help@r-project.org ] mailing list -- To >> UNSUBSCRIBE and more, see >> [ https://stat.ethz.ch/mailman/listinfo/r-help | >> https://stat.ethz.ch/mailman/listinfo/r-help ] >> PLEASE do read the posting guide [ >> http://www.r-project.org/posting-guide.html | >> http://www.R-project.org/posting-guide.html ] >> and provide commented, minimal, self-contained, reproducible code. -- Chris Evans (he/him) <ch...@psyctc.org> Visiting Professor, University of Sheffield and UDLA, Quito, Ecuador I do some consultation work for the University of Roehampton <chris.ev...@roehampton.ac.uk> and other places but <ch...@psyctc.org> 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. ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
