Following from the unresolved closed topic.
I have an Rmd file that knits and renders uneventfully with the knit button when the R session is fresh, but if the code is run in the console the knit button becomes dysfunctional and knitting halts at a certain point through the document without any error or warning messages. The red stop sign just disappears and nothing happens. I've noted no problems with the Rstudio session whatsoever, everything functions fine, codes run in the console with the expected output and I can still use Rmarkdown::render in the console and get my pdf output.
Interestingly -similar to the closed but unresolved post- this project also contains a biggish data file (3.5 mb xlsx) with 22.5K rows. Below is a screenshot of my latest attempt with the knit button.
Below is the sessioninfo
R version 3.5.2 (2018-12-20)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 LTS
Matrix products: default
BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0
LAPACK: /usr/lib/atlas-base/atlas/liblapack.so.3.0
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8
[6] LC_MESSAGES=C.UTF-8 LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] broom_0.5.2 lme4_1.1-21 Matrix_1.2-15 zoo_1.8-5 lubridate_1.7.4 ggalluvial_0.9.1
[7] kableExtra_1.1.0 forcats_0.4.0 stringr_1.4.0 dplyr_0.8.0.1 purrr_0.3.2 readr_1.3.1
[13] tidyr_0.8.3 tibble_2.1.1 ggplot2_3.1.1 tidyverse_1.2.1 readxl_1.3.1
loaded via a namespace (and not attached):
[1] tidyselect_0.2.5 xfun_0.6 splines_3.5.2 haven_2.1.0 lattice_0.20-38 colorspace_1.4-1
[7] generics_0.0.2 htmltools_0.3.6 viridisLite_0.3.0 yaml_2.2.0 rlang_0.3.4 nloptr_1.2.1
[13] pillar_1.3.1 glue_1.3.1 withr_2.1.2 selectr_0.4-1 RColorBrewer_1.1-2 modelr_0.1.4
[19] plyr_1.8.4 munsell_0.5.0 gtable_0.3.0 cellranger_1.1.0 rvest_0.3.3 evaluate_0.13
[25] labeling_0.3 knitr_1.22 highr_0.8 Rcpp_1.0.1 scales_1.0.0 backports_1.1.4
[31] webshot_0.5.1 jsonlite_1.6 hms_0.4.2 digest_0.6.18 stringi_1.4.3 bookdown_0.9
[37] grid_3.5.2 cli_1.1.0 tools_3.5.2 magrittr_1.5 lazyeval_0.2.2 crayon_1.3.4
[43] pkgconfig_2.0.2 ellipsis_0.1.0 MASS_7.3-51.1 xml2_1.2.0 minqa_1.2.4 assertthat_0.2.1
[49] rmarkdown_1.12 httr_1.4.0 rstudioapi_0.10 boot_1.3-20 R6_2.4.0 nlme_3.1-137
[55] compiler_3.5.2