Fail to reproduce the correlate analysis

[chongma8903]

Hi Youyi,

I am trying to reproduce the correlate analysis by cloning this repository. When I try to restore the renv.lock file, there are two packages flevr and psbinary not existing and I cannot install them. I tried to run the test using your example, "bash test_before_submit cor_coxph", however, I could see some results when it ran in terminal, but it failed generating the report. As following is the bug, and I wonder if you could please help me fix this out. Thank you very much.

[1] "Thu Jul 13 22:03:31 2023"
Bootstrap marginalized risks using models without markers prev.plac prev.vacc overall.ve
est 0.108367 0.00543281 0.949866
2.5% 0.105589 0.00407550 0.943828
97.5% 0.112916 0.00631714 0.961624
Error in prettyNum(.Internal(format(x, trim, digits, nsmall, width, 3L, :
invalid value 0 for 'digits' argument
Calls: source ... paste0 -> format -> format -> format.default -> prettyNum
Execution halted
make: *** [Makefile:11: cor_coxph] Error 1
make: Target 'all' not remade because of errors.
make: Leaving directory '/mnt/correlates_reporting2/cor_coxph'
moderna_mock

Analysis-ready data: /mnt/correlates_reporting2/data_clean/moderna_mock_data_processed_with_riskscore.csv
! LaTeX Error: File `cor_coxph/output/moderna_mock/D29D57/barplot_mixed' not fo
und.

Error: LaTeX failed to compile covpn_correlates_cor_coxph_moderna_mock.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See covpn_correlates_cor_coxph_moderna_mock.log for more info.
In addition: Warning messages:
1: In eval(ei, envir) :
No COR. This is okay if _common.R is sourced just to load common functions. If needed, COR can be defined through command line argument or in R script before _common.R is sourced.
2: In utils::citation(..., lib.loc = lib.loc) :
no date field in DESCRIPTION file of package 'kyotil'
Execution halted