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epiforecasts / bpmodels

[No longer being developed. Use the epichains package instead]. Methods for simulating and analysing the sizes and lengths of chains from branching process models
https://epiforecasts.io/bpmodels/
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Fix HTML validation problems #83

Closed jamesmbaazam closed 1 year ago

jamesmbaazam commented 1 year ago 
❯ checking HTML version of manual ... NOTE
  Found the following HTML validation problems:
  bpmodels-package.html:4:1 (bpmodels-package.Rd:7): Warning: <link> inserting "type" attribute
  bpmodels-package.html:12:1 (bpmodels-package.Rd:7): Warning: <script> proprietary attribute "onload"
  bpmodels-package.html:12:1 (bpmodels-package.Rd:7): Warning: <script> inserting "type" attribute
  bpmodels-package.html:17:1 (bpmodels-package.Rd:7): Warning: <table> lacks "summary" attribute
  chain_ll.html:4:1 (chain_ll.Rd:5): Warning: <link> inserting "type" attribute
  chain_ll.html:12:1 (chain_ll.Rd:5): Warning: <script> proprietary attribute "onload"
  chain_ll.html:12:1 (chain_ll.Rd:5): Warning: <script> inserting "type" attribute
  chain_ll.html:17:1 (chain_ll.Rd:5): Warning: <table> lacks "summary" attribute
  chain_ll.html:45:1 (chain_ll.Rd:20): Warning: <table> lacks "summary" attribute
  chain_sim.html:4:1 (chain_sim.Rd:5): Warning: <link> inserting "type" attribute
  chain_sim.html:12:1 (chain_sim.Rd:5): Warning: <script> proprietary attribute "onload"
  chain_sim.html:12:1 (chain_sim.Rd:5): Warning: <script> inserting "type" attribute
  chain_sim.html:17:1 (chain_sim.Rd:5): Warning: <table> lacks "summary" attribute
  chain_sim.html:47:1 (chain_sim.Rd:20): Warning: <table> lacks "summary" attribute
  chain_sim_susc.html:4:1 (chain_sim_susc.Rd:5): Warning: <link> inserting "type" attribute
  chain_sim_susc.html:12:1 (chain_sim_susc.Rd:5): Warning: <script> proprietary attribute "onload"
  chain_sim_susc.html:12:1 (chain_sim_susc.Rd:5): Warning: <script> inserting "type" attribute
  chain_sim_susc.html:17:1 (chain_sim_susc.Rd:5): Warning: <table> lacks "summary" attribute
  chain_sim_susc.html:46:1 (chain_sim_susc.Rd:20): Warning: <table> lacks "summary" attribute
  complementary_logprob.html:4:1 (complementary_logprob.Rd:5): Warning: <link> inserting "type" attribute
  complementary_logprob.html:12:1 (complementary_logprob.Rd:5): Warning: <script> proprietary attribute "onload"
  complementary_logprob.html:12:1 (complementary_logprob.Rd:5): Warning: <script> inserting "type" attribute
  complementary_logprob.html:17:1 (complementary_logprob.Rd:5): Warning: <table> lacks "summary" attribute
  complementary_logprob.html:35:1 (complementary_logprob.Rd:10): Warning: <table> lacks "summary" attribute
  covid19_sa.html:4:1 (covid19_sa.Rd:6): Warning: <link> inserting "type" attribute
  covid19_sa.html:12:1 (covid19_sa.Rd:6): Warning: <script> proprietary attribute "onload"
  covid19_sa.html:12:1 (covid19_sa.Rd:6): Warning: <script> inserting "type" attribute
  covid19_sa.html:17:1 (covid19_sa.Rd:6): Warning: <table> lacks "summary" attribute
  dborel.html:4:1 (dborel.Rd:5): Warning: <link> inserting "type" attribute
  dborel.html:12:1 (dborel.Rd:5): Warning: <script> proprietary attribute "onload"
  dborel.html:12:1 (dborel.Rd:5): Warning: <script> inserting "type" attribute
  dborel.html:17:1 (dborel.Rd:5): Warning: <table> lacks "summary" attribute
  dborel.html:35:1 (dborel.Rd:10): Warning: <table> lacks "summary" attribute
  find_function_name.html:4:1 (find_function_name.Rd:5): Warning: <link> inserting "type" attribute
  find_function_name.html:12:1 (find_function_name.Rd:5): Warning: <script> proprietary attribute "onload"
  find_function_name.html:12:1 (find_function_name.Rd:5): Warning: <script> inserting "type" attribute
  find_function_name.html:17:1 (find_function_name.Rd:5): Warning: <table> lacks "summary" attribute
  find_function_name.html:37:1 (find_function_name.Rd:10): Warning: <table> lacks "summary" attribute
  gborel_size_ll.html:4:1 (gborel_size_ll.Rd:5): Warning: <link> inserting "type" attribute
  gborel_size_ll.html:12:1 (gborel_size_ll.Rd:5): Warning: <script> proprietary attribute "onload"
  gborel_size_ll.html:12:1 (gborel_size_ll.Rd:5): Warning: <script> inserting "type" attribute
  gborel_size_ll.html:17:1 (gborel_size_ll.Rd:5): Warning: <table> lacks "summary" attribute
  gborel_size_ll.html:35:1 (gborel_size_ll.Rd:10): Warning: <table> lacks "summary" attribute
  geom_length_ll.html:4:1 (geom_length_ll.Rd:5): Warning: <link> inserting "type" attribute
  geom_length_ll.html:12:1 (geom_length_ll.Rd:5): Warning: <script> proprietary attribute "onload"
  geom_length_ll.html:12:1 (geom_length_ll.Rd:5): Warning: <script> inserting "type" attribute
  geom_length_ll.html:17:1 (geom_length_ll.Rd:5): Warning: <table> lacks "summary" attribute
  geom_length_ll.html:35:1 (geom_length_ll.Rd:10): Warning: <table> lacks "summary" attribute
  nbinom_size_ll.html:4:1 (nbinom_size_ll.Rd:5): Warning: <link> inserting "type" attribute
  nbinom_size_ll.html:12:1 (nbinom_size_ll.Rd:5): Warning: <script> proprietary attribute "onload"
  nbinom_size_ll.html:12:1 (nbinom_size_ll.Rd:5): Warning: <script> inserting "type" attribute
  nbinom_size_ll.html:17:1 (nbinom_size_ll.Rd:5): Warning: <table> lacks "summary" attribute
  nbinom_size_ll.html:37:1 (nbinom_size_ll.Rd:11): Warning: <table> lacks "summary" attribute
  offspring_ll.html:4:1 (offspring_ll.Rd:5): Warning: <link> inserting "type" attribute
  offspring_ll.html:12:1 (offspring_ll.Rd:5): Warning: <script> proprietary attribute "onload"
  offspring_ll.html:12:1 (offspring_ll.Rd:5): Warning: <script> inserting "type" attribute
  offspring_ll.html:17:1 (offspring_ll.Rd:5): Warning: <table> lacks "summary" attribute
  offspring_ll.html:37:1 (offspring_ll.Rd:10): Warning: <table> lacks "summary" attribute
  pois_length_ll.html:4:1 (pois_length_ll.Rd:5): Warning: <link> inserting "type" attribute
  pois_length_ll.html:12:1 (pois_length_ll.Rd:5): Warning: <script> proprietary attribute "onload"
  pois_length_ll.html:12:1 (pois_length_ll.Rd:5): Warning: <script> inserting "type" attribute
  pois_length_ll.html:17:1 (pois_length_ll.Rd:5): Warning: <table> lacks "summary" attribute
  pois_length_ll.html:35:1 (pois_length_ll.Rd:10): Warning: <table> lacks "summary" attribute
  pois_size_ll.html:4:1 (pois_size_ll.Rd:5): Warning: <link> inserting "type" attribute
  pois_size_ll.html:12:1 (pois_size_ll.Rd:5): Warning: <script> proprietary attribute "onload"
  pois_size_ll.html:12:1 (pois_size_ll.Rd:5): Warning: <script> inserting "type" attribute
  pois_size_ll.html:17:1 (pois_size_ll.Rd:5): Warning: <table> lacks "summary" attribute
  pois_size_ll.html:35:1 (pois_size_ll.Rd:10): Warning: <table> lacks "summary" attribute
  rbinom_size.html:4:1 (rbinom_size.Rd:5): Warning: <link> inserting "type" attribute
  rbinom_size.html:12:1 (rbinom_size.Rd:5): Warning: <script> proprietary attribute "onload"
  rbinom_size.html:12:1 (rbinom_size.Rd:5): Warning: <script> inserting "type" attribute
  rbinom_size.html:17:1 (rbinom_size.Rd:5): Warning: <table> lacks "summary" attribute
  rbinom_size.html:36:1 (rbinom_size.Rd:10): Warning: <table> lacks "summary" attribute
  rborel.html:4:1 (rborel.Rd:5): Warning: <link> inserting "type" attribute
  rborel.html:12:1 (rborel.Rd:5): Warning: <script> proprietary attribute "onload"
  rborel.html:12:1 (rborel.Rd:5): Warning: <script> inserting "type" attribute
  rborel.html:17:1 (rborel.Rd:5): Warning: <table> lacks "summary" attribute
  rborel.html:35:1 (rborel.Rd:10): Warning: <table> lacks "summary" attribute
  rgen_length.html:4:1 (rgen_length.Rd:5): Warning: <link> inserting "type" attribute
  rgen_length.html:12:1 (rgen_length.Rd:5): Warning: <script> proprietary attribute "onload"
  rgen_length.html:12:1 (rgen_length.Rd:5): Warning: <script> inserting "type" attribute
  rgen_length.html:17:1 (rgen_length.Rd:5): Warning: <table> lacks "summary" attribute
  rgen_length.html:37:1 (rgen_length.Rd:10): Warning: <table> lacks "summary" attribute
  rnbinom_mean_disp.html:4:1 (rnbinom_mean_disp.Rd:5): Warning: <link> inserting "type" attribute
  rnbinom_mean_disp.html:12:1 (rnbinom_mean_disp.Rd:5): Warning: <script> proprietary attribute "onload"
  rnbinom_mean_disp.html:12:1 (rnbinom_mean_disp.Rd:5): Warning: <script> inserting "type" attribute
  rnbinom_mean_disp.html:17:1 (rnbinom_mean_disp.Rd:5): Warning: <table> lacks "summary" attribute
  rnbinom_mean_disp.html:37:1 (rnbinom_mean_disp.Rd:11): Warning: <table> lacks "summary" attribute
sbfnk commented 1 year ago

see https://groups.google.com/g/r-sig-mac/c/7u_ivEj4zhM/m/TnkDs0CPAwAJ

jamesmbaazam commented 1 year ago

Amazing! Thanks, Seb.

If anyone wants the TLDR, the answer is:

" So the simplest thing for someone wanting to do an -as-cran check is to install html-tidy 5.8.0. R CMD check --as-cran also makes use of ‘HTML Tidy’. macOS has a version in /usr/bin/tidy dating from 2006 which is far too old and is skipped. Up-to-date versions can be installed from http://binaries.html-tidy.org/."

jamesmbaazam commented 1 year ago

This issue was fixed by installing HTML-tidy from http://binaries.html-tidy.org/.

Closing the issue now.