BiocCheck findings should be addressed

[vjcitn]

I have been assigned all the biodb* packages. I had a look at biodb to start off. Please run BiocCheck as you maintain your software.

BiocCheck FAILED.
$error
[1] ".Rbuildignore file includes the 'tests' folder."

$warning
...
[2] " Avoid T/F variables; If logical, use TRUE/FALSE (found 1 times)"                                                                               

$note
[1] " 'sessionInfo' not found in vignette(s)"   

End your vignettes with an R chunk that runs sessionInfo(). This will allow readers to know exactly which package versions were used to compile the vignette.

[vjcitn]

Here is the sessionInfo that corresponds to the BiocCheck run noted above:

> sessionInfo()
R version 4.1.1 Patched (2021-09-30 r81005)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS

Matrix products: default
BLAS:   /home/stvjc/R-4-1-dist/lib/R/lib/libRblas.so
LAPACK: /home/stvjc/R-4-1-dist/lib/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] biodb_1.1.11   rmarkdown_2.11

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.7           stringdist_0.9.8     prettyunits_1.1.1   
 [4] assertthat_0.2.1     digest_0.6.28        utf8_1.2.2          
 [7] BiocFileCache_2.1.1  R6_2.5.1             plyr_1.8.6          
[10] stats4_4.1.1         RSQLite_2.2.8        evaluate_0.14       
[13] httr_1.4.2           pillar_1.6.3         biocViews_1.61.1    
[16] rlang_0.4.11         progress_1.2.2       curl_4.3.2          
[19] rstudioapi_0.13      blob_1.2.2           RUnit_0.4.32        
[22] startup_0.15.0       stringr_1.4.0        RCurl_1.98-1.5      
[25] bit_4.0.4            compiler_4.1.1       xfun_0.26           
[28] pkgconfig_2.0.3      askpass_1.1          BiocGenerics_0.39.2 
[31] htmltools_0.5.2      openssl_1.4.5        tidyselect_1.1.1    
[34] tibble_3.1.5         lgr_0.4.3            codetools_0.2-18    
[37] BiocCheck_1.29.14001 XML_3.99-0.8         fansi_0.5.0         
[40] crayon_1.4.1         dplyr_1.0.7          dbplyr_2.1.1        
[43] withr_2.4.2          bitops_1.0-7         rappdirs_0.3.3      
[46] RBGL_1.69.0          jsonlite_1.7.2       lifecycle_1.0.1     
[49] DBI_1.1.1            magrittr_2.0.1       graph_1.71.2        
[52] stringi_1.7.5        cachem_1.0.6         getopt_1.20.3       
[55] optparse_1.6.6       ellipsis_0.3.2       chk_0.7.0           
[58] filelock_1.0.2       generics_0.1.0       vctrs_0.3.8         
[61] tools_4.1.1          bit64_4.0.5          Biobase_2.53.0      
[64] glue_1.4.2           purrr_0.3.4          hms_1.1.1           
[67] parallel_4.1.1       fastmap_1.1.0        yaml_2.2.1          
[70] BiocManager_1.30.16  memoise_2.0.0        knitr_1.36   

Note that BiocCheck has an unusual version number. If you have a problem with the standard BiocCheck at this time, use BiocManager::install('vjcitn/BiocCheck', ref="vjcitn-patch-1") to get a patched version.

[pkrog]

I always run BiocCheck. However I do not see those messages. I will try with the version you suggest.

[pkrog]

OK. now I get the error about T/F variables. Not the other too, must because they have been solved I guess.

[pkrog]

A new version 1.1.13 has been pushed yesterday.