Open vjcitn opened 2 years ago
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.
I always run BiocCheck. However I do not see those messages. I will try with the version you suggest.
OK. now I get the error about T/F variables. Not the other too, must because they have been solved I guess.
A new version 1.1.13 has been pushed yesterday.
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.
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.