search

ropensci / bold

Interface to the Bold Systems barcode webservice
https://docs.ropensci.org/bold
Other
17 stars 11 forks source link

Guidelines to install `sangerseqR` with R3.6.0 in the README file #65

Closed KevCaz closed 5 years ago

KevCaz commented 5 years ago

Hi @sckott,

A quick comment about the README: with R 3.6.0, things have slightly changed on Bioconductor https://www.bioconductor.org/install/ and so now source("http://bioconductor.org/biocLite.R") returns the following error:

Error: With R version 3.5 or greater, install Bioconductor packages using BiocManager; see https://bioconductor.org/install

I guess, you simply need to update the README, mentioning that for R >= 3.6.9, one must use:

install.packages('BiocManager')
BiocManager::install('sangerseqR')

Thanks for your work on this!

Session Info ```r R version 3.6.0 (2019-04-26) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 10 (buster) Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.3.5.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] usethis_1.4.0 devtools_2.0.1 loaded via a namespace (and not attached): [1] Rcpp_1.0.1 ps_1.3.0 prettyunits_1.0.2 digest_0.6.18 [5] crayon_1.3.4 withr_2.1.2 rprojroot_1.3-2 assertthat_0.2.1 [9] R6_2.4.0 backports_1.1.3 magrittr_1.5 rlang_0.4.0 [13] cli_1.0.1 fs_1.2.6 remotes_2.0.2 testthat_2.0.1 [17] callr_3.1.1 desc_1.2.0 tools_3.6.0 glue_1.3.1 [21] compiler_3.6.0 pkgload_1.0.2 processx_3.2.1 pkgbuild_1.0.2 [25] sessioninfo_1.1.1 memoise_1.1.0 ```
sckott commented 5 years ago

thanks very much @KevCaz ! had no idea