Merge release candidate dev into master before submitting to CRAN

[jooolia]

Hello,

As described in Issue #102 we are hoping to submit a new version of rsnps to CRAN that fixes many issues we have encountered recently.

@sckott would you mind having a look at this PR to see if things look ok for this go-around?

Thanks! Julia and Sina

[jooolia]

Thanks a lot @sckott. We will work on addressing all of your helpful comments.

[jooolia]

Ok thanks for the explanation! That helps!

…

On Mon, 27 Jul 2020 at 17:40, Scott Chamberlain ***@***.***> wrote: ***@***.**** commented on this pull request. ------------------------------ In R/ncbi_snp_api.R <#114 (comment)>: > + + message(paste0("Getting info about the following rsIDs: ", + paste(SNPs, + collapse = ", "))) + ## transform all SNPs into numbers (rsid) + SNPs_num <- gsub("rs", "", SNPs) + + out <- as.data.frame(matrix(0, nrow = length(SNPs_num), ncol = 15)) + names(out) <- c("Query", "Chromosome", "BP", "Class", "rsid", "Gene", "Alleles", "AncestralAllele", "VariationAllele", "seqname", "hgvs", "assembly", "ref_seq", "Minor", "MAF") + + ## as far as I understand from https://api.ncbi.nlm.nih.gov/variation/v0/#/RefSNP/ we + ## can only send one query at a time and max 1 per second. + for (i in seq_along(SNPs_num)) { + + variant.url <- paste0("https://api.ncbi.nlm.nih.gov/variation/v0/refsnp/", SNPs_num[i]) + variant.response <- httr::GET(variant.url) e.g. httr::verbose() httr::timeout(), see ?httr::config - You could just remove the ... from the function definition though and then users if they wanted to set curl options could still do so by doing httr::set_config/ httr::with_config — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#114 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAOPZSUFBRREKX4VOGSODBDR5WNV7ANCNFSM4OZSVARQ> .

[jooolia]

Hi @sinarueeger,
We are getting 7 failed tests because of "SSL certificate problem: certificate has expired" type errors. This is the reason for the failed Travis CI build and I can also reproduce this locally. I will re-run the tests tomorrow to see if it still remains an issue.

[sinarueeger]

Hi @jooolia , the ssl error is because of https://opensnp.org/ I think. I asked them to extend their ssl certificate: https://gitter.im/openSNP/.

[jooolia]

ok well this morning it seems to be ok. :)

…

On Mon, 24 Aug 2020 at 08:02, Sina Rüeger ***@***.***> wrote: Hi @jooolia <https://github.com/jooolia> , the ssl error is because of https://opensnp.org/ I think. I asked them to extend their ssl certificate: https://gitter.im/openSNP/. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#114 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAOPZSSEC7HNBFSGS37SMN3SCH7BBANCNFSM4OZSVARQ> .

[jooolia]

Hi @sinarueeger,
I think that we have addressed all the current issues (and I cannot get the travis-ci/push test to be redone but I think it should now be ok again for the moment, but the most recent win-builder https://win-builder.r-project.org/0D7lBEzduf98/ is as expected). Are you ok with merging this branch into master and then we submit (as in #102). Anything else that you would like to see done?

Thanks, Julia

[sinarueeger]

Hi @Joolia, thanks! This looks ok to me :-)