Fix #150 fix #149 fix#152 (#151)

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: rang
 Title: Reconstructing Reproducible R Computational Environments
-Version: 0.2.4
+Version: 0.2.5
 Authors@R: 
     c(person("Chung-hong", "Chan", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-6232-7530")),

R/memo_misc.R

@@ -5,7 +5,25 @@ NULL
 
 ## one hr
 
-.memo_search <- memoise::memoise(pkgsearch::cran_package_history, cache = cachem::cache_mem(max_age = 60 * 60))
+.cran_package_history <- function(package, max_retries = 5) {
+    n_retries <- 0
+    while(n_retries < max_retries) {
+        tryCatch({
+            return(pkgsearch::cran_package_history(package))
+        }, error = function(e) {
+            if (grepl("parse error: premature EOF", e$message)) {
+                n_retries <<- n_retries + 1
+                ##message("retrying in 2s...")
+                Sys.sleep(2)
+            } else {
+                stop(e)
+            }
+        })
+    }
+    stop("Can't query this package: ", package, call. = FALSE)
+}
+
+.memo_search <- memoise::memoise(.cran_package_history, cache = cachem::cache_mem(max_age = 60 * 60))
 
 .rver <- function() {
     suppressWarnings(jsonlite::fromJSON(readLines("https://api.r-hub.io/rversions/r-versions"), simplifyVector = TRUE))

R/resolve.R

@@ -479,17 +479,17 @@ print.rang <- function(x, all_pkgs = FALSE, ...) {
     return(res)
 }
 
-.gh <- function(path,ref = NULL,...){
+.gh <- function(path,ref = NULL,...) {
     url <- httr::parse_url("https://api.github.com/")
     url <- httr::modify_url(url, path = path)
     token <- Sys.getenv("GITHUB_PAT", NA_character_)
-    if(is.na(token)){
+    if(is.na(token)) {
         token <- Sys.getenv("GITHUB_TOKEN", NA_character_)
     }
-    if(is.na(token)){
+    if(is.na(token)) {
         token <- ""
     }
-    config <- httr::add_headers(Accept = "application/vnd.github.v3+json",Authorization=token)
+    config <- httr::add_headers(Accept = "application/vnd.github.v3+json", Authorization = paste0("token ", token))
     params <- list(ref = ref,...)
     request_results <- httr::GET(httr::modify_url(url, path = path), config, query = params)
     status_code <- httr::status_code(request_results)

README.Rmd

@@ -27,11 +27,7 @@ To reconstruct a historical R computational environment, this package assumes on
 
 Please cite this package as:
 
-Chan CH, Schoch D (2023) rang: Reconstructing reproducible R computational environments. arXiv preprint:[2303.04758](https://doi.org/10.48550/arXiv.2303.04758)
-
-Please cite this package as:
-
-Chan CH, Schoch D (2023) rang: Reconstructing reproducible R computational environments. arXiv preprint:[2303.04758](https://doi.org/10.48550/arXiv.2303.04758)
+Chan CH, Schoch D (2023) rang: Reconstructing reproducible R computational environments. PLOS ONE [https://doi.org/10.1371/journal.pone.0286761](https://doi.org/10.1371/journal.pone.0286761)
 
 ## Installation
 

README.md

@@ -30,8 +30,8 @@ of R.
 Please cite this package as:
 
 Chan CH, Schoch D (2023) rang: Reconstructing reproducible R
-computational environments. arXiv
-preprint:[2303.04758](https://doi.org/10.48550/arXiv.2303.04758)
+computational environments. PLOS ONE
+<https://doi.org/10.1371/journal.pone.0286761>
 
 ## Installation
 

inst/CITATION

@@ -3,8 +3,8 @@ citHeader("To cite rang in publications use:")
 
 bibentry(bibtype = "article",
          title = "rang: Reconstructing reproducible R computational environments",
-         journal = "arXiv preprint 2303.04758",
+         journal = "PLOS ONE",
          author = c(person("Chung-hong", "Chan"), person("David", "Schoch")),
          url = "https://github.com/chainsawriot/rang",
          year = 2023,
-         doi = "10.48550/arXiv.2303.04758")
+         doi = "10.1371/journal.pone.0286761")

tests/testthat/test_resolve.R

@@ -153,6 +153,8 @@ test_that("Non-cran must enforce caching ref #22", {
 ## })
 
 test_that("Integration of as_pkgrefs() in resolve() for sessionInfo()", {
+    skip_if_offline()
+    skip_on_cran()
     x <- resolve(c("cran::sna"), snapshot_date = "2020-05-01", query_sysreqs = FALSE)
     si <- readRDS("../testdata/sessionInfo2.RDS")
     expect_error(graph <- resolve(si, snapshot_date = "2020-05-01", query_sysreqs = FALSE), NA)