CRAN errors for R 3.5.2/dataone 2.1.1

[gothub]

The following errors occurred with the new version of R (3.5.2, released 2018 12 20) during the routine CRAN checks. Note that duplicate checks across the various platform types have been omitted in this listing:

Version: 2.1.1 Check: tests Result: ERROR Running ‘testthat.R’ [29s/82s] Running the tests in ‘tests/testthat.R’ failed. Complete output:

library(testthat) test_check("dataone") Loading required package: dataone ── 1. Error: D1Client downloadObject (@test.D1Client.R#548) ─────────────────── trying to get slot "obsoletedBy" from an object of a basic class ("NULL") with no slots 1: downloadObject(d1cKNB, pid, path) at testthat/test.D1Client.R:548 2: downloadObject(d1cKNB, pid, path) 3: .local(x, identifier, ...)

 ══ testthat results ═══════════════════════════════════════════════════════════
 OK: 200 SKIPPED: 37 FAILED: 1
 1. Error: D1Client downloadObject (@test.D1Client.R#548)

 Error: testthat unit tests failed
 Execution halted

Flavor: r-devel-linux-x86_64-debian-clang

Version: 2.1.1 Check: re-building of vignette outputs Result: WARN Error(s) in re-building vignettes: ... duplicated vignette title: ‘Uploading Data to DataONE’

--- re-building ‘dataone-federation.Rmd’ using rmarkdown
--- finished re-building ‘dataone-federation.Rmd’

--- re-building ‘dataone-overview.Rmd’ using rmarkdown
--- finished re-building ‘dataone-overview.Rmd’

--- re-building ‘download-data.Rmd’ using rmarkdown
--- finished re-building ‘download-data.Rmd’

--- re-building ‘known-issues.Rmd’ using rmarkdown
--- finished re-building ‘known-issues.Rmd’

--- re-building ‘searching-dataone.Rmd’ using rmarkdown
--- finished re-building ‘searching-dataone.Rmd’

--- re-building ‘update-package.Rmd’ using rmarkdown
--- finished re-building ‘update-package.Rmd’

--- re-building ‘upload-data.Rmd’ using rmarkdown
--- finished re-building ‘upload-data.Rmd’

Error: Duplicate vignette titles.
 Ensure that the %\VignetteIndexEntry lines in the vignette sources
 correspond to the vignette titles.
Execution halted

Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 2.1.1 Check: tests Result: ERROR Running ‘testthat.R’ [89s/200s] Running the tests in ‘tests/testthat.R’ failed. Complete output:

library(testthat) test_check("dataone") Loading required package: dataone ── 1. Error: D1Client getDataObject (@test.D1Client.R#99) ───────────────────── Timeout was reached: Operation timed out after 10002 milliseconds with 0 out of 0 bytes received 1: getDataObject(d1cKNB, pid) at testthat/test.D1Client.R:99 2: getDataObject(d1cKNB, pid) 3: .local(x, identifier, ...) 4: getSystemMetadata(currentMN, identifier) 5: getSystemMetadata(currentMN, identifier) 6: .local(x, ...) 7: auth_get(url, node = x) 8: GET(url, config = nconfig, user_agent(get_user_agent()), write_path) 9: request_perform(req, hu$handle$handle) 10: request_fetch(req$output, req$url, handle) 11: request_fetch.write_memory(req$output, req$url, handle) 12: curl::curl_fetch_memory(url, handle = handle)

 ── 2. Error: D1Client downloadObject (@test.D1Client.R#548) ───────────────────
 trying to get slot "obsoletedBy" from an object of a basic class ("NULL") with no slots
 1: downloadObject(d1cKNB, pid, path) at testthat/test.D1Client.R:548
 2: downloadObject(d1cKNB, pid, path)
 3: .local(x, identifier, ...)

 ══ testthat results ═══════════════════════════════════════════════════════════
 OK: 195 SKIPPED: 37 FAILED: 2
 1. Error: D1Client getDataObject (@test.D1Client.R#99)
 2. Error: D1Client downloadObject (@test.D1Client.R#548)

 Error: testthat unit tests failed
 Execution halted

Flavor: r-patched-solaris-x86

[gothub]

The trying to get slot "obsoletedBy" from an object of a basic class ("NULL") errors were due to a retired DataONE tests MNs, problem with DataONE production MN certs, and inadequate error handling by the dataone R service accessing them. Fixes are in commits e50f4ce555a398b872be86f2f442dd61cecadf8c 1d7eb3d0299f9c0bf8a2ea17d81e16a5c1f7fb1f.

Note that unit tests run locally will continue generate warnings regarding the expired MN certs, and that the 2 related tests are being skipped on CRAN. We still want to see that there is a problem when run locally, but don't want this problem to prevent the package from being accepted by CRAN, as it may be a few days before the certs are updated.

The duplicate vignette error "Error: Duplicate vignette titles" has been resolved in commit c16d01d395aeb7dc6529a14b10ec28e506673406

Note that a v 2.1.2 release will be submitted when win-builder results are returned from CRAN.

[gothub]

All CRAN errors for dataone 2.1.1/R 3.5.2, reported from https://cran.r-project.org/web/checks/check_results_dataone.html have been resolved with the v 2.1.2 dataone package release.