Merge pull request #47 from hugheylab/grace

added new rhub and more graceful error handling.

.github/workflows/rhub.yaml

@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 1.1.3
-Date: 2023-05-23 23:24:27 UTC
-SHA: 82211b24fe055620ddf60bc02b75576318738495
+Version: 1.1.5
+Date: 2024-01-22 18:38:12 UTC
+SHA: 235a640089660206e3a1cd6489b43dfee2f6ff38

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: seeker
 Type: Package
 Title: Simplified Fetching and Processing of Microarray and RNA-Seq Data
-Version: 1.1.5
+Version: 1.1.6
 Authors@R: c(
   person('Jake', 'Hughey', , '[email protected]', role = c('aut', 'cre')),
   person('Josh', 'Schoenbachler', , '[email protected]', role = 'aut'))
@@ -26,7 +26,7 @@ URL: https://seeker.hugheylab.org, https://github.com/hugheylab/seeker
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)
 Depends: R (>= 3.5)
 Imports:

NEWS.md

@@ -1,3 +1,6 @@
+# seeker 1.1.6
+* Made error handling more graceful.
+
 # seeker 1.1.5
 * Added support for GPL17811 (thanks to @jacorvar).
 

R/fetch.R

@@ -39,7 +39,12 @@ fetchMetadata = function(
       '?save=efetch&db=sra&rettype=runinfo&term=', bioproject)
     sep = ','}
 
-  raw = curl::curl_fetch_memory(url)
+  raw = tryCatch(curl::curl_fetch_memory(url), error = \(e) e)
+  metadata = if (inherits(raw, 'error')) {
+    message('Unable to fetch metadata. Host may be temporarily unavailable.')
+    return(data.table())
+  }
+
   metadata = fread(text = rawToChar(raw$content), sep = sep, na.strings = '')
   data.table::setorder(metadata)
   if (!is.null(file)) fwrite(metadata, file)

R/install_sys_deps.R

@@ -32,7 +32,12 @@ installSraToolkit = function(installDir, rprofileDir) {
     sraVersion = max(regmatches(x, m))
 
     # Based on operating system, download correct version to correct path
-    sraOsTar = if (Sys.info()[['sysname']] == 'Darwin') 'mac64' else 'ubuntu64'
+    sraOsTar = if (Sys.info()[['sysname']] == 'Darwin') {
+      uname = system('uname -m', intern = TRUE)
+      if (uname == 'x86_64') 'mac-x86_64' else 'mac-arm64'
+    } else {
+      'ubuntu64'
+    }
     sraTar = glue('sratoolkit.{sraVersion}-{sraOsTar}.tar.gz')
 
     # Download based on version and OS, unzip, then rename directory

cran-comments.md

@@ -8,19 +8,9 @@
 
 ### R-hub
 
-`devtools::check_rhub()`:
-
-  0 errors ✓ | 0 warnings ✓ | 2 notes ✓
-
-❯ checking for non-standard things in the check directory ... NOTE
-  Found the following files/directories:
-    ''NULL''
-
-❯ checking for detritus in the temp directory ... NOTE
-  Found the following files/directories:
-    'lastMiKTeXException'
+  0 errors ✓ | 0 warnings ✓ | 0 notes ✓
 
-See results for [Windows](https://builder.r-hub.io/status/seeker_1.1.5.tar.gz-8a323a68035846eb827c4bcdd88625b5), [Ubuntu](https://builder.r-hub.io/status/seeker_1.1.5.tar.gz-0e06ae6f6ad84e0bb98821147bf0488c), and [Fedora](https://builder.r-hub.io/status/seeker_1.1.5.tar.gz-6d6c440ee7bd4a6d98c0b01f1f7fb3af).
+See results for Mac, Windows, and Linux [here]().
 
 ### GitHub Actions
 
@@ -30,4 +20,4 @@ See results for Mac, Windows, and Ubuntu [here]().
 
 ## Changes from current CRAN release
 
-* Added support for GPL17811.
+* Made error handling related to internet resources more graceful.

tests/testthat/test-fetch.R

@@ -4,6 +4,8 @@ test_that('fetchMetadata', {
   paramsNow = params[[step]]
 
   metadataObs = fetchMetadata(paramsNow$bioproject)
+  skip_if(nrow(metadataObs) == 0L)
+
   idx = metadataObs[[paramsNow$include$colname]] %in% paramsNow$include$values
   metadataObs = metadataObs[idx]