update ca-certs for linux

update permissions

add cert manually

add cert chain

reordeR:

use full chain:

update packages

add letenrcrpt certs

skip verification

.github/workflows/check-standard.yaml

@@ -29,6 +29,32 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
+      - name: Add custom certificate to trusted store
+        if: matrix.config.os == 'ubuntu-latest'
+        run: |
+          sudo apt install --only-upgrade ca-certificates
+          sudo apt install --only-upgrade openssl
+          # Download or access the certificate
+           echo "${{ secrets.CERT_CHAIN }}" > website_cert_chain.pem
+           sudo curl -k https://letsencrypt.org/certs/isrgrootx1.pem.txt -o /usr/local/share/ca-certificates/isrgrootx1.crt
+          sudo curl -k https://letsencrypt.org/certs/letsencryptauthorityx1.pem.txt -o /usr/local/share/ca-certificates/letsencryptauthorityx1.crt
+          sudo curl -k https://letsencrypt.org/certs/letsencryptauthorityx2.pem.txt -o /usr/local/share/ca-certificates/letsencryptauthorityx2.crt
+          sudo curl -k https://letsencrypt.org/certs/lets-encrypt-x1-cross-signed.pem.txt -o /usr/local/share/ca-certificates/letsencryptx1.crt
+          sudo curl -k https://letsencrypt.org/certs/lets-encrypt-x2-cross-signed.pem.txt -o /usr/local/share/ca-certificates/letsencryptx2.crt
+          sudo curl -k https://letsencrypt.org/certs/lets-encrypt-x3-cross-signed.pem.txt -o /usr/local/share/ca-certificates/letsencryptx3.crt
+          sudo curl -k https://letsencrypt.org/certs/lets-encrypt-x4-cross-signed.pem.txt -o /usr/local/share/ca-certificates/letsencryptx4.crt
+
+          sudo dpkg-reconfigure ca-certificates
+  
+          # Add the certificate to the system's trusted certificates
+          sudo cp website_cert_chain.pem /usr/local/share/ca-certificates/website_cert_chain.crt
+          sudo update-ca-certificates
+          sudo dpkg-reconfigure ca-certificates
+          # Verify the certificate is trusted
+          # openssl verify /usr/local/share/ca-certificates/website_cert_chain.crt
+
+        shell: bash
+
       - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-pandoc@v2

DESCRIPTION

@@ -1,9 +1,9 @@
 Package: clinicalomicsdbR
-Title: Interface with the ClinicalOmicsDB API, Allowing for Easy Data Downloading and Importing
+Title: Interface with the 'ClinicalOmicsDB' API, Allowing for Easy Data Downloading and Importing
 Version: 1.0.4
 Authors@R: 
     person("John", "Elizarraras", , "john.elizarraras@bcm.edu", role = c("aut", "cre", "ctb"))
-Description: Provides an interface to the ClinicalOmicsDB API, allowing for easy data downloading and importing. ClinicalOmicsDB is a database of clinical and omics data from cancer patients. The database is accessible at <http://trials.linkedomics.org>.
+Description: Provides an interface to the 'ClinicalOmicsDB' API, allowing for easy data downloading and importing. 'ClinicalOmicsDB' is a database of clinical and 'omics' data from cancer patients. The database is accessible at <http://trials.linkedomics.org>.
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)