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Submission of the 10th release

  • Increased maximum allowed variants in LDmatrix to 2500
  • Added base pair window size parameter to LDproxy
  • Added base pair window size parameter to LDproxy_batch
  • Added Zenodo DOI badge

Test environments

  • local R installation, R 4.3.2, MacOS Sonoma v.14.3.1
  • win-builder (devel, release, oldrelease)
  • Rhub
    • Windows Server 2022, R-devel, 64 bit
    • Ubuntu Linux 20.04.1 LTS, R-release, GCC
    • Fedora Linux, R-devel, clang, gfortran
  • Github actions
    • macos-latest (release)
    • ubuntu-latest (devel)
    • ubuntu-latest (oldrel-1)
    • ubuntu-latest (release)
    • windows-latested (release)

R CMD check results

0 errors | 0 warnings | 5 notes

There were five NOTEs:

  • This NOTE is only found during Rhub Fedora Linux, R-devel, clang, gfortran and Rhub Ubuntu Linux 20.04.1 LTS, R-release, GCC
* checking HTML version of manual ... NOTE
Skipping checking HTML validation: no command 'tidy' found

The HTML version of the manual validated locally and on all other platforms. This would seem to be an issue with the path to tidy on the external Linux servers.

  • The following two NOTEs were only found during Rhub Windows Server 2022, R-devel, 64 bit:
* checking for detritus in the temp directory ... NOTE
Found the following files/directories:
  'lastMiKTeXException'

As noted in R-hub issue #503, this could be due to a bug/crash in MiKTeX and can likely be ignored.

* checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
  ''NULL''

As noted in R-hub issue #506, this is probably an R-hub issue and can be ignored.

  • The following two NOTEs were only found intermittently during R CMD checks on a local macOS system:
Found the following (possibly) invalid URLs:
    URL: https://ldlink.nih.gov/?tab=apiaccess
    From:....
    Status: Error
      Message: libcurl error code 35:

The URL in question is operated and maintained by a USA government research institute. It is accessible via browsers, suggesting an intermittent network or SSL handshake issue.

Found the following HTML validation problems:
  LDexpress.html:4:1 (LDexpress.Rd:5): Warning: <link> inserting "type" attribute
  LDexpress.html:12:1 (LDexpress.Rd:5): Warning: <script> proprietary attribute "onload"
  ....

The validation notes are intermittent and arise from automatically generated documentation. These do not impact functionality or user accessibility and reflect the output of current documentation tools.

revdepcheck results

We checked 2 reverse dependencies (1 from CRAN + 1 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.

  • We saw 0 problems with 1 package from CRAN
  • One check failed for 1 package from Bioconductor

The maintainer of the Bioconductor package (GRaNIE) was notified on 2024-03-20 (~3 weeks ago) via email of the upcoming new release of LDlinkR.