CI: lintr updates (#4743)
CI: lintr updates (#4743)

- fix function that emits a deprecation warning
- also output line (can't hurt)
gregvonkuster/tools-iuc,jj-umn/tools-iuc,nsoranzo/tools-iuc,galaxyproject/tools-iuc,pavanvidem/tools-iuc,galaxyproject/tools-iuc,jj-umn/tools-iuc,pavanvidem/tools-iuc,loraine-gueguen/tools-iuc,galaxyproject/tools-iuc,jj-umn/tools-iuc,gregvonkuster/tools-iuc,nsoranzo/tools-iuc,gregvonkuster/tools-iuc,pavanvidem/tools-iuc,gregvonkuster/tools-iuc,jj-umn/tools-iuc,pavanvidem/tools-iuc,pavanvidem/tools-iuc,loraine-gueguen/tools-iuc,gregvonkuster/tools-iuc,loraine-gueguen/tools-iuc,galaxyproject/tools-iuc,loraine-gueguen/tools-iuc,jj-umn/tools-iuc,pavanvidem/tools-iuc,loraine-gueguen/tools-iuc,pavanvidem/tools-iuc,jj-umn/tools-iuc,jj-umn/tools-iuc,loraine-gueguen/tools-iuc,nsoranzo/tools-iuc,galaxyproject/tools-iuc,gregvonkuster/tools-iuc,galaxyproject/tools-iuc,galaxyproject/tools-iuc,nsoranzo/tools-iuc,nsoranzo/tools-iuc,loraine-gueguen/tools-iuc,nsoranzo/tools-iuc,gregvonkuster/tools-iuc,nsoranzo/tools-iuc