We run BiocCheckGitClone on a raw clone of the github directory. If you are running it locally and had .gitignored those files before pushing to github then you should be okay. A way to test this would be to do a git clone​ of your github repository, in a different, temporary location to see if those files are still present when you do a git clone and running BiocCheckGitClone on that temporary cloned copy.
Cheers Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 ________________________________ From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Emilie Secherre <emiseche...@gmail.com> Sent: Tuesday, September 22, 2020 4:57 AM To: bioc-devel@r-project.org <bioc-devel@r-project.org> Subject: [Bioc-devel] BiocCheckGitClone error Hello, When i run R CMD and BiocCheck, i get no error or warnings. But, when running BiocCheckGitClone, i'm getting this error : System files found that should not be tracked : famat.Rproj, .Rhistory The issue is that both files are in .gitignore, but this error isn't removed... I'm using BiocCheckGitClone on the same file as BiocCheck. Thank you in advance for your answer, Emilie Secherre <https://secure-web.cisco.com/1lwre-aHHcRizwgWLTysqlxTkQiybIA-Ps00M-PLKpqFVzJ64aTPySscIJyAnB8wINYl6Wsd_ltPJc8U5_1kHh6b6TDxaWvrB9i-FIKc_zu3ZOWI2irLvOWfyB-xEN1-NQq2ZiloDniTzfDEFtTRs87pcEz0oTQNyG5GtwQXpC3M3F2Eox3UixhBzpARysKMIYCbPbVuSmVxzchWnD4j4KgrxbcxPs61hCx0H-GoRXd7K_0oiIFq1wIg4YUAEP_66v4VUR3_ajkfABp01qcaJCnIjKHswCiAKb9Ta_tQTbiTb93glCt883z5FmK3T0pGo/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail> Garanti sans virus. http://secure-web.cisco.com/1dpic_w7RKEppZqqs_Yss0WOlzxlFcgXQS9dTNgAck28Z4H--TRKKnEOu7DkBkYh4uI1v2iDQWoPnb-1lZuxZkxly8iOjadcs_GtP6slHhaA0r3px5xJX0Lyh_eBLQwJLOqvbP3wmQ0uTRem2-wSPhpNzqvnVu1nwNBcDWzN8gievsPXOUg1C0kxueCoPAU-irC58E9JwH1EJtFZINi4UZCHKD5cHwpoMNs5MZHQw4vBH8jyo2TuuuL3K8KeKTxTsGEi11Q2oky72N-x6851KYx7Qb4h2YVlZFKW8Z-SfbBB36f-nlMcb2MT8MhCEKwvT/http%3A%2F%2Fwww.avast.com <https://secure-web.cisco.com/1lwre-aHHcRizwgWLTysqlxTkQiybIA-Ps00M-PLKpqFVzJ64aTPySscIJyAnB8wINYl6Wsd_ltPJc8U5_1kHh6b6TDxaWvrB9i-FIKc_zu3ZOWI2irLvOWfyB-xEN1-NQq2ZiloDniTzfDEFtTRs87pcEz0oTQNyG5GtwQXpC3M3F2Eox3UixhBzpARysKMIYCbPbVuSmVxzchWnD4j4KgrxbcxPs61hCx0H-GoRXd7K_0oiIFq1wIg4YUAEP_66v4VUR3_ajkfABp01qcaJCnIjKHswCiAKb9Ta_tQTbiTb93glCt883z5FmK3T0pGo/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://secure-web.cisco.com/1-GUsUWfilq2QbmuQ1z-hcm1ypTsGXBFaIfcc0hfxzMSLdoMG9mj6JC4Wtu9pYCfJOrR38uuWeK6tdCYeogdaDAnlINKU2kll9o7CoUCHCj3g1dpQWDPt36iecit-pF17FYfsWqK-Ys8oHAcX8i9IowIZ0sn36OUtc0Tbc6bu2FRkWM4jpYSiRSRDQuVN5fQQvgd5RBPs-T2yN6uT5WOIXV0j7TCdv5Nawu-ps1-u_Lr8IgcwcbK9ZF8Qdd5ZWwvnLqnyaRybzZP6xGHr7usUF_-7NUTT1OJx6OaEjD9Y99984YMUDWYJkuwKy7SfixwD/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
