So I think the file probably got pushed up before you added it to .gitignore. So you would probably want to git rm the files, commit, and push. Then you could add them back in after and if they were still listed in the .gitignore then they would be ignored.
Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 ________________________________ From: Emilie Secherre <emiseche...@gmail.com> Sent: Tuesday, September 22, 2020 9:04 AM To: Shepherd, Lori <lori.sheph...@roswellpark.org> Cc: bioc-devel@r-project.org <bioc-devel@r-project.org> Subject: Re: [Bioc-devel] BiocCheckGitClone error This time I used Git clone folder. Though, when I push famat package in github, .gitignore file isn't uploaded, so I created a .gitignore file in the github repository with "famat.Rproj" in it before pushing the whole package. Unfortunately, the "famat.Rproj" file is still in the git clone folder... [https://secure-web.cisco.com/14HlJ6pYPmc3ca4y-t8kMrtl9__nsZZIVdh1FyubkHtI_uHav7g8NmQ3g-Ddrj8crOerXSz7-BGWmj25QldqKh3CziRw4-vIC05u5I75Qo3f0daNrBjyscENAIKQkhC87QNrfNSTXCTnRjEpzGPHtVFS6uzyXWChEq5nFnl-74b4Fcg092PiTaoGdd1X_Rg4D9CpCcT2XMQv7sIH2ep_u3gbh6cOAd_ELgRxwS30KMyWcEqRLglF7qSBH_7DOghdgZbaD1ZGO_eexhcDLj3Vq46ylckVe1nX6YLAESP1vV1hUpZ7guAhahUlHcW-7w6iM/https%3A%2F%2Fipmcdn.avast.com%2Fimages%2Ficons%2Ficon-envelope-tick-round-orange-animated-no-repeat-v1.gif]<https://secure-web.cisco.com/1kUcjeK1l5uJLWUgk1BEPSSsClwf6nXlSgM5k14zf32z1bnZJmqgWRn1b1BpkEBSNysDnSMiukeI70FhY3w7_9VXHSZxuSFyPsoZOCeYdt6XZmvRyG1y-kHEda2Ffe3Vy6uhqWccL_pE3Ru9s5EQyoBoVuNEs56AUlsD4cWsBjcfXiCDL6EBRbgmOIwR9l9iRR6VAMTQ5o8azDl8DAocIGa6H7VwNFbowLLmnLuTIUqMKK0TiEcIPataXipooaiyDu95bM1X0bo-7BHtGzt2UocrIT9TTtSxudid7Dk4nuBjLFCRbpxuVJYLfsEwA0-hU/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail> Garanti sans virus. www.avast.com<https://secure-web.cisco.com/1kUcjeK1l5uJLWUgk1BEPSSsClwf6nXlSgM5k14zf32z1bnZJmqgWRn1b1BpkEBSNysDnSMiukeI70FhY3w7_9VXHSZxuSFyPsoZOCeYdt6XZmvRyG1y-kHEda2Ffe3Vy6uhqWccL_pE3Ru9s5EQyoBoVuNEs56AUlsD4cWsBjcfXiCDL6EBRbgmOIwR9l9iRR6VAMTQ5o8azDl8DAocIGa6H7VwNFbowLLmnLuTIUqMKK0TiEcIPataXipooaiyDu95bM1X0bo-7BHtGzt2UocrIT9TTtSxudid7Dk4nuBjLFCRbpxuVJYLfsEwA0-hU/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail> Le mar. 22 sept. 2020 � 14:12, Shepherd, Lori <lori.sheph...@roswellpark.org<mailto:lori.sheph...@roswellpark.org>> a �crit : 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<mailto:bioc-devel-boun...@r-project.org>> on behalf of Emilie Secherre <emiseche...@gmail.com<mailto:emiseche...@gmail.com>> Sent: Tuesday, September 22, 2020 4:57 AM To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> <bioc-devel@r-project.org<mailto: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<mailto: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. 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