[Bioc-devel] BiocCheckGitClone error

[Emilie Secherre]

I still couldn't fix the issue, therefore is that allowed to just don't
push the .Rproj file in github ?
Thanks in advance for your answer
Emilie

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Le mar. 22 sept. 2020 à 15:36, Emilie Secherre <emisecherre using gmail.com> a
écrit :

> I pushed famat.Rproj after .gitignore was created and pushed with
> "famat.Rproj" in it. That's why i don't understand why famat.Rproj is still
> in the clone folder.
>
>
> <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> Garanti
> sans virus. www.avast.com
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> Le mar. 22 sept. 2020 à 15:32, Shepherd, Lori <
> Lori.Shepherd using roswellpark.org> a écrit :
>
>> 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 <emisecherre using gmail.com>
>> *Sent:* Tuesday, September 22, 2020 9:04 AM
>> *To:* Shepherd, Lori <Lori.Shepherd using RoswellPark.org>
>> *Cc:* bioc-devel using r-project.org <bioc-devel using 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/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>
>> <#m_5808152295650690142_m_-1353067446180599254_x_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>>
>> Le mar. 22 sept. 2020 à 14:12, Shepherd, Lori <
>> Lori.Shepherd using roswellpark.org> a écrit :
>>
>> 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-bounces using r-project.org> on behalf of
>> Emilie Secherre <emisecherre using gmail.com>
>> *Sent:* Tuesday, September 22, 2020 4:57 AM
>> *To:* bioc-devel using r-project.org <bioc-devel using 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
>> >
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