[Bioc-devel] BiocCheckGitClone error

Wed Sep 23 13:52:32 CEST 2020

Yes.  Go ahead and submit the package to the tracker.  We can investigate this further with your assigned reviewer.  Sorry for the inconvenience.

Cheers,

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: Wednesday, September 23, 2020 3:35 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

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

[https://secure-web.cisco.com/1HQT4avzpKVe6j7PuRRxrsuWMDf9cWUZuvWvcmpy-Hm9ylUZcF1ZK9nij0XmQseltPyNpiVmy97v-prEItcNCrEAqe9fIjUDyu0csq6FZafOd080slA_qK4RzvNTFpksPzhjCbqJXkoQCSo1LZBF77jZxj3MjR8FCoZMJJ4U34udEfaunOUDkSlbg8LQPaGHtHgwcnYoVrpHPwzErSn4gBD2ViioFX0Ih7UCTGBvlWD1s5570xDsW6bkezIp2St53vPw6zUrY7552Hb1Flo43oOYZU90q15k8vJV2UjMlfP9FzDiX9wEkI4CumAgAmcQw/https%3A%2F%2Fipmcdn.avast.com%2Fimages%2Ficons%2Ficon-envelope-tick-round-orange-animated-no-repeat-v1.gif]<https://secure-web.cisco.com/17l9BTXu1ngxN75bEPvs7hsonthCqIcSnKrCD9HCnP5tOgrGU5-zej7v0522uC4i4IlpHOf0dxvuBmjmp-mYGyLhOYm6G5dz0qxy97sD-4hkfK2s7jtNVPTC8-M2oeFhjkSXd0EDiTJId30qyV1gokBTajOy93gX-6Bx39Ot39ZeuXxBgVHHsd1p6GI31OoRT8s04vOXupH16uslqopreYCdf-PEpBNdUHVb1lVMIgzxxZxnYLAVPcKf5JD52Ft_kBpHjxgPSJW0_dLWw7IckfVXudVlCvf5Jb6tYp5WEqaRZ72fBgYDr_He-ocy8agax/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/17l9BTXu1ngxN75bEPvs7hsonthCqIcSnKrCD9HCnP5tOgrGU5-zej7v0522uC4i4IlpHOf0dxvuBmjmp-mYGyLhOYm6G5dz0qxy97sD-4hkfK2s7jtNVPTC8-M2oeFhjkSXd0EDiTJId30qyV1gokBTajOy93gX-6Bx39Ot39ZeuXxBgVHHsd1p6GI31OoRT8s04vOXupH16uslqopreYCdf-PEpBNdUHVb1lVMIgzxxZxnYLAVPcKf5JD52Ft_kBpHjxgPSJW0_dLWw7IckfVXudVlCvf5Jb6tYp5WEqaRZ72fBgYDr_He-ocy8agax/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 � 15:36, Emilie Secherre <emisecherre using gmail.com<mailto:emisecherre using gmail.com>> a �crit :
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://secure-web.cisco.com/1HQT4avzpKVe6j7PuRRxrsuWMDf9cWUZuvWvcmpy-Hm9ylUZcF1ZK9nij0XmQseltPyNpiVmy97v-prEItcNCrEAqe9fIjUDyu0csq6FZafOd080slA_qK4RzvNTFpksPzhjCbqJXkoQCSo1LZBF77jZxj3MjR8FCoZMJJ4U34udEfaunOUDkSlbg8LQPaGHtHgwcnYoVrpHPwzErSn4gBD2ViioFX0Ih7UCTGBvlWD1s5570xDsW6bkezIp2St53vPw6zUrY7552Hb1Flo43oOYZU90q15k8vJV2UjMlfP9FzDiX9wEkI4CumAgAmcQw/https%3A%2F%2Fipmcdn.avast.com%2Fimages%2Ficons%2Ficon-envelope-tick-round-orange-animated-no-repeat-v1.gif]<https://secure-web.cisco.com/17l9BTXu1ngxN75bEPvs7hsonthCqIcSnKrCD9HCnP5tOgrGU5-zej7v0522uC4i4IlpHOf0dxvuBmjmp-mYGyLhOYm6G5dz0qxy97sD-4hkfK2s7jtNVPTC8-M2oeFhjkSXd0EDiTJId30qyV1gokBTajOy93gX-6Bx39Ot39ZeuXxBgVHHsd1p6GI31OoRT8s04vOXupH16uslqopreYCdf-PEpBNdUHVb1lVMIgzxxZxnYLAVPcKf5JD52Ft_kBpHjxgPSJW0_dLWw7IckfVXudVlCvf5Jb6tYp5WEqaRZ72fBgYDr_He-ocy8agax/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/17l9BTXu1ngxN75bEPvs7hsonthCqIcSnKrCD9HCnP5tOgrGU5-zej7v0522uC4i4IlpHOf0dxvuBmjmp-mYGyLhOYm6G5dz0qxy97sD-4hkfK2s7jtNVPTC8-M2oeFhjkSXd0EDiTJId30qyV1gokBTajOy93gX-6Bx39Ot39ZeuXxBgVHHsd1p6GI31OoRT8s04vOXupH16uslqopreYCdf-PEpBNdUHVb1lVMIgzxxZxnYLAVPcKf5JD52Ft_kBpHjxgPSJW0_dLWw7IckfVXudVlCvf5Jb6tYp5WEqaRZ72fBgYDr_He-ocy8agax/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 � 15:32, Shepherd, Lori <Lori.Shepherd using roswellpark.org<mailto:Lori.Shepherd using roswellpark.org>> a �crit :
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<mailto: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<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org<mailto: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/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.Shepherd using roswellpark.org<mailto:Lori.Shepherd using 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-bounces using r-project.org<mailto:bioc-devel-bounces using r-project.org>> on behalf of Emilie Secherre <emisecherre using gmail.com<mailto:emisecherre using gmail.com>>
Sent: Tuesday, September 22, 2020 4:57 AM
To: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org<mailto: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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