If you have further trouble, I think you should submit your key again to the google form. And wait for the new key to be added.
It might also help to read the instructions here again, bioconductor.org/developers/how-to/git/. > On Oct 17, 2017, at 11:39 AM, Zhao, Shilin <shilin.zha...@vanderbilt.edu> > wrote: > > See below. Thanks! > > ssh -v g...@git.bioconductor.org > OpenSSH_5.3p1, OpenSSL 1.0.1e-fips 11 Feb 2013 > debug1: Reading configuration data /etc/ssh/ssh_config > debug1: Applying options for * > debug1: Connecting to git.bioconductor.org [34.192.48.227] port 22. > debug1: Connection established. > debug1: identity file /home/zhaos/.ssh/identity type -1 > debug1: identity file /home/zhaos/.ssh/identity-cert type -1 > debug1: identity file /home/zhaos/.ssh/id_rsa type 1 > debug1: identity file /home/zhaos/.ssh/id_rsa-cert type -1 > debug1: identity file /home/zhaos/.ssh/id_dsa type -1 > debug1: identity file /home/zhaos/.ssh/id_dsa-cert type -1 > debug1: identity file /home/zhaos/.ssh/id_ecdsa type -1 > debug1: identity file /home/zhaos/.ssh/id_ecdsa-cert type -1 > debug1: Remote protocol version 2.0, remote software version OpenSSH_7.2p2 > Ubuntu-4ubuntu2.2 > debug1: match: OpenSSH_7.2p2 Ubuntu-4ubuntu2.2 pat OpenSSH* > debug1: Enabling compatibility mode for protocol 2.0 > debug1: Local version string SSH-2.0-OpenSSH_5.3 > debug1: SSH2_MSG_KEXINIT sent > debug1: SSH2_MSG_KEXINIT received > debug1: kex: server->client aes128-ctr hmac-sha1 none > debug1: kex: client->server aes128-ctr hmac-sha1 none > debug1: SSH2_MSG_KEX_DH_GEX_REQUEST(1024<2048<8192) sent > debug1: expecting SSH2_MSG_KEX_DH_GEX_GROUP > debug1: SSH2_MSG_KEX_DH_GEX_INIT sent > debug1: expecting SSH2_MSG_KEX_DH_GEX_REPLY > debug1: Host 'git.bioconductor.org' is known and matches the RSA host key. > debug1: Found key in /home/zhaos/.ssh/known_hosts:12 > debug1: ssh_rsa_verify: signature correct > debug1: SSH2_MSG_NEWKEYS sent > debug1: expecting SSH2_MSG_NEWKEYS > debug1: SSH2_MSG_NEWKEYS received > debug1: SSH2_MSG_SERVICE_REQUEST sent > debug1: SSH2_MSG_SERVICE_ACCEPT received > debug1: Authentications that can continue: publickey > debug1: Next authentication method: publickey > debug1: Trying private key: /home/zhaos/.ssh/identity > debug1: Offering public key: /home/zhaos/.ssh/id_rsa > debug1: Authentications that can continue: publickey > debug1: Trying private key: /home/zhaos/.ssh/id_dsa > debug1: Trying private key: /home/zhaos/.ssh/id_ecdsa > debug1: No more authentication methods to try. > Permission denied (publickey). > > > more /home/zhaos/.ssh/id_rsa.pub > ssh-rsa > AAAAB3NzaC1yc2EAAAABIwAAAgEAnTHeitBs6pakp2KmWdsAcqE7XJ3EAHZUsVP9t5AsN0FWG0gJg5V7I5jCckzfW2aYL4HdbKO39fpVzixNpa3Tqi6QPNoBBo7SKkpBhxQrsh8xRvFlGmV27qXJUbRhOEOkvWhJFuSXZ1Di+xvwFpvjUFOYWafItOjHTuI5TTkVQRTydu9sw3n15PN1BWhvA > pnLmKJzQNWJvskQINMgMpO0L+cswF9dtDcStkK7hVuow0Gz7Z3/kKxgTNd9becUHEteK0RpXKm0SLgAphvQfvYe7FLDEQ1JlSwaZ42lS74f+5uFFUPNtzc1IuvdWPKxsNxODhOLFCX8Xao6fO3X7KpcLEc5o0SX8SxSLFI4U8l/1V3xYcDFklp786zfb0BsnSilIErcbtTeMJOG6FdlHO3gjzScwkS9u1 > mw8ZIu3CvOFV1/IarMuuTTrYLI8b22ho4TTo/aiQOm1zYayxVsp65tMwNbjwSBLjOvR9A9a+sGbVk9xZRvGeH8DYYaPQoJHLJwMXEiULLAjaL4HJaV9pEuaWD6cLnRxqkoSILIsSboele5H4A2EKZXztfdq8rzS4pgw0tv9fap+Y0+DiDk5P98Wf8Cm5dzrpMty7xBvMDFBAWJTnRlakFv5kA5pLWJtc5 > +o6pXv4QK5+VuHrHGrj3V/ViYMoYGqZYck2lAm2WNMSk= zhaoshi...@gmail.com > > > -----Original Message----- > From: Turaga, Nitesh [mailto:nitesh.tur...@roswellpark.org] > Sent: Tuesday, October 17, 2017 6:05 AM > To: Zhao, Shilin <shilin.zha...@vanderbilt.edu> > Cc: Shepherd, Lori <lori.sheph...@roswellpark.org> > Subject: Re: EXTERNAL: RE: Failing bioconductor package KEGGprofile > > Try this command and send the output, it is likely you are not using the > correct key on your machine. Your key is in our system already. > > ssh -v g...@git.bioconductor.org > > See, if the public key you submitted is being used. > > ssh-rsa > AAAAB3NzaC1yc2EAAAABIwAAAgEAnTHeitBs6pakp2KmWdsAcqE7XJ3EAHZUsVP9t5AsN0FWG0gJg5V7I5jCckzfW2aYL4HdbKO39fpVzixNpa3Tqi6QPNoBBo7SKkpBhxQrsh8xRvFlGmV27qXJUbRhOEOkvWhJFuSXZ1Di+xvwFpvjUFOYWafItOjHTuI5TTkVQRTydu9sw3n15PN1BWh > > vApnLmKJzQNWJvskQINMgMpO0L+cswF9dtDcStkK7hVuow0Gz7Z3/kKxgTNd9becUHEteK0RpXKm0SLgAphvQfvYe7FLDEQ1JlSwaZ42lS74f+5uFFUPNtzc1IuvdWPKxsNxODhOLFCX8Xao6fO3X7KpcLEc5o0SX8SxSLFI4U8l/1V3xYcDFklp786zfb0BsnSilIErcbtTeMJOG6FdlHO3gjzScwk > > S9u1mw8ZIu3CvOFV1/IarMuuTTrYLI8b22ho4TTo/aiQOm1zYayxVsp65tMwNbjwSBLjOvR9A9a+sGbVk9xZRvGeH8DYYaPQoJHLJwMXEiULLAjaL4HJaV9pEuaWD6cLnRxqkoSILIsSboele5H4A2EKZXztfdq8rzS4pgw0tv9fap+Y0+DiDk5P98Wf8Cm5dzrpMty7xBvMDFBAWJTnRlakFv5kA5p > LWJtc5+o6pXv4QK5+VuHrHGrj3V/ViYMoYGqZYck2lAm2WNMSk= zhaoshi...@gmail.com > > > On Oct 17, 2017, at 12:34 AM, Zhao, Shilin <shilin.zha...@vanderbilt.edu> > > wrote: > > > > Hi Nitesh, > > > > I was not able to fetch KEGGprofile from Bioconductor. Would you please > > help with it? Thanks! > > > > git remote add upstream > > g...@git.bioconductor.org:packages/KEGGprofile.git > > git fetch upstream > > Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (RSA) to > > the list of known hosts. > > Permission denied (publickey). > > fatal: Could not read from remote repository. > > > > Please make sure you have the correct access rights and the repository > > exists. > > > > #I have submitted my SSH public key to Bioconductor, and my SSH key works > > in github: > > ssh -T g...@github.com > > Hi slzhao! You've successfully authenticated, but GitHub does not provide > > shell access. > > > > Thanks! > > > > Best, > > Shilin > > > > -----Original Message----- > > From: Turaga, Nitesh [mailto:nitesh.tur...@roswellpark.org] > > Sent: Tuesday, October 10, 2017 10:01 AM > > To: Zhao, Shilin <shilin.zha...@vanderbilt.edu> > > Cc: Shepherd, Lori <lori.sheph...@roswellpark.org> > > Subject: Re: Failing bioconductor package KEGGprofile > > > > Bump the version. It should redo the whole thing. > > > > Consider adding > > importFrom("grDevices", "dev.off", "png", "rainbow") > > importFrom("graphics", "abline", "axis", "box", "boxplot", "image", > > "legend", "matplot", "par", "plot", "polygon", > > "rasterImage", "text") > > importFrom("stats", "cor", "median", "p.adjust", "phyper", "sd", "var", > > "wilcox.test") > > importFrom("utils", "download.file", "flush.console”) > > > > > > > > > On Oct 9, 2017, at 3:13 PM, Zhao, Shilin <shilin.zha...@vanderbilt.edu> > > > wrote: > > > > > > Hello Nitesh, > > > > > > Would you please help with my package bug-fix? > > > > > > For Development version, the error message is here: > > > https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmast > > > er > > > .bioconductor.org%2FcheckResults%2F3.6%2Fbioc-LATEST%2FKEGGprofile%2 > > > Fm > > > albec1-checksrc.html&data=02%7C01%7Cshilin.zhao.1%40vanderbilt.edu%7 > > > C3 > > > 02d9906c2fc42d58c8008d50fefb5df%7Cba5a7f39e3be4ab3b45067fa80faecad%7 > > > C0 > > > %7C0%7C636432444583862185&sdata=idhR7L%2BMkKDfi1p8GphCYLWfux4HHyIWoU > > > 6d > > > Db5Hk%2B8%3D&reserved=0 > > > > > > It says “Error: XML content does not seem to be XML: > > > '/home/biocbuild/bbs-3.6-bioc/meat/KEGGprofile.Rcheck/KEGGprofile/extdata/hsa00020.xml' > > > ” > > > > > > This file should be downloaded from KEGG website and there was a bug and > > > I have fixed it. You can see the vignette and example of > > > download_KEGGfile are running successfully now, which means the > > > “download” function is good now. And the exactly same version can be run > > > on my side. So I think the code is good now. > > > > > > But I guess the xml file on the server was not re-generated. It was an > > > old version (broken) on the server. So it made the error. Do you have a > > > way to deleted the whole “KEGGprofile.Rcheck” folder and re-run the > > > checking? Thanks! > > > > > > Best, > > > Shilin > > > > > > > > > > > > > > > From: Turaga, Nitesh [mailto:nitesh.tur...@roswellpark.org] > > > Sent: Wednesday, September 27, 2017 11:15 AM > > > To: Zhao, Shilin <shilin.zha...@vanderbilt.edu> > > > Subject: Fwd: Failing bioconductor package KEGGprofile > > > > > > > > > > > > > > > Begin forwarded message: > > > > > > From: ni41435_ca <nitesh.tur...@roswellpark.org> > > > Subject: Failing bioconductor package KEGGprofile > > > Date: September 27, 2017 at 12:13:36 PM EDT > > > To: Shilin Zhao <shilin.z...@vanderbilt.edu> > > > > > > Dear KEGGprofile maintainer, > > > > > > The KEGGprofile package is failing to pass 'R CMD check' on all platforms > > > in the devel version of Bioconductor (i.e. BioC 3.6): > > > > > > https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww > > > .b > > > ioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FKEGGprofile%2 > > > F& > > > data=02%7C01%7Cshilin.zhao.1%40vanderbilt.edu%7C302d9906c2fc42d58c80 > > > 08 > > > d50fefb5df%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C636432444583 > > > 86 > > > 2185&sdata=369J8NOSI2IrPSHJ8Cl1qs42werz5DB3cFBTGgqvif8%3D&reserved=0 > > > > > > This is your first warning. If no action is taken over the next few > > > weeks we will begin the deprecation process for your package. Thank you > > > for your time and effort. > > > > > > Thanks for your contribution to Bioconductor. > > > > > > Pleae be advised that Bioconductor has switched from svn to Git. > > > Some helpful links can be found here: > > > > > > https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbio > > > co > > > nductor.org%2Fdevelopers%2Fhow-to%2Fgit%2F&data=02%7C01%7Cshilin.zhao. > > > 1%40vanderbilt.edu%7C302d9906c2fc42d58c8008d50fefb5df%7Cba5a7f39e3be > > > 4a > > > b3b45067fa80faecad%7C0%7C0%7C636432444583862185&sdata=Bg5qXKBz%2BWem > > > A4 > > > Ktd773WVEE59uqFk%2B8GD8T6XklP5M%3D&reserved=0 > > > > > > Best, > > > > > > Nitesh Turaga > > > Bioconductor Core Team > > > > > > > > > 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. > > > > > > > > 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. > > > > 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. 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. 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