On Oct 17, 2017, at 11:39 AM, Zhao, Shilin <shilin.zhao.1 at vanderbilt.edu> wrote:
See below. Thanks!
ssh -v git at 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= zhaoshilin at gmail.com
-----Original Message-----
From: Turaga, Nitesh [mailto:Nitesh.Turaga at RoswellPark.org]
Sent: Tuesday, October 17, 2017 6:05 AM
To: Zhao, Shilin <shilin.zhao.1 at vanderbilt.edu>
Cc: Shepherd, Lori <Lori.Shepherd at 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 git at 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= zhaoshilin at gmail.com
On Oct 17, 2017, at 12:34 AM, Zhao, Shilin <shilin.zhao.1 at 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
git at 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 git at 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.Turaga at RoswellPark.org]
Sent: Tuesday, October 10, 2017 10:01 AM
To: Zhao, Shilin <shilin.zhao.1 at vanderbilt.edu>
Cc: Shepherd, Lori <Lori.Shepherd at 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.zhao.1 at 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.Turaga at RoswellPark.org]
Sent: Wednesday, September 27, 2017 11:15 AM
To: Zhao, Shilin <shilin.zhao.1 at vanderbilt.edu>
Subject: Fwd: Failing bioconductor package KEGGprofile
Begin forwarded message:
From: ni41435_ca <nitesh.turaga at roswellpark.org>
Subject: Failing bioconductor package KEGGprofile
Date: September 27, 2017 at 12:13:36 PM EDT
To: Shilin Zhao <shilin.zhao at 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
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