e build system
over the next two builds
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
From: Bioc-devel on behalf of cstrato
Sent: Saturd
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
From: Bioc-devel on behalf of cstrato
Sent: Saturday, April 6, 2019 7:23:39 AM
To: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] celaya2 and merida2 are running d
Dear Lori,
Since you have just mentioned that users need to satisfy 'celaya2' since
'merida2' will be taken offline shortly, may I remind you that 'xps' is
still missing the ROOT framework on 'celaya2', see:
https://stat.ethz.ch/pipermail/bioc-devel/2019-February/014670.html
Best regards,
Chr
of weeks. Martin
On 2/18/19, 9:16 AM, "Bioc-devel on behalf of cstrato"
wrote:
Dear All,
End of January you have set up a new Mac server, called 'celaya2'.
The problem is that since the setup of 'celaya2' my package xps reports
laya2'.
I would appreciate if this could be done within the next few weeks.
Thank you in advance.
Best regards,
Christian
_._._._._._._._._._._._._._._._._._
C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a
V.i.e.n.n.a A.u.s.t.r.i.a
e.m.a.i.l: cstrato at aon.at
_._._._._._._._._._._._._._
flicts in version change
1 file changed, 4 deletions(-)
$ git push origin master
Enter passphrase for key '/Users/cstrato/.ssh/id_rsa':
Counting objects: 3, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (3/3), done.
Writing objects: 100% (3/3), 324 bytes | 0 b
...@git.bioconductor.org:packages/xps (fetch)
upstreamg...@git.bioconductor.org:packages/xps (push)
$ git checkout master
Already on 'master'
Your branch is up-to-date with 'origin/master'.
$ git pull upstream master
Enter passphrase for key '/Users/cstrato/.ssh/
Dear Nitesh,
Thank you for your fast reply. Here is what I tried now,
including using 'git pull':
$ cd /Volumes/T3Data/CRAN/GIT/xps
$ git checkout master
Already on 'master'
Your branch is up-to-date with 'origin/master'.
$ git pull
Enter passphrase for k
Dear GIT experts,
On Saturday I wanted to update my development package to xps_1.41.1,
however until now it was not updated in the 'Multiple platform
build/check report' although I could confirm the changes with Firefox:
https://github.com/cstrato/xps
For this reason I trie
were finally uploaded to:
http://bioconductor.org/checkResults/devel/bioc-LATEST/xps/
Finally I was able to upload the 'xps' code to:
https://github.com/cstrato/xps
by running:
$ git push -u origin master
Enter passphrase for key '/Users/rabbitus/.ssh/id_rsa':
Counting objects: 2
ust admit that I was astonished since I did not expect this (and I
did not want this!)
So I changed it to:
# This is Git's per-user configuration file.
[user]
# Please adapt and uncomment the following lines:
name = cstrato
email = cstr...@aon.at
My other question was:
D
low.com/questions/10946893/git-name-and-email-address-configuration
and did:
$ git config --global user.name "cstrato"
$ git config --global user.email cstr...@aon.at
Now the file '~/.gitconfig' does contain the corrected name and email.
Afterwards, I tried:
$ git commit
10/15/2017 06:00 PM, cstrato wrote:
I have just seen the update 2017-10-15 of the BUILD/CHECK report:
http://bioconductor.org/checkResults/devel/bioc-LATEST/xps/
which was not available when I have sent my former mail.
For some reason my commit to version xps_1.37.2 was not accepted.
Please te
this problem.
Best regards,
Christian
On 10/15/17 21:37, cstrato wrote:
Hi,
Since 'https://github.com/cstrato/xps' does only contain information how
to create or push a repository I tried to follow again:
http://master.bioconductor.org/developers/how-to/git/push-to-github-bioc/
Hi,
Since 'https://github.com/cstrato/xps' does only contain information how
to create or push a repository I tried to follow again:
http://master.bioconductor.org/developers/how-to/git/push-to-github-bioc/
2. View existing remotes
$ git remote -v
origin g...@github.com:cstra
/cstrato/xps is still empty.
Do you know what the problem might be?
Could it be that the 'git/svn transition: ssh keys' form did not accept
my SSH public key?
Or could it be that I am running Firefox in 'private browsing' mode
(although cookies are activated)?
To test thi
hrase for key '/Users/rabbitus/.ssh/id_rsa':
Everything up-to-date
$ git push upstream master
Enter passphrase for key '/Users/rabbitus/.ssh/id_rsa':
Everything up-to-date
I hope that I could commit my changes and my development version on
https://github.com/cstrato/xps
will
and why my correct key is not accepted.
According to 'https://caius.github.io/github_id/' my user id is:
cstrato is github user #32616897
My public key at 'https://github.com/cstrato.keys' is still empty.
I am not sure what I need to do next?
Thank you.
Best regards,
Christian
SVN user id.
Is this correct, or how do I get my SVN user id?
3, I created a new GitHub repository:
https://github.com/cstrato/xps
4, Then I tried to clone the empty repository from GitHub. Here is the
result:
iMac:GIT cstrato$ git clone https://github.com/cstrato/xps.git
Cloning into &#x
Dear Herve,
I have just seen that now both files have been updated.
Thank you,
Christian
On 04/30/17 00:07, cstrato wrote:
Dear Herve,
Sorry to contact you again, but I have yesterday uploaded new versions,
'xps_1.36.1' (release branch) and 'xps_1.37.1' (devel branch)
Dear Herve,
Sorry to contact you again, but I have yesterday uploaded new versions,
'xps_1.36.1' (release branch) and 'xps_1.37.1' (devel branch), which
contain both updated versions of the README and INSTALL files.
While the documentation of the development branch contains the updated
files
Yes, I know.
I wanted only to mention that this error is hopefully corrected in
today's update.
Christian
On 04/23/17 22:19, Hervé Pagès wrote:
On 04/23/2017 12:15 PM, cstrato wrote:
Dear Herve,
I have just seen that the newest build xps_1.3.3:
https://urldefense.proofpoint.com/v2/
this dependency
(see my mail below).
Best regards,
Christian
On 04/23/17 17:31, cstrato wrote:
Dear Herve,
Since some users report problems since many years that the libs are
found in '/usr/local/root/lib/root', I agree that it is a good idea
to set LDFLAGS also to
LDFLAGS = ... -rpa
OS Sierra (Oct 2016), see:
https://root-forum.cern.ch/t/compilation-problem-with-os-sierra-xcode-8-root-6-06-08/22102/6
There was an interesting reply:
Better don't use -j4 when using cmake, just when using make.
I am not sure whether this is still true, since it seems to work in your
case.
bit libraries of root and not the 32 bit ones.
For me the 64 bit libraries were located in /usr/local/lib/root while
the 32 bit ones were in /usr/local/root/lib/root.
I am not sure what this means and if it is helpful for you.
Best regards,
Christian
On 04/22/17 23:57, cstrato wrote:
Dear
file (which BTW should preferably be named
INSTALL).
Thanks,
H.
On 04/22/2017 05:15 AM, cstrato wrote:
Dear Herve,
I am glad to inform you that I have just uploaded version xps_1.35.3 to
BioC-dev branch. I have followed your suggestion to use -rpath and have
eliminated the environment vari
quot;Hervé Pagès"
To: "cstrato" , "Dan Tenenbaum"
Cc: "bioc-devel"
Sent: Thursday, April 20, 2017 3:17:23 PM
Subject: Re: [Bioc-devel] xps build problem on veracruz2
On 04/20/2017 03:01 PM, cstrato wrote:
Dear Herve,
Doing 'csrutil disable' does
ood place to seek help
for this.
Cheers,
H.
On 04/20/2017 10:53 AM, cstrato wrote:
Dear Herve,
Thank you for your efforts to try to install xps. I am glad to hear that
you could build ROOT 5 from source.
It's a pity that Apple does no longer allow the use of
DYLD_LIBRARY_PATH. This see
;>>
On 03/23/17 17:47, Hervé Pagès wrote:
Hi Christian,
The CRAN folks are currently experimenting with clang 4.0.0 for
producing the Mac binaries of R and CRAN packages so we are
using
the same on veracruz2. This is a version of clang that is
ahead of
what's in XCode 8.x or XCode
On 03/24/17 19:55, Hervé Pagès wrote:
On 03/24/2017 11:37 AM, cstrato wrote:
On 03/24/17 19:23, Hervé Pagès wrote:
On 03/24/2017 11:10 AM, cstrato wrote:
On 03/24/17 18:02, Hervé Pagès wrote:
On 03/24/2017 06:52 AM, cstrato wrote:
R/Bioc is still building on Mavericks,
Not for R
On 03/24/17 19:23, Hervé Pagès wrote:
On 03/24/2017 11:10 AM, cstrato wrote:
On 03/24/17 18:02, Hervé Pagès wrote:
On 03/24/2017 06:52 AM, cstrato wrote:
R/Bioc is still building on Mavericks,
Not for R devel (3.4). The R folks have switched to El Capitan a few
days ago:
You are
On 03/24/17 18:02, Hervé Pagès wrote:
On 03/24/2017 06:52 AM, cstrato wrote:
R/Bioc is still building on Mavericks,
Not for R devel (3.4). The R folks have switched to El Capitan a few
days ago:
You are right, I did not check R devel.
https://r.research.att.com/
and before was
:
- Original Message -
From: "Hervé Pagès"
To: "cstrato" , "bioc-devel"
Sent: Thursday, March 23, 2017 12:14:38 PM
Subject: Re: [Bioc-devel] xps build problem on veracruz2
On 03/23/2017 11:09 AM, cstrato wrote:
Dear Herve,
Thank you for your explanation.
means we'll have
to compile ROOT from source on veracruz2.
BTW any reason not to make xps work with ROOT 6?
Cheers,
H.
On 03/23/2017 07:28 AM, cstrato wrote:
Dear Valerie,
I have seen that you have set up a new Mac server, veracruz2, running El
Capitan.
Although the development version of xps
V.i.e.n.n.a A.u.s.t.r.i.a
e.m.a.i.l:cstrato at aon.at
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___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
lem may be
more wide spread and it's helpful to have more than one person looking
at it.
Valerie
On 01/27/2017 09:53 AM, cstrato wrote:
Dear Valerie,
Thank you for your extensive reply.
I understand that it does not affect any users. It was only a reminder.
Usually, I have contacted D
he mailing lists when
toluca2 officially replaces oaxaca and at that point you'll only see
toluca2 on the build report.
Valerie
On 01/26/2017 10:08 AM, cstrato wrote:
Dear all,
Since Dan, who was always very helpful and took care of the special
requirements of my package 'xps', is n
d be no problem to transfer ROOT and the corresponding settings to
toluca2.
Thank you in advance.
Best regards,
Christian
_._._._._._._._._._._._._._._._._._
C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a
V.i.e.n.n.a A.u.s.t.r
Dear all,
Looking at the alphabetical list of functions/methods in BioGenerics I
have the feeling that all functions are really generic, i.e. general,
with the exception of function 'annotation' which in my opinion should
be part of BioBase as method for one or more of the BioBase classes.
T
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