[Rd] install_github and survival

[Therneau, Terry M., Ph.D. via R-devel]

I treat CRAN as the main repository for survival, but I have also had a github 
(therneau/survival) version for a couple of years.  It has a vignette2 
directory, for 
instance, that contains extra vignettes that either take too long to run or 
depend on 
other packages.  It also gets updated more often than CRAN (though those 
updates mght not 
be as well tested yet).

In any case, since it is there, people will of course run install_github 
against it.   
I've added a config script to do the one extra step necessary, but when I try 
install_github it fails.   I'm clearly doing something wrong.  If someone were 
willing to 
contribute a fix I would be most grateful.

survival3.1-0 is almost ready for CRAN, by the way.   Reverse dependency checks 
of hdnom 
turned up one last thing to repair...


Terry Therneau


[[alternative HTML version deleted]]

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Re: [R-pkg-devel] set pkg_config for 3rd party software

[Ralf Stubner]

On Thu, Sep 5, 2019 at 12:27 PM Martin Maechler
 wrote:

> Now what is the officially / best way to have either 'configure'
> or  Makevars.{in,win}  use the 'pkg-config' information
> *dynamically*, i.e.,
> if I update my MPFR from 4.0.1 to 4.0.2  the newer 4.0.2 is found ?

I don't know what is best, but here are three alternatives:

* Use PKG_CHECK_MODULES which sets up default variables with _CFLAGS
and _LIBS suffix after searching for a library with pkg-config, c.f.
https://autotools.io/pkgconfig/pkg_check_modules.html
* Call pkg-config by hand in configure.ac (and hence configure).
Example: 
https://github.com/eddelbuettel/rcppredis/blob/master/configure.ac#L47-L60
* Call pkg-config within an "Anticonf" configure script. Example:
https://github.com/jeroen/curl/blob/master/configure#L16-L24

cheerio
ralf

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Re: [Bioc-devel] Build error due to TensorFlow installation

[Vincent Carey]

how about TF for platforms that support it and C++ for those that don't,
eventually
migrating away from C++ as support grows?   a little messy for the moment
but let's
get some mileage on the TF solution ASAP

On Thu, Sep 5, 2019 at 9:21 AM Dirmeier Simon  wrote:

> Hi Herve,
>
> > All this means that if you replace some old C++ code with TensorFlow
> > then we will need to mark your package as unavailable on Windows and
> > Mac, at least for now. Sorry. I wonder if there was something wrong
> > with this old C++ code. I would recommend that you stick to it if you
> can.
> >
> The code is fine, but still an impractical complexity that doesn't need
> to exist:
>
> 1) It's hard to extend and read for others.
>
> 2) It needs a custom configure.ac.
>
> 3) Extending the package to other models/families is a huge pain, as one
> needs to derive custom coordinate descents (or other optimizers for that
> matter) for each.
>
> On the other side:
>
> 1) TF allowed me to replace like 5000 lines of source code with 100
> lines of R.
>
> 2) TF allows to easily extend with other models with just a few lines.
>
> 3) I don't need a huge test suite.
>
> 4) On GPUs it's a huge speedup.
>
> So, for now I'll revert the changes back on Bioc devel and continue
> development on another branch.
>
> Cheers,
>
> S
>
>
> Am 04.09.19 um 16:53 schrieb Pages, Herve:
> >
> > Hi Simon,
> >
> > On 9/3/19 09:11, Simon Dirmeier wrote:
> >> ...
> >> Do you think it would be possible to install TensorFlow and
> >> TensorFlow-Probability on the builders? I'd assume that many would
> >> profit from that.
> >>
> > As Lori mentioned at the end of her email (see below), we can't make
> > the tensorflow Python module available on our Windows builders at the
> > moment because we need to update Python to Python 3 on these machines
> > first (AFAIK tensorflow is only available for Python 3 on Windows).
> > This is something that we are currently working on.
> >
> > As for the Mac builders, we have tensorflow there but unfortunately
> > it's an old version because recent versions of are broken on El
> > Capitan (this is the Mac OS version that, for various reasons, we are
> > stuck with at the moment). This prevents us from installing the
> > tensorflow_probability module which requires a recent version of
> > tensorflow.
> >
> > The tensorflow and tensorflow_probability modules are available on our
> > Linux builders.
> >
> > All this means that if you replace some old C++ code with TensorFlow
> > then we will need to mark your package as unavailable on Windows and
> > Mac, at least for now. Sorry. I wonder if there was something wrong
> > with this old C++ code. I would recommend that you stick to it if you
> can.
> >
> > Best,
> >
> > H.
> >
> >
> >>> Right now tensorflow is unavailable on our windows server (tokay1)�as
> >>> we have not updated to python 3 (but will be in the near future)� The
> >>> windows error can be ignored for now.
> >>>
> >>>
> >>>
> >>> 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
> >>> Simon Dirmeier
> >>> *Sent:* Monday, September 2, 2019 6:08:45 AM
> >>> *To:*bioc-devel@r-project.org  
> >>> *Subject:* [Bioc-devel] Build error due to TensorFlow installation
> >>> Dear all,
> >>>
> >>> since I replaced some old C++ code with TensorFlow I am getting some
> >>> build errors on merida1 and tokay1 regarding installation (even though
> I
> >>> install TF and TF Probability during /.onLoad/)
> >>>
> >>>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_netReg_merida1-2Dbuildsrc.html=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Iy8WHNH6twF-8QkJjKa7MOIXm9mYjGg4pBlLb2CGiq8=wjC8b2uCm0PJgQ1LRO_CTrqNvfGKpEKN0N6QN23Sbd0=
>
> >>>
> >>> Does anyone know how I can fix this or did anyone use TF with
> >>> Bioconductor so far?
> >>>
> >>> Many thanks in advance.
> >>>
> >>> Best,
> >>>
> >>> Simon
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> ��� [[alternative HTML version deleted]]
> >>>
> >>> ___
> >>> Bioc-devel@r-project.org  mailing list
> >>>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Iy8WHNH6twF-8QkJjKa7MOIXm9mYjGg4pBlLb2CGiq8=98vYdk5e2ryxlWN99O68ty2dUHnoE23VPU9TwSF8rPc=
>
> >>>
> >>> 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,
> >>> 

Re: [Bioc-devel] Version number error

[Martin Morgan]

this needs to be fixed on our end, so please just be patient (I would expect a 
fix later today...) Martin

On 9/5/19, 6:48 AM, "Christopher John"  wrote:

Still stuck here trying to update. I think I may have been a bit special 
with my version numbering.


Well let me know if there is a solution or do I just wait until the next 
release..(?)



remote: Error: Illegal version bump from '1.7.999' to '1.7.1000'. Check 
remote: http://bioconductor.org/developers/how-to/version-numbering/
remote: for details
To git.bioconductor.org:packages/M3C.git
 ! [remote rejected] master -> master (pre-receive hook declined)
error: failed to push some refs to 
'g...@git.bioconductor.org:packages/M3C.git'


Chris



On Thu, 5 Sep 2019 at 11:17, Martin Morgan  wrote:


This seems like a bug in the version check code.

The next number after '999' is '1000', but '9991' is larger than '999', 
too, so I think both 1000 and 9991 are valid version bumps; '10' is less than 
'999' so is not a valid version bump.

Note that .99... has no special significance in the third position (your 
package will be bumped to 1.8.0 in release / 1.9.0 in devel at the next release 
regardless...) so one would usually only get to '999' if one were a very 
'commit'ed person... ;)

Martin

On 9/5/19, 2:02 AM, "Bioc-devel on behalf of Christopher John" 
 wrote:

This is just the update in the normal way to github, see the below code.

Please note the change from '1.7.999' to '1.7.10' as requested by Lori
unfortunately gives the same error message as before. Previously I tried
version 1.7.9991 which didn't work.

Any ideas? What is the correct version number to change to?

Thanks,

Chris

### update commands

christopher@RA-MAP:~/M3C$ git checkout master
M DESCRIPTION
Already on 'master'
Your branch is up-to-date with 'origin/master'.
christopher@RA-MAP:~/M3C$ git add .
christopher@RA-MAP:~/M3C$ git commit -m "v no change"
[master 600273a] v no change
 1 file changed, 1 insertion(+), 1 deletion(-)
christopher@RA-MAP:~/M3C$ git push origin master
Username for 'https://github.com': crj32
Password for 'https://cr...@github.com':
Counting objects: 3, done.
Delta compression using up to 16 threads.
Compressing objects: 100% (3/3), done.
Writing objects: 100% (3/3), 290 bytes | 290.00 KiB/s, done.
Total 3 (delta 2), reused 0 (delta 0)
remote: Resolving deltas: 100% (2/2), completed with 2 local objects.
To https://github.com/crj32/M3C
   942ea47..600273a  master -> master
christopher@RA-MAP:~/M3C$ git push upstream master
Counting objects: 8, done.
Delta compression using up to 16 threads.
Compressing objects: 100% (8/8), done.
Writing objects: 100% (8/8), 1.24 KiB | 1.24 MiB/s, done.
Total 8 (delta 6), reused 0 (delta 0)

### error

remote: Error: Illegal version bump from '1.7.999' to '1.7.10'. Check
remote: 
http://bioconductor.org/developers/how-to/version-numbering/ 

remote: for details
To git.bioconductor.org:packages/M3C.git
 ! [remote rejected] master -> master (pre-receive hook declined)
error: failed to push some refs to 'g...@git.bioconductor.org:
packages/M3C.git'

On Wed, 4 Sep 2019 at 14:57, Turaga, Nitesh 

wrote:

> I suspect this was a Bioconductor hook rejecting the "version" 
number? Is
> that correct Chris?
>
> Please also reply with the exact error message.
>
> Best,
>
> Nitesh
>
> > On Sep 4, 2019, at 7:58 AM, Shepherd, Lori 

> wrote:
> >
> > Or perhaps just providing the git commands you tried and the ERROR 
that
> was produced with the original  1.7.9991 would be a better place to 
start
> so we can evaluate the ERROR.
> >
> >
> > Cheers,
> >
> >
> > 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
> Christopher John 
> > Sent: Wednesday, September 4, 2019 5:48:54 AM
> > To: bioc-devel@r-project.org 
> > Subject: [Bioc-devel] Version number error
> >
> > Hi
> >
> > I tried to update M3C as follows, and I got an 

Re: [Bioc-devel] Fwd: Re: Build error due to TensorFlow installation

[Kasper Daniel Hansen]

It might be true that the code is much easier on your end, but it comes
with the complexity of using TensorFlow, which is a huge dependency. And
that library can be easy or impossible to install depending on your box.  I
am not saying people shouldn't use TensorFlow, but I am saying it brings a
lot of complexities with it.

And (trying to) installing TensorFlow as part of .onLoad seems ... not the
right way to deal with this.

On Thu, Sep 5, 2019 at 6:27 AM Simon Dirmeier  wrote:

>
> Hi Herve,
>
> > All this means that if you replace some old C++ code with TensorFlow
> > then we will need to mark your package as unavailable on Windows and
> > Mac, at least for now. Sorry. I wonder if there was something wrong
> > with this old C++ code. I would recommend that you stick to it if you
> can.
> >
> The code is fine, but still an impractical complexity that doesn't need
> to exist:
>
> 1) It's hard to extend and read for others.
>
> 2) It needs a custom configure.ac.
>
> 3) Extending the package to other models/families is a huge pain, as one
> needs to derive custom coordinate descents (or other optimizers for that
> matter) for each.
>
> On the other side:
>
> 1) TF allowed me to replace like 5000 lines of source code with 100
> lines of R.
>
> 2) TF allows to easily extend with other models with just a few lines.
>
> 3) I don't need a huge test suite.
>
> 4) On GPUs it's a huge speedup.
>
> So, I'll revert the changes back on Bioc devel for now and continue
> development on another branch.
>
> Cheers,
>
> Simon
>
>
> Am 04.09.19 um 16:53 schrieb Pages, Herve:
> >
> > Hi Simon,
> >
> > On 9/3/19 09:11, Simon Dirmeier wrote:
> >> ...
> >> Do you think it would be possible to install TensorFlow and
> >> TensorFlow-Probability on the builders? I'd assume that many would
> >> profit from that.
> >>
> > As Lori mentioned at the end of her email (see below), we can't make
> > the tensorflow Python module available on our Windows builders at the
> > moment because we need to update Python to Python 3 on these machines
> > first (AFAIK tensorflow is only available for Python 3 on Windows).
> > This is something that we are currently working on.
> >
> > As for the Mac builders, we have tensorflow there but unfortunately
> > it's an old version because recent versions of are broken on El
> > Capitan (this is the Mac OS version that, for various reasons, we are
> > stuck with at the moment). This prevents us from installing the
> > tensorflow_probability module which requires a recent version of
> > tensorflow.
> >
> > The tensorflow and tensorflow_probability modules are available on our
> > Linux builders.
> >
> > All this means that if you replace some old C++ code with TensorFlow
> > then we will need to mark your package as unavailable on Windows and
> > Mac, at least for now. Sorry. I wonder if there was something wrong
> > with this old C++ code. I would recommend that you stick to it if you
> can.
> >
> > Best,
> >
> > H.
> >
> >
> >>> Right now tensorflow is unavailable on our windows server (tokay1)�as
> >>> we have not updated to python 3 (but will be in the near future)� The
> >>> windows error can be ignored for now.
> >>>
> >>>
> >>>
> >>> 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
> >>> Simon Dirmeier
> >>> *Sent:* Monday, September 2, 2019 6:08:45 AM
> >>> *To:*bioc-devel@r-project.org  
> >>> *Subject:* [Bioc-devel] Build error due to TensorFlow installation
> >>> Dear all,
> >>>
> >>> since I replaced some old C++ code with TensorFlow I am getting some
> >>> build errors on merida1 and tokay1 regarding installation (even though
> I
> >>> install TF and TF Probability during /.onLoad/)
> >>>
> >>>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_netReg_merida1-2Dbuildsrc.html=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Iy8WHNH6twF-8QkJjKa7MOIXm9mYjGg4pBlLb2CGiq8=wjC8b2uCm0PJgQ1LRO_CTrqNvfGKpEKN0N6QN23Sbd0=
> >>>
> >>> Does anyone know how I can fix this or did anyone use TF with
> >>> Bioconductor so far?
> >>>
> >>> Many thanks in advance.
> >>>
> >>> Best,
> >>>
> >>> Simon
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> ��� [[alternative HTML version deleted]]
> >>>
> >>> ___
> >>> Bioc-devel@r-project.org  mailing list
> >>>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Iy8WHNH6twF-8QkJjKa7MOIXm9mYjGg4pBlLb2CGiq8=98vYdk5e2ryxlWN99O68ty2dUHnoE23VPU9TwSF8rPc=
> >>>
> >>> This email message may contain legally privileged and/or confidential
> >>> information. If 

Re: [R-pkg-devel] set pkg_config for 3rd party software

[Serguei Sokol]

On 05/09/2019 12:26, Martin Maechler wrote:

Sameh M Abdulah
 on Fri, 30 Aug 2019 18:50:55 + writes:


 > Hi,
 > I recently asked some questions about my R package which were well 
responded by Dirk.

 > I have another question related to pkg_config path,

 > I am using this command to add the installation path to the 
PKG_CONFIG_PATH   so that all cmake commands can get the required libraries from 
this path,

 > 
Sys.setenv(PKG_CONFIG_PATH=paste(Sys.getenv("PKG_CONFIG_PATH"),paste(.libPaths(),"exageostat/lib/pkgconfig",sep='/',collapse=':'),sep=':'))

 > Is there a simple way to set this path without explicitly calling this 
line before installing my package? OR is there any other path that I can use so 
that all software CMake commands can easily find the required libraries?

 > --Sameh

Not an answer, but a  #METOO   with a hopefull very related
question, also on using 'pkg-config' (Note: "-", not "_" here)
for package configuration.

I'm maintainer of CRAN package Rmpfr (for arbitrary precise arithmetic..),
 https://cran.r-project.org/package=Rmpfr
development & source on R-forge
  http://rmpfr.r-forge.r-project.org/
and  https://r-forge.r-project.org/scm/viewvc.php/pkg/?root=rmpfr
which "down there"  is principally an interface to the GNU MPFR
C library (which also needs the GNU  GMP C library).

I do have a  Rmpfr/configure.ac from which to produce
Rmpfr/configure which then ensures that both libraries (MPFR and GMP)
are found and are "working".
The 'configure' script then (supposedly, but not on Windows?) takes
either src/Makevars.in  (non-Windows)
or src/Makevars.win (Windows)
to produce  src/Makevars
which then is used during compilation of the C sources of my
package.

I have a small marginal remark about this.
Makevars.win is not windows equivalent of Makevars.in but of plain 
Makevars (see
https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Package-subdirectories 
)
On windows, you can use configure.win which in turn can use 
Makevars.win.in to produce Makevars.win. The latter will be used by make 
on that platform (see 
https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Configure-and-cleanup 
)


Best,
Serguei.



Notably it will contain   '-lmpfr -lgmp'  among the LDFLAGS in
any case.

Now back to the 'pkg-config' : The compiler *also* needs correct

-I  (the path used  by ' #include <...> ' statement)

and for linking a correct  -L.

Now, my main OS,  Linux Fedora (as all other decent Linux distributions)
does provide MPFR and GMP libraries (and include headers) as OS
packages, installed in  /usr/lib/ (actually /lib64 nowadays)
and /usr/include respectively.

However, for some reasons I don't know the *version* of the MPFR
library that the OS provides is outdate (to my taste), and I'd
really want a newer version of MPFR,  which I easily install in
a version of /usr/local/. *and* I also make sure that

 pkg-config --libs mpfr
and pkg-config --cflags mpfr

list the corresponding LDFLAGS  and CFLAGS

(the first giving

   -L/usr/local.../mpfr/4.0.1/lib -lmpfr -lgmp

  the 2nd

   -I/usr/local.../mpfr/4.0.1/include
)

Now what is the officially / best way to have either 'configure'
or  Makevars.{in,win}  use the 'pkg-config' information
*dynamically*, i.e.,
if I update my MPFR from 4.0.1 to 4.0.2  the newer 4.0.2 is found ?

My current setup would not even work on some platforms to really
end up using my local version of MPFR instead of the system-wide
OS default (using /lib64 and /usr/include/ and then
which even with quite new Fedora 30 is still MPFR 3.1.6 .. much
too old for some of the things I want).

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Re: [R-pkg-devel] Single character in Fortran function and FCONE and FCLEN macros

[Dirk Eddelbuettel]

On 3 September 2019 at 15:37, Tomas Kalibera wrote:
| Yes, that seems to be an upstream problem.

Maybe checking with the documentation for Armadillo documentation at
http://arma.sourceforge.net/docs.html (large page, see about the various
#define in config.hpp near the bottom) could be of help. Might be worth
trying to set ARMA_DONT_USE_FORTRAN_HIDDEN_ARGS.

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

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Re: [Bioc-devel] Version number error

[Christopher John]

Still stuck here trying to update. I think I may have been a bit special
with my version numbering.

Well let me know if there is a solution or do I just wait until the next
release..(?)

remote: Error: Illegal version bump from '1.7.999' to '1.7.1000'. Check
remote: http://bioconductor.org/developers/how-to/version-numbering/
remote: for details
To git.bioconductor.org:packages/M3C.git
 ! [remote rejected] master -> master (pre-receive hook declined)
error: failed to push some refs to 'g...@git.bioconductor.org:
packages/M3C.git'

Chris

On Thu, 5 Sep 2019 at 11:17, Martin Morgan  wrote:

> This seems like a bug in the version check code.
>
> The next number after '999' is '1000', but '9991' is larger than '999',
> too, so I think both 1000 and 9991 are valid version bumps; '10' is less
> than '999' so is not a valid version bump.
>
> Note that .99... has no special significance in the third position (your
> package will be bumped to 1.8.0 in release / 1.9.0 in devel at the next
> release regardless...) so one would usually only get to '999' if one were a
> very 'commit'ed person... ;)
>
> Martin
>
> On 9/5/19, 2:02 AM, "Bioc-devel on behalf of Christopher John" <
> bioc-devel-boun...@r-project.org on behalf of chris.r.joh...@gmail.com>
> wrote:
>
> This is just the update in the normal way to github, see the below
> code.
>
> Please note the change from '1.7.999' to '1.7.10' as requested by Lori
> unfortunately gives the same error message as before. Previously I
> tried
> version 1.7.9991 which didn't work.
>
> Any ideas? What is the correct version number to change to?
>
> Thanks,
>
> Chris
>
> ### update commands
>
> christopher@RA-MAP:~/M3C$ git checkout master
> M DESCRIPTION
> Already on 'master'
> Your branch is up-to-date with 'origin/master'.
> christopher@RA-MAP:~/M3C$ git add .
> christopher@RA-MAP:~/M3C$ git commit -m "v no change"
> [master 600273a] v no change
>  1 file changed, 1 insertion(+), 1 deletion(-)
> christopher@RA-MAP:~/M3C$ git push origin master
> Username for 'https://github.com': crj32
> Password for 'https://cr...@github.com':
> Counting objects: 3, done.
> Delta compression using up to 16 threads.
> Compressing objects: 100% (3/3), done.
> Writing objects: 100% (3/3), 290 bytes | 290.00 KiB/s, done.
> Total 3 (delta 2), reused 0 (delta 0)
> remote: Resolving deltas: 100% (2/2), completed with 2 local objects.
> To https://github.com/crj32/M3C
>942ea47..600273a  master -> master
> christopher@RA-MAP:~/M3C$ git push upstream master
> Counting objects: 8, done.
> Delta compression using up to 16 threads.
> Compressing objects: 100% (8/8), done.
> Writing objects: 100% (8/8), 1.24 KiB | 1.24 MiB/s, done.
> Total 8 (delta 6), reused 0 (delta 0)
>
> ### error
>
> remote: Error: Illegal version bump from '1.7.999' to '1.7.10'. Check
> remote: http://bioconductor.org/developers/how-to/version-numbering/
> remote: for details
> To git.bioconductor.org:packages/M3C.git
>  ! [remote rejected] master -> master (pre-receive hook declined)
> error: failed to push some refs to 'g...@git.bioconductor.org:
> packages/M3C.git'
>
> On Wed, 4 Sep 2019 at 14:57, Turaga, Nitesh <
> nitesh.tur...@roswellpark.org>
> wrote:
>
> > I suspect this was a Bioconductor hook rejecting the "version"
> number? Is
> > that correct Chris?
> >
> > Please also reply with the exact error message.
> >
> > Best,
> >
> > Nitesh
> >
> > > On Sep 4, 2019, at 7:58 AM, Shepherd, Lori
> 
> > wrote:
> > >
> > > Or perhaps just providing the git commands you tried and the ERROR
> that
> > was produced with the original  1.7.9991 would be a better place to
> start
> > so we can evaluate the ERROR.
> > >
> > >
> > > Cheers,
> > >
> > >
> > > 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
> > Christopher John 
> > > Sent: Wednesday, September 4, 2019 5:48:54 AM
> > > To: bioc-devel@r-project.org 
> > > Subject: [Bioc-devel] Version number error
> > >
> > > Hi
> > >
> > > I tried to update M3C as follows, and I got an error. What is
> wrong with
> > > the new version number please? What should it be?
> > >
> > > Version: 1.7.999 --> Version: 1.7.9991
> > >
> > > Thanks,
> > >
> > > Chris
> > >
> > >[[alternative HTML version deleted]]
> > >
> > > ___
> > > Bioc-devel@r-project.org mailing list
> > > 

[Bioc-devel] Fwd: Re: Build error due to TensorFlow installation

[Simon Dirmeier]

Hi Herve,

> All this means that if you replace some old C++ code with TensorFlow
> then we will need to mark your package as unavailable on Windows and
> Mac, at least for now. Sorry. I wonder if there was something wrong
> with this old C++ code. I would recommend that you stick to it if you can.
>
The code is fine, but still an impractical complexity that doesn't need
to exist:

1) It's hard to extend and read for others.

2) It needs a custom configure.ac.

3) Extending the package to other models/families is a huge pain, as one
needs to derive custom coordinate descents (or other optimizers for that
matter) for each.

On the other side:

1) TF allowed me to replace like 5000 lines of source code with 100
lines of R.

2) TF allows to easily extend with other models with just a few lines.

3) I don't need a huge test suite.

4) On GPUs it's a huge speedup.

So, I'll revert the changes back on Bioc devel for now and continue
development on another branch.

Cheers,

Simon


Am 04.09.19 um 16:53 schrieb Pages, Herve:
>
> Hi Simon,
>
> On 9/3/19 09:11, Simon Dirmeier wrote:
>> ...
>> Do you think it would be possible to install TensorFlow and
>> TensorFlow-Probability on the builders? I'd assume that many would
>> profit from that.
>>
> As Lori mentioned at the end of her email (see below), we can't make
> the tensorflow Python module available on our Windows builders at the
> moment because we need to update Python to Python 3 on these machines
> first (AFAIK tensorflow is only available for Python 3 on Windows).
> This is something that we are currently working on.
>
> As for the Mac builders, we have tensorflow there but unfortunately
> it's an old version because recent versions of are broken on El
> Capitan (this is the Mac OS version that, for various reasons, we are
> stuck with at the moment). This prevents us from installing the
> tensorflow_probability module which requires a recent version of
> tensorflow.
>
> The tensorflow and tensorflow_probability modules are available on our
> Linux builders.
>
> All this means that if you replace some old C++ code with TensorFlow
> then we will need to mark your package as unavailable on Windows and
> Mac, at least for now. Sorry. I wonder if there was something wrong
> with this old C++ code. I would recommend that you stick to it if you can.
>
> Best,
>
> H.
>
>
>>> Right now tensorflow is unavailable on our windows server (tokay1)�as
>>> we have not updated to python 3 (but will be in the near future)� The
>>> windows error can be ignored for now.
>>>
>>>
>>>
>>> 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
>>> Simon Dirmeier
>>> *Sent:* Monday, September 2, 2019 6:08:45 AM
>>> *To:*bioc-devel@r-project.org  
>>> *Subject:* [Bioc-devel] Build error due to TensorFlow installation
>>> Dear all,
>>>
>>> since I replaced some old C++ code with TensorFlow I am getting some
>>> build errors on merida1 and tokay1 regarding installation (even though I
>>> install TF and TF Probability during /.onLoad/)
>>>
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_netReg_merida1-2Dbuildsrc.html=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Iy8WHNH6twF-8QkJjKa7MOIXm9mYjGg4pBlLb2CGiq8=wjC8b2uCm0PJgQ1LRO_CTrqNvfGKpEKN0N6QN23Sbd0=
>>>
>>> Does anyone know how I can fix this or did anyone use TF with
>>> Bioconductor so far?
>>>
>>> Many thanks in advance.
>>>
>>> Best,
>>>
>>> Simon
>>>
>>>
>>>
>>>
>>>
>>> ��� [[alternative HTML version deleted]]
>>>
>>> ___
>>> Bioc-devel@r-project.org  mailing list
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Iy8WHNH6twF-8QkJjKa7MOIXm9mYjGg4pBlLb2CGiq8=98vYdk5e2ryxlWN99O68ty2dUHnoE23VPU9TwSF8rPc=
>>>
>>> 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.
>>  [[alternative HTML version deleted]]
>>
>>
>> ___
>> Bioc-devel@r-project.org  mailing list
>> 

Re: [R-pkg-devel] set pkg_config for 3rd party software

[Martin Maechler]

> Sameh M Abdulah 
> on Fri, 30 Aug 2019 18:50:55 + writes:

> Hi,
> I recently asked some questions about my R package which were well 
responded by Dirk.

> I have another question related to pkg_config path,

> I am using this command to add the installation path to the 
PKG_CONFIG_PATH   so that all cmake commands can get the required libraries 
from this path,

> 
Sys.setenv(PKG_CONFIG_PATH=paste(Sys.getenv("PKG_CONFIG_PATH"),paste(.libPaths(),"exageostat/lib/pkgconfig",sep='/',collapse=':'),sep=':'))

> Is there a simple way to set this path without explicitly calling this 
line before installing my package? OR is there any other path that I can use so 
that all software CMake commands can easily find the required libraries?

> --Sameh

Not an answer, but a  #METOO   with a hopefull very related
question, also on using 'pkg-config' (Note: "-", not "_" here)
for package configuration.

I'm maintainer of CRAN package Rmpfr (for arbitrary precise arithmetic..),
https://cran.r-project.org/package=Rmpfr
development & source on R-forge
 http://rmpfr.r-forge.r-project.org/
and  https://r-forge.r-project.org/scm/viewvc.php/pkg/?root=rmpfr
which "down there"  is principally an interface to the GNU MPFR
C library (which also needs the GNU  GMP C library).

I do have a  Rmpfr/configure.ac from which to produce
Rmpfr/configure which then ensures that both libraries (MPFR and GMP)
are found and are "working".
The 'configure' script then (supposedly, but not on Windows?) takes
either src/Makevars.in  (non-Windows)
or src/Makevars.win (Windows)
to produce  src/Makevars
which then is used during compilation of the C sources of my
package.

Notably it will contain   '-lmpfr -lgmp'  among the LDFLAGS in
any case.

Now back to the 'pkg-config' : The compiler *also* needs correct

-I  (the path used  by ' #include <...> ' statement)

and for linking a correct  -L.

Now, my main OS,  Linux Fedora (as all other decent Linux distributions)
does provide MPFR and GMP libraries (and include headers) as OS
packages, installed in  /usr/lib/ (actually /lib64 nowadays)
and /usr/include respectively.

However, for some reasons I don't know the *version* of the MPFR
library that the OS provides is outdate (to my taste), and I'd
really want a newer version of MPFR,  which I easily install in
a version of /usr/local/. *and* I also make sure that

pkg-config --libs mpfr
and pkg-config --cflags mpfr

list the corresponding LDFLAGS  and CFLAGS

(the first giving

  -L/usr/local.../mpfr/4.0.1/lib -lmpfr -lgmp 

 the 2nd

  -I/usr/local.../mpfr/4.0.1/include 
)

Now what is the officially / best way to have either 'configure'
or  Makevars.{in,win}  use the 'pkg-config' information
*dynamically*, i.e.,
if I update my MPFR from 4.0.1 to 4.0.2  the newer 4.0.2 is found ?

My current setup would not even work on some platforms to really
end up using my local version of MPFR instead of the system-wide
OS default (using /lib64 and /usr/include/ and then
which even with quite new Fedora 30 is still MPFR 3.1.6 .. much
too old for some of the things I want).

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [Bioc-devel] Version number error

[Martin Morgan]

This seems like a bug in the version check code.

The next number after '999' is '1000', but '9991' is larger than '999', too, so 
I think both 1000 and 9991 are valid version bumps; '10' is less than '999' so 
is not a valid version bump.

Note that .99... has no special significance in the third position (your 
package will be bumped to 1.8.0 in release / 1.9.0 in devel at the next release 
regardless...) so one would usually only get to '999' if one were a very 
'commit'ed person... ;)

Martin

On 9/5/19, 2:02 AM, "Bioc-devel on behalf of Christopher John" 
 wrote:

This is just the update in the normal way to github, see the below code.

Please note the change from '1.7.999' to '1.7.10' as requested by Lori
unfortunately gives the same error message as before. Previously I tried
version 1.7.9991 which didn't work.

Any ideas? What is the correct version number to change to?

Thanks,

Chris

### update commands

christopher@RA-MAP:~/M3C$ git checkout master
M DESCRIPTION
Already on 'master'
Your branch is up-to-date with 'origin/master'.
christopher@RA-MAP:~/M3C$ git add .
christopher@RA-MAP:~/M3C$ git commit -m "v no change"
[master 600273a] v no change
 1 file changed, 1 insertion(+), 1 deletion(-)
christopher@RA-MAP:~/M3C$ git push origin master
Username for 'https://github.com': crj32
Password for 'https://cr...@github.com':
Counting objects: 3, done.
Delta compression using up to 16 threads.
Compressing objects: 100% (3/3), done.
Writing objects: 100% (3/3), 290 bytes | 290.00 KiB/s, done.
Total 3 (delta 2), reused 0 (delta 0)
remote: Resolving deltas: 100% (2/2), completed with 2 local objects.
To https://github.com/crj32/M3C
   942ea47..600273a  master -> master
christopher@RA-MAP:~/M3C$ git push upstream master
Counting objects: 8, done.
Delta compression using up to 16 threads.
Compressing objects: 100% (8/8), done.
Writing objects: 100% (8/8), 1.24 KiB | 1.24 MiB/s, done.
Total 8 (delta 6), reused 0 (delta 0)

### error

remote: Error: Illegal version bump from '1.7.999' to '1.7.10'. Check
remote: http://bioconductor.org/developers/how-to/version-numbering/
remote: for details
To git.bioconductor.org:packages/M3C.git
 ! [remote rejected] master -> master (pre-receive hook declined)
error: failed to push some refs to 'g...@git.bioconductor.org:
packages/M3C.git'

On Wed, 4 Sep 2019 at 14:57, Turaga, Nitesh 
wrote:

> I suspect this was a Bioconductor hook rejecting the "version" number? Is
> that correct Chris?
>
> Please also reply with the exact error message.
>
> Best,
>
> Nitesh
>
> > On Sep 4, 2019, at 7:58 AM, Shepherd, Lori 

> wrote:
> >
> > Or perhaps just providing the git commands you tried and the ERROR that
> was produced with the original  1.7.9991 would be a better place to start
> so we can evaluate the ERROR.
> >
> >
> > Cheers,
> >
> >
> > 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
> Christopher John 
> > Sent: Wednesday, September 4, 2019 5:48:54 AM
> > To: bioc-devel@r-project.org 
> > Subject: [Bioc-devel] Version number error
> >
> > Hi
> >
> > I tried to update M3C as follows, and I got an error. What is wrong with
> > the new version number please? What should it be?
> >
> > Version: 1.7.999 --> Version: 1.7.9991
> >
> > Thanks,
> >
> > Chris
> >
> >[[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> >
> > 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.
> >   [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>
> This email message may contain legally privileged and/or confidential
> information.  If you are 

Re: [Bioc-devel] Version number error

[Christopher John]

This is just the update in the normal way to github, see the below code.

Please note the change from '1.7.999' to '1.7.10' as requested by Lori
unfortunately gives the same error message as before. Previously I tried
version 1.7.9991 which didn't work.

Any ideas? What is the correct version number to change to?

Thanks,

Chris

### update commands

christopher@RA-MAP:~/M3C$ git checkout master
M DESCRIPTION
Already on 'master'
Your branch is up-to-date with 'origin/master'.
christopher@RA-MAP:~/M3C$ git add .
christopher@RA-MAP:~/M3C$ git commit -m "v no change"
[master 600273a] v no change
 1 file changed, 1 insertion(+), 1 deletion(-)
christopher@RA-MAP:~/M3C$ git push origin master
Username for 'https://github.com': crj32
Password for 'https://cr...@github.com':
Counting objects: 3, done.
Delta compression using up to 16 threads.
Compressing objects: 100% (3/3), done.
Writing objects: 100% (3/3), 290 bytes | 290.00 KiB/s, done.
Total 3 (delta 2), reused 0 (delta 0)
remote: Resolving deltas: 100% (2/2), completed with 2 local objects.
To https://github.com/crj32/M3C
   942ea47..600273a  master -> master
christopher@RA-MAP:~/M3C$ git push upstream master
Counting objects: 8, done.
Delta compression using up to 16 threads.
Compressing objects: 100% (8/8), done.
Writing objects: 100% (8/8), 1.24 KiB | 1.24 MiB/s, done.
Total 8 (delta 6), reused 0 (delta 0)

### error

remote: Error: Illegal version bump from '1.7.999' to '1.7.10'. Check
remote: http://bioconductor.org/developers/how-to/version-numbering/
remote: for details
To git.bioconductor.org:packages/M3C.git
 ! [remote rejected] master -> master (pre-receive hook declined)
error: failed to push some refs to 'g...@git.bioconductor.org:
packages/M3C.git'

On Wed, 4 Sep 2019 at 14:57, Turaga, Nitesh 
wrote:

> I suspect this was a Bioconductor hook rejecting the "version" number? Is
> that correct Chris?
>
> Please also reply with the exact error message.
>
> Best,
>
> Nitesh
>
> > On Sep 4, 2019, at 7:58 AM, Shepherd, Lori 
> wrote:
> >
> > Or perhaps just providing the git commands you tried and the ERROR that
> was produced with the original  1.7.9991 would be a better place to start
> so we can evaluate the ERROR.
> >
> >
> > Cheers,
> >
> >
> > 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
> Christopher John 
> > Sent: Wednesday, September 4, 2019 5:48:54 AM
> > To: bioc-devel@r-project.org 
> > Subject: [Bioc-devel] Version number error
> >
> > Hi
> >
> > I tried to update M3C as follows, and I got an error. What is wrong with
> > the new version number please? What should it be?
> >
> > Version: 1.7.999 --> Version: 1.7.9991
> >
> > Thanks,
> >
> > Chris
> >
> >[[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> >
> > 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.
> >   [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>
> 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.
>

[[alternative HTML version deleted]]

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