Re: [Bioc-devel] "Error: duplicate commits" when pushing FamAgg to Bioconductor git

[Rainer Johannes]

Thanks Nitesh for your quick reply!

> On 13 Feb 2018, at 16:47, Turaga, Nitesh  
> wrote:
> 
> Hi,
> 
> It seems that there are multiple levels of duplication on your repository. 
> 
> You seem to have issued the “merge” with not the current bioconductor devel 
> but the (now deprecated) GitHub- bioconductor mirror, multiple times. Please 
> correct me if this is not accurate. I’m wondering why the merge was issued so 
> many times? 
> 

could be that I pushed several time (wasn't aware of that) - eventually I was 
just puzzled that it didn't resolve the problem so I tried again...

> As far as the fix goes, it would take me a while to track down the “merge” 
> commits and then “cherry-pick" on to the master branch the commits that are 
> not duplicated. These seem to be stemming right from the beginning of your 
> development history. 
> 
> The steps you need are:
> 
> 1. Back up master branch (git branch master_backup)
> 2. Check merge commit SHA’s (git log --oneline maste)
> 3. Reset to commit before the merge, (git reset --hard )
> 4. Then, overlay commits on top that reset, with latest non-duplicated 
> commits (git cherry-pick )
> 
> You’d have to repeat these steps quite extensively depending on how many 
> merges you have.
> 
> Take a look at this manual as further help to do this, 
> http://sethrobertson.github.io/GitFixUm/fixup.html. 
> 
> Do these steps on your local repository and push to Github. Once you have 
> done that, let me know and I’ll take a look at your Github repo, and sync 
> with Bioconductor if history looks clean.
> 
> If you are unable to fix the repo, then the best way forward it to remove the 
> pre-receive hook from your repository and deal with the history as is. This 
> will not effect your package in anyway, just that the git history won’t be 
> clean. 
> 

honestly - I'm afraid my git-knowledge isn't good enough so that I can fix the 
duplicated commits (I think they still derive from the git git-svn setup). I 
could live with the git history not being clean. So, from my side, you could go 
ahead and remove the pre-receive hook.

funnily, I have also duplicated commits in ensembldb, but there I'm still able 
to push to Bioconductor git without problems.

best, jo

> 
> Best,
> 
> Nitesh 
> 
> 
>> On Feb 12, 2018, at 5:41 AM, Rainer Johannes  
>> wrote:
>> 
>> Dear all,
>> 
>> I'm unable to push my recent changes to FamAgg to the Bioconductor git repo 
>> (see below for the error message). I did try the suggested fix but without 
>> any success - seems the duplicated commits are in Bioconductor and not 
>> github.
>> 
>> thankful for any help or advise
>> 
>> The error message is:
>> 
>> macbookjo:FamAgg jo$ git push origin master
>> Everything up-to-date
>> macbookjo:FamAgg jo$ git push upstream master
>> Counting objects: 13, done.
>> Delta compression using up to 8 threads.
>> Compressing objects: 100% (13/13), done.
>> Writing objects: 100% (13/13), 2.17 KiB | 2.17 MiB/s, done.
>> Total 13 (delta 11), reused 0 (delta 0)
>> remote: Error: duplicate commits.
>> remote: 
>> remote: There are duplicate commits in your commit history, These cannot be
>> remote: pushed to the Bioconductor git server. Please make sure that this is
>> remote: resolved.
>> remote: 
>> remote: Take a look at the documentation to fix this,
>> remote: 
>> https://bioconductor.org/developers/how-to/git/sync-existing-repositories/,
>> remote: particularly, point #8 (force Bioconductor master to Github master).
>> remote: 
>> remote: For more information, or help resolving this issue, contact
>> remote: . Provide the error, the package name and
>> remote: any other details we might need.
>> remote: 
>> remote: Use
>> remote: 
>> remote: git show 397d05e8ba7d301a9145573210c277f1c6dd66a5
>> remote: git show 6a0c683477b78e231a7eb1b59171baa0bc582ef2
>> remote: 
>> remote: to see body of commits.
>> remote: 
>> To git.bioconductor.org:packages/FamAgg
>> ! [remote rejected] master -> master (pre-receive hook declined)
>> error: failed to push some refs to 
>> 'g...@git.bioconductor.org:packages/FamAgg'
>> 
>> 
>> macbookjo:FamAgg jo$ git show 397d05e8ba7d301a9145573210c277f1c6dd66a5
>> commit 397d05e8ba7d301a9145573210c277f1c6dd66a5
>> Author: Herve Pages 
>> Date:   Mon Apr 24 19:50:57 2017 +
>> 
>>   bump x.y.z versions to odd y after creation of 3_5 branch
>> 
>>   git-svn-id: 
>> file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/FamAgg@129129
>>  bc3139a8-67e5-0310-9ffc-ced21a209358
>> 
>> diff --git a/DESCRIPTION b/DESCRIPTION
>> index c9cb1b7..948b777 100644
>> --- a/DESCRIPTION
>> +++ b/DESCRIPTION
>> @@ -1,7 +1,7 @@
>> Package: FamAgg
>> Type: Package
>> Title: Pedigree Analysis and Familial Aggregation
>> -Version: 1.4.0
>> +Version: 1.5.0
>> Author: J. Rainer, D. Taliun, C.X. Weichenberger
>> Maintainer: Johannes Rainer 
>> URL: 

Re: [R-pkg-devel] Lapack: undefined symbol: zgbsv_

[Baptiste Auguie]

On 13 February 2018 at 22:07, Ralf Stubner 
wrote:

> On 13.02.2018 05:49, Baptiste Auguie wrote:
> > On 13 February 2018 at 01:05, Dirk Eddelbuettel  > > wrote:
> > Maybe we are setting a more global "no advanced lapack" for Windows
> that
> > assures success when we assume that the other system will always
> > have it.
> >
> >
> > it sounds plausible, but it would be nice to know for sure.
>
> It is the case, c.f.
> https://github.com/RcppCore/RcppArmadillo/blob/master/inst/i
> nclude/RcppArmadilloConfig.h#L96-L106
>
> > In
> > particular, it doesn't explain why the external Lapack on linux appears
> > to be missing these symbols (they're not very recent, as far as I can
> > tell). I don't really know how to figure this out, but it seems to be
> key.
>
> My understanding:
>
> * On Windows internal LAPACK is used but it is not affected due to the
> defines quoted above.
> * At least Debian & Co but probably also other Linux distributions
> compile R with external LAPACK and are not affected.
> * CRAN (and probably r-hub) use R compiled with internal LAPACK and is
> therefore affected.
>


Thanks Ralf, now it makes more sense to me. I had misunderstood the
situation on CRAN and r-hub and thought they used an external Lapack on
linux.



> * I do not understand why Mac OS is not affected. The FAQ [1] implies
> that by default the internal BLAS/LAPACK is used. But then I do not see
> the mentioned alternative libRblas.vecLib.dylib on a test system.
>
> [1]
> https://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html#Which
> -BLAS-is-used-and-how-can-it-be-changed_003f
>
>
> > Or, be brutal, and set '#define ARMA_CRIPPLED_LAPACK 1' everywhere.
> See
> > lines 67 to 95 of RcppArmadillo's configure.ac  >:
> > https://github.com/RcppCore/RcppArmadillo/blob/master/confi
> gure.ac#L67-L95
> >
> > while this might solve the CRAN problem, it doesn't feel right to
> > enforce the use of suboptimal routines throughout and on all platforms,
> > including those that do in fact provide a full-fledged external Lapack.
>
> You could use this as a first step to get the package back into CRAN.
> Later on you can try to only set the flag when an internal LAPACK is
> detected, similar to the way RcppArmadillo does it. If my understanding
> above is correct, the number of users with ARMA_CRIPPLED_LAPACK in your
> package but not in RcppArmadillo will be quite small.
>

It would make sense to test for internal vs external Lapack and decide
based on that (regardless of the OS); as you say, the results should be
essentially identical to what happens when the same user installs
RcppArmadillo on their machine. Unfortunately I don't know how to proceed.
I copied RcppArmadillo's configure.ac script and tried to extract just the
Lapack testing bits, but these macro and configure concepts are totally
foreign to me. I believe it would be helpful to have a minimal example of
this type of configuration for the dummy isolve package (
https://github.com/baptiste/isolve), if someone with such expertise and a
linux machine is willing to help.

Thanks,

baptiste


>
> Greetings
> Ralf
>
> --
> Ralf Stubner
> Senior Software Engineer / Trainer
>
> R Institute GmbH
> Dortustraße 48
> 14467 Potsdam
>
> T: +49 331 23 70 81 66
> F: +49 331 23 70 81 67
> M: +49 162 20 91 196
>
> Mail: ralf.stub...@r-institute.com
>
> Sitz: Potsdam
> Register: AG Potsdam HRB 27966 P
> Ust.-IdNr.: DE300072622
> Geschäftsführer: Prof. Dr. Dr. Karl-Kuno Kunze
>
>

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Re: [Bioc-devel] rsvg on mac

[Hervé Pagès]

Hi Kevin,

As Val said, some CRAN packages with native code won't compile
on our Windows or Mac builders because of missing components,
and rsvg is one of them. Please keep in mind that we already
install many external components required for the compilation
of Bioconductor packages. The process of doing so on a fresh
Mac El Capitan system is documented here:


https://github.com/Bioconductor/BBS/blob/master/Doc/Prepare-MacOSX-El-Capitan-HOWTO.TXT

Installing these components is time consuming and there is always
the risk to introduce some conflicts/instabilities when installing
new components. Given that our resources are limited, it wouldn't
make much sense that we do this for those CRAN packages for which
the binaries are only temporarily unavailable.

Cheers,
H.


On 02/13/2018 12:56 PM, Kevin Horan wrote:

Valerie,

  Ok, I understand the difference now. Would it be possible to
install the system requirement for rsvg ( just on devel)?

  I'm trying to generate plots in either PNG or SVG with OpenBabel.
For PNG, OpenBabel requires it's own Cario library be installed on the
system (doesn't seem to work with what is built into R, as it needs to
be linked with OpenBabel). I've not been successful getting the Cairo
lib installed on windows, but using SVG with OpenBabel, and then reading
that back into R with rsvg, works fine. So it seems I'll need a extra
system library either way ( either Cairo, or librsvg2).

Thanks.

Kevin


On 02/13/2018 06:43 AM, Obenchain, Valerie wrote:

Hi,

By default, the build system installs CRAN dependencies on the Mac and
Windows builders with 'type=both':

   install.packages("mypackage", type="both")

This means it first tries to install the binary and if that fails, it
tries to install from source. Packages without native code or
SystemRequirements usually install fine from source. This is the case
for DiagrammeR which can be installed on the build machines. rsvg is
in the Suggests field of DiagrammeR so rsvg is not needed to install
or load the package.

The rsvg package is different in that it has 'librsvg2' as a
SystemRequirement which is not installed on the Mac (or Windows) build
machine:

https://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-2Dproject.org_web_packages_rsvg_index.html=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=y_AVoDJvCaCexHFznr_ua93-DoFexhIDSKUK1NcBzNs=ykWNmVUAiB_w-DbtSqe1v5yWUnT_KpcxPCqUSLt873w=

We do install all SystemRequirements for Bioconductor packages on the
Mac and Windows builders but not for CRAN packages. Installing all
third party requirements of CRAN dependencies would add significantly
to the build system maintenance and really only serves a purpose in
this window of time where binaries are not available for devel.

cc'ing Herve in case he has more to add.


Valerie




On 02/12/2018 12:25 PM, Kevin Horan wrote:

Valerie,
 I'm not sure I understand. I looked at another package that is
currently installed on the mac devel machine, DiagrammeR
(https://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-2Dproject.org_package-3DDiagrammeR=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=y_AVoDJvCaCexHFznr_ua93-DoFexhIDSKUK1NcBzNs=7UDK9omF9qsdLzWH6wEh_fyNE5BuQbNbJzc0v925ElE=),
 and it has the same
set of links on the CRAN site as rsvg does. In particular, it does
not show a  r-devel version for El Capitan.
 Also, rsvg is not installed on the release mac build machine
either, which it should have a version for.

Kevin

On 02/07/2018 09:09 AM, Obenchain, Valerie wrote:

Hi Kevin,

CRAN binaries for El Capitan in devel aren't available. You can see
this on the rsvg landing page:

https://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-2Dproject.org_web_packages_rsvg_index.html=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=y_AVoDJvCaCexHFznr_ua93-DoFexhIDSKUK1NcBzNs=ykWNmVUAiB_w-DbtSqe1v5yWUnT_KpcxPCqUSLt873w=

Nothing we can do until CRAN makes them available.

Valerie


On 02/07/2018 08:29 AM, Kevin Horan wrote:

The ChemmineR build is failing on the mac due to a new dependency not
being available, the package "rsvg". Would it be possible to install
that on the mac build machine? Thanks.

https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_ChemmineR_merida2-2Dinstall.html=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=y_AVoDJvCaCexHFznr_ua93-DoFexhIDSKUK1NcBzNs=B43U-waIixUyD4yJS4OySSIX5jVaAXp98jUM348m8oU=


Kevin

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Re: [R-pkg-devel] Solaris and ggplot2

[Kevin Ushey]

Hi,

Glancing at the R CMD check errors, available at:

https://www.r-project.org/nosvn/R.check/r-patched-solaris-x86/RJafroc-00install.html)

It seems like the issues relate to ambiguous calls to 'sqrt()'. This
particular issue is discussed in R-exts, at:

https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Portable-C-and-C_002b_002b-code

You would likely be able to resolve this by calling e.g. 'sqrt(2.0)'
instead of 'sqrt(2)'.

Best,
Kevin

On Tue, Feb 13, 2018 at 2:58 PM, Dev Chakraborty  wrote:
> My package RJafroc, which is currently on CRAN, passes all operating
> systems except solaris-x86-patched, and as a result has been flagged for
> removal. Using R-hub builder, I am unable to reproduce the log file because
> a required package, ggplot2, does not exist for Solaris. I found the
> following conversation on GitHub at the following URL:
> https://github.com/tidyverse/ggplot2/issues/2273 (the conversation is
> reproduced below).
>
> Could use any advice. Thanks.
>
> Dev
>
> **
> tdhock commented on Sep 23, 2017
> Hey there, it seems that ggplot2 on CRAN has an ERROR on solaris
> https://www.r-project.org/nosvn/R.check/r-patched-so
> laris-x86/ggplot2-00check.html because of a test about date scales that
> does not pass. Do you have any plan to fix?
>
> This is an issue for me because I have a package that imports ggplot2, and
> I would like to use rhub to check it on solaris before submitting it to
> CRAN. *However rhub can not perform the check because the ggplot2 package
> is not available on solaris*. Here is the related issue at rhub
> r-hub/rhub#83
>
>  @hadley
>  Owner
> hadley commented on Oct 30, 2017
> *Probably not, since solaris is going away.*
>
> [[alternative HTML version deleted]]
>
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Re: [R-pkg-devel] Solaris and ggplot2

[Gábor Csárdi]

This is probably because stringi does not compile on r-hub, and
ggplot2 depends on stringi.
This is a known and as of yet unsolved issue:
https://github.com/gagolews/stringi/issues/275

Gabor

On Tue, Feb 13, 2018 at 10:58 PM, Dev Chakraborty  wrote:
> My package RJafroc, which is currently on CRAN, passes all operating
> systems except solaris-x86-patched, and as a result has been flagged for
> removal. Using R-hub builder, I am unable to reproduce the log file because
> a required package, ggplot2, does not exist for Solaris. I found the
> following conversation on GitHub at the following URL:
> https://github.com/tidyverse/ggplot2/issues/2273 (the conversation is
> reproduced below).
>
> Could use any advice. Thanks.
>
> Dev
>
> **
> tdhock commented on Sep 23, 2017
> Hey there, it seems that ggplot2 on CRAN has an ERROR on solaris
> https://www.r-project.org/nosvn/R.check/r-patched-so
> laris-x86/ggplot2-00check.html because of a test about date scales that
> does not pass. Do you have any plan to fix?
>
> This is an issue for me because I have a package that imports ggplot2, and
> I would like to use rhub to check it on solaris before submitting it to
> CRAN. *However rhub can not perform the check because the ggplot2 package
> is not available on solaris*. Here is the related issue at rhub
> r-hub/rhub#83
>
>  @hadley
>  Owner
> hadley commented on Oct 30, 2017
> *Probably not, since solaris is going away.*
>
> [[alternative HTML version deleted]]
>
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[R-pkg-devel] Solaris and ggplot2

[Dev Chakraborty]

My package RJafroc, which is currently on CRAN, passes all operating
systems except solaris-x86-patched, and as a result has been flagged for
removal. Using R-hub builder, I am unable to reproduce the log file because
a required package, ggplot2, does not exist for Solaris. I found the
following conversation on GitHub at the following URL:
https://github.com/tidyverse/ggplot2/issues/2273 (the conversation is
reproduced below).

Could use any advice. Thanks.

Dev

**
tdhock commented on Sep 23, 2017
Hey there, it seems that ggplot2 on CRAN has an ERROR on solaris
https://www.r-project.org/nosvn/R.check/r-patched-so
laris-x86/ggplot2-00check.html because of a test about date scales that
does not pass. Do you have any plan to fix?

This is an issue for me because I have a package that imports ggplot2, and
I would like to use rhub to check it on solaris before submitting it to
CRAN. *However rhub can not perform the check because the ggplot2 package
is not available on solaris*. Here is the related issue at rhub
r-hub/rhub#83

 @hadley
 Owner
hadley commented on Oct 30, 2017
*Probably not, since solaris is going away.*

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Re: [Bioc-devel] rsvg on mac

[Kevin Horan]

Valerie,

 Ok, I understand the difference now. Would it be possible to 
install the system requirement for rsvg ( just on devel)?

 I'm trying to generate plots in either PNG or SVG with OpenBabel. 
For PNG, OpenBabel requires it's own Cario library be installed on the 
system (doesn't seem to work with what is built into R, as it needs to 
be linked with OpenBabel). I've not been successful getting the Cairo 
lib installed on windows, but using SVG with OpenBabel, and then reading 
that back into R with rsvg, works fine. So it seems I'll need a extra 
system library either way ( either Cairo, or librsvg2).

Thanks.

Kevin


On 02/13/2018 06:43 AM, Obenchain, Valerie wrote:
> Hi,
>
> By default, the build system installs CRAN dependencies on the Mac and 
> Windows builders with 'type=both':
>
>   install.packages("mypackage", type="both")
>
> This means it first tries to install the binary and if that fails, it 
> tries to install from source. Packages without native code or 
> SystemRequirements usually install fine from source. This is the case 
> for DiagrammeR which can be installed on the build machines. rsvg is 
> in the Suggests field of DiagrammeR so rsvg is not needed to install 
> or load the package.
>
> The rsvg package is different in that it has 'librsvg2' as a 
> SystemRequirement which is not installed on the Mac (or Windows) build 
> machine:
>
> https://cran.r-project.org/web/packages/rsvg/index.html
>
> We do install all SystemRequirements for Bioconductor packages on the 
> Mac and Windows builders but not for CRAN packages. Installing all 
> third party requirements of CRAN dependencies would add significantly 
> to the build system maintenance and really only serves a purpose in 
> this window of time where binaries are not available for devel.
>
> cc'ing Herve in case he has more to add.
>
>
> Valerie
>
>
>
>
> On 02/12/2018 12:25 PM, Kevin Horan wrote:
>> Valerie,
>> I'm not sure I understand. I looked at another package that is 
>> currently installed on the mac devel machine, DiagrammeR 
>> (https://cran.r-project.org/package=DiagrammeR), and it has the same 
>> set of links on the CRAN site as rsvg does. In particular, it does 
>> not show a  r-devel version for El Capitan.
>> Also, rsvg is not installed on the release mac build machine 
>> either, which it should have a version for.
>>
>> Kevin
>>
>> On 02/07/2018 09:09 AM, Obenchain, Valerie wrote:
>>> Hi Kevin,
>>>
>>> CRAN binaries for El Capitan in devel aren't available. You can see 
>>> this on the rsvg landing page:
>>>
>>> https://cran.r-project.org/web/packages/rsvg/index.html
>>>
>>> Nothing we can do until CRAN makes them available.
>>>
>>> Valerie
>>>
>>>
>>> On 02/07/2018 08:29 AM, Kevin Horan wrote:
 The ChemmineR build is failing on the mac due to a new dependency not
 being available, the package "rsvg". Would it be possible to install
 that on the mac build machine? Thanks.

 http://bioconductor.org/checkResults/devel/bioc-LATEST/ChemmineR/merida2-install.html


 Kevin

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Re: [Bioc-devel] Access to push to pacakges Polyester and Ballgown

[Obenchain, Valerie]

Thanks Jack. I've added you to both packages. Before you have access, you'll 
need to fill out this form

  
https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480vo4tNufs0ziNyNmexegNZgNieIovbAA/viewform

Please use your github username on the form - we'll get your ssh keys from that 
account.

Valerie


On 02/13/2018 07:53 AM, Jack Fu wrote:
Thanks for checking Valerie. My github id is jmf47.

Thanks!
Jack

On Feb 13, 2018, at 10:22 AM, Obenchain, Valerie 
> 
wrote:

Hi,

Jack, It doesn't look like you currently have access to other Bioconductor 
packages - is that correct? If you don't currently have access, I need to know 
your github username.

Jeff, are we adding Jack to both polyester and ballgown?

Valerie


On 02/13/2018 02:57 AM, Jeff Leek wrote:

HI Bioc Team

If you could please add Jack that would be great!

Jeff

On Mon, Feb 12, 2018 at 7:53 AM Jack Fu  
wrote:



Hi Bioc team,

I'm currently maintaining the packages Ballgown and polyester. However,
I haven't been able to access the new system since the change in system.
I'm wondering if I would be able to be give access? I have included the
maintainers on file for those packages as well.

Best,
Jack



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Re: [Bioc-devel] Access to push to pacakges Polyester and Ballgown

[Jeff Leek]

Yes we are adding him to both

On Tue, Feb 13, 2018, 10:53 AM Jack Fu  wrote:

> Thanks for checking Valerie. My github id is jmf47.
>
> Thanks!
> Jack
>
> On Feb 13, 2018, at 10:22 AM, Obenchain, Valerie <
> valerie.obench...@roswellpark.org> wrote:
>
> Hi,
>
> Jack, It doesn't look like you currently have access to other Bioconductor
> packages - is that correct? If you don't currently have access, I need to
> know your github username.
>
> Jeff, are we adding Jack to both polyester and ballgown?
>
> Valerie
>
>
> On 02/13/2018 02:57 AM, Jeff Leek wrote:
>
> HI Bioc Team
>
> If you could please add Jack that would be great!
>
> Jeff
>
> On Mon, Feb 12, 2018 at 7:53 AM Jack Fu   wrote:
>
>
> Hi Bioc team,
>
> I'm currently maintaining the packages Ballgown and polyester. However,
> I haven't been able to access the new system since the change in system.
> I'm wondering if I would be able to be give access? I have included the
> maintainers on file for those packages as well.
>
> Best,
> Jack
>
>
>   [[alternative HTML version deleted]]
>
> ___bioc-de...@r-project.org 
> mailing listhttps://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>
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> agent responsible for the delivery of this message to the intended
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Re: [Bioc-devel] "Error: duplicate commits" when pushing FamAgg to Bioconductor git

[Turaga, Nitesh]

Hi,

It seems that there are multiple levels of duplication on your repository. 

You seem to have issued the “merge” with not the current bioconductor devel but 
the (now deprecated) GitHub- bioconductor mirror, multiple times. Please 
correct me if this is not accurate. I’m wondering why the merge was issued so 
many times? 

As far as the fix goes, it would take me a while to track down the “merge” 
commits and then “cherry-pick" on to the master branch the commits that are not 
duplicated. These seem to be stemming right from the beginning of your 
development history. 

The steps you need are:

1. Back up master branch (git branch master_backup)
2. Check merge commit SHA’s (git log --oneline maste)
3. Reset to commit before the merge, (git reset --hard )
4. Then, overlay commits on top that reset, with latest non-duplicated commits 
(git cherry-pick )

You’d have to repeat these steps quite extensively depending on how many merges 
you have.

Take a look at this manual as further help to do this, 
http://sethrobertson.github.io/GitFixUm/fixup.html. 

Do these steps on your local repository and push to Github. Once you have done 
that, let me know and I’ll take a look at your Github repo, and sync with 
Bioconductor if history looks clean.

If you are unable to fix the repo, then the best way forward it to remove the 
pre-receive hook from your repository and deal with the history as is. This 
will not effect your package in anyway, just that the git history won’t be 
clean. 


Best,

Nitesh 


> On Feb 12, 2018, at 5:41 AM, Rainer Johannes  
> wrote:
> 
> Dear all,
> 
> I'm unable to push my recent changes to FamAgg to the Bioconductor git repo 
> (see below for the error message). I did try the suggested fix but without 
> any success - seems the duplicated commits are in Bioconductor and not github.
> 
> thankful for any help or advise
> 
> The error message is:
> 
> macbookjo:FamAgg jo$ git push origin master
> Everything up-to-date
> macbookjo:FamAgg jo$ git push upstream master
> Counting objects: 13, done.
> Delta compression using up to 8 threads.
> Compressing objects: 100% (13/13), done.
> Writing objects: 100% (13/13), 2.17 KiB | 2.17 MiB/s, done.
> Total 13 (delta 11), reused 0 (delta 0)
> remote: Error: duplicate commits.
> remote: 
> remote: There are duplicate commits in your commit history, These cannot be
> remote: pushed to the Bioconductor git server. Please make sure that this is
> remote: resolved.
> remote: 
> remote: Take a look at the documentation to fix this,
> remote: 
> https://bioconductor.org/developers/how-to/git/sync-existing-repositories/,
> remote: particularly, point #8 (force Bioconductor master to Github master).
> remote: 
> remote: For more information, or help resolving this issue, contact
> remote: . Provide the error, the package name and
> remote: any other details we might need.
> remote: 
> remote: Use
> remote: 
> remote: git show 397d05e8ba7d301a9145573210c277f1c6dd66a5
> remote: git show 6a0c683477b78e231a7eb1b59171baa0bc582ef2
> remote: 
> remote: to see body of commits.
> remote: 
> To git.bioconductor.org:packages/FamAgg
> ! [remote rejected] master -> master (pre-receive hook declined)
> error: failed to push some refs to 'g...@git.bioconductor.org:packages/FamAgg'
> 
> 
> macbookjo:FamAgg jo$ git show 397d05e8ba7d301a9145573210c277f1c6dd66a5
> commit 397d05e8ba7d301a9145573210c277f1c6dd66a5
> Author: Herve Pages 
> Date:   Mon Apr 24 19:50:57 2017 +
> 
>bump x.y.z versions to odd y after creation of 3_5 branch
> 
>git-svn-id: 
> file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/FamAgg@129129
>  bc3139a8-67e5-0310-9ffc-ced21a209358
> 
> diff --git a/DESCRIPTION b/DESCRIPTION
> index c9cb1b7..948b777 100644
> --- a/DESCRIPTION
> +++ b/DESCRIPTION
> @@ -1,7 +1,7 @@
> Package: FamAgg
> Type: Package
> Title: Pedigree Analysis and Familial Aggregation
> -Version: 1.4.0
> +Version: 1.5.0
> Author: J. Rainer, D. Taliun, C.X. Weichenberger
> Maintainer: Johannes Rainer 
> URL: https://github.com/jotsetung/FamAgg
> 
> macbookjo:FamAgg jo$ git show 6a0c683477b78e231a7eb1b59171baa0bc582ef2
> commit 6a0c683477b78e231a7eb1b59171baa0bc582ef2
> Author: hpa...@fhcrc.org 
> 
> Date:   Mon Apr 24 19:50:57 2017 +
> 
>bump x.y.z versions to odd y after creation of 3_5 branch
> 
>git-svn-id: 
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/FamAgg@129129 
> bc3139a8-67e5-0310-9ffc-ced21a209358
> 
> diff --git a/DESCRIPTION b/DESCRIPTION
> index c9cb1b7..948b777 100644
> --- a/DESCRIPTION
> +++ b/DESCRIPTION
> @@ -1,7 +1,7 @@
> Package: FamAgg
> Type: Package
> Title: Pedigree Analysis and Familial Aggregation
> -Version: 1.4.0
> +Version: 1.5.0
> Author: J. Rainer, D. Taliun, C.X. Weichenberger
> Maintainer: Johannes Rainer 
> 

Re: [Bioc-devel] Access to push to pacakges Polyester and Ballgown

[Jack Fu]

Thanks for checking Valerie. My github id is jmf47.

Thanks!
Jack

On Feb 13, 2018, at 10:22 AM, Obenchain, Valerie 
> 
wrote:

Hi,

Jack, It doesn't look like you currently have access to other Bioconductor 
packages - is that correct? If you don't currently have access, I need to know 
your github username.

Jeff, are we adding Jack to both polyester and ballgown?

Valerie


On 02/13/2018 02:57 AM, Jeff Leek wrote:

HI Bioc Team

If you could please add Jack that would be great!

Jeff

On Mon, Feb 12, 2018 at 7:53 AM Jack Fu  
wrote:



Hi Bioc team,

I'm currently maintaining the packages Ballgown and polyester. However,
I haven't been able to access the new system since the change in system.
I'm wondering if I would be able to be give access? I have included the
maintainers on file for those packages as well.

Best,
Jack



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Re: [Bioc-devel] Access to push to pacakges Polyester and Ballgown

[Obenchain, Valerie]

Hi,

Jack, It doesn't look like you currently have access to other Bioconductor 
packages - is that correct? If you don't currently have access, I need to know 
your github username.

Jeff, are we adding Jack to both polyester and ballgown?

Valerie


On 02/13/2018 02:57 AM, Jeff Leek wrote:

HI Bioc Team

If you could please add Jack that would be great!

Jeff

On Mon, Feb 12, 2018 at 7:53 AM Jack Fu  
wrote:



Hi Bioc team,

I'm currently maintaining the packages Ballgown and polyester. However,
I haven't been able to access the new system since the change in system.
I'm wondering if I would be able to be give access? I have included the
maintainers on file for those packages as well.

Best,
Jack




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Re: [Bioc-devel] rsvg on mac

[Obenchain, Valerie]

Hi,

By default, the build system installs CRAN dependencies on the Mac and Windows 
builders with 'type=both':

  install.packages("mypackage", type="both")

This means it first tries to install the binary and if that fails, it tries to 
install from source. Packages without native code or SystemRequirements usually 
install fine from source. This is the case for DiagrammeR which can be 
installed on the build machines. rsvg is in the Suggests field of DiagrammeR so 
rsvg is not needed to install or load the package.

The rsvg package is different in that it has 'librsvg2' as a SystemRequirement 
which is not installed on the Mac (or Windows) build machine:

  https://cran.r-project.org/web/packages/rsvg/index.html

We do install all SystemRequirements for Bioconductor packages on the Mac and 
Windows builders but not for CRAN packages. Installing all third party 
requirements of CRAN dependencies would add significantly to the build system 
maintenance and really only serves a purpose in this window of time where 
binaries are not available for devel.

cc'ing Herve in case he has more to add.

Valerie




On 02/12/2018 12:25 PM, Kevin Horan wrote:
Valerie,
I'm not sure I understand. I looked at another package that is currently 
installed on the mac devel machine, DiagrammeR 
(https://cran.r-project.org/package=DiagrammeR), and it has the same set of 
links on the CRAN site as rsvg does. In particular, it does not show a  r-devel 
version for El Capitan.
Also, rsvg is not installed on the release mac build machine either, which 
it should have a version for.

Kevin

On 02/07/2018 09:09 AM, Obenchain, Valerie wrote:
Hi Kevin,

CRAN binaries for El Capitan in devel aren't available. You can see this on the 
rsvg landing page:

https://cran.r-project.org/web/packages/rsvg/index.html

Nothing we can do until CRAN makes them available.

Valerie


On 02/07/2018 08:29 AM, Kevin Horan wrote:

The ChemmineR build is failing on the mac due to a new dependency not
being available, the package "rsvg". Would it be possible to install
that on the mac build machine? Thanks.

http://bioconductor.org/checkResults/devel/bioc-LATEST/ChemmineR/merida2-install.html


Kevin

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Re: [Rd] R Compilation gets stuck on Windows 64

[Avraham Adler]

Set the location of atlas path in mkrules.local to what you need, then edit
arc/extra/blas/makevars.win to read lopenblas_haswell-r0.2.20 instead of
the two libraries there in the atlas section. I think I described this in
my more recent instructions.

Avi

On Tue, Feb 13, 2018 at 8:18 AM Indrajit Sen Gupta 
wrote:

> In the file MkRules.local.in, I see the line: USE_ATLAS = NO which I
> believe needs to be changed to YES. But how do I specify the BLAS file 
> *libopenblas_haswell-r0.2.20.a
> *and its location?
>
> Regards,
> Indrajit
>
> On Tue, Feb 13, 2018 at 6:41 PM, Indrajit Sen Gupta 
> wrote:
>
>> I was able to compile the R from the github by running build-r-devel.bat!
>>
>> Now need to see how to compile it with BLAS.
>>
>> Regard,
>> Indrajit
>>
>> On Tue, Feb 13, 2018 at 5:45 PM, Jeroen Ooms 
>> wrote:
>>
>>> On Tue, Feb 13, 2018 at 12:22 PM, Indrajit Sen Gupta
>>>  wrote:
>>> > Hi Avraham,
>>> >
>>> > I tried with the patched version. The same error message.
>>> >
>>> > gcc -std=gnu99 -m64 -shared -s -mwindows -o R.dll R.def console.o
>>> dynload.o
>>> > editor.o embeddedR.o extra.o malloc.o opt.o pager.o preferences.o
>>> psignal.o
>>> > rhome.o rt_complete.o rui.o run.o shext.o sys-win32.o system.o
>>> dos_wglob.o
>>> > dllversion.o ../main/libmain.a ../appl/libappl.a ../nmath/libnmath.a
>>> > getline/gl.a ../extra/xdr/libxdr.a ../extra/intl/libintl.a
>>> > ../extra/trio/libtrio.a ../extra/tzone/libtz.a ../extra/tre/libtre.a
>>> > -fopenmp -L. -lgfortran -lquadmath -lRblas -L../../lib -lRgraphapp
>>> -lRiconv
>>> > -lcomctl32 -lversion -L"D:/R64/extsoft"/lib/x64 -lpcre -lz -lbz2 -llzma
>>> > -L"D:/home/ICU"/lib/x64 -lsicuin -lsicuuc -lsicudt -lstdc++
>>> >
>>> D:/Rtools/mingw_64/bin/../lib/gcc/x86_64-w64-mingw32/4.9.3/../../../../x86_64-w64-mingw32/bin/ld.exe:
>>> > cannot find -lRgraphapp
>>> > collect2.exe: error: ld returned 1 exit status
>>> > make[4]: *** [R.dll] Error 1
>>> > make[3]: *** [../../bin/x64/R.dll] Error 2
>>> > make[2]: *** [rbuild] Error 2
>>> > make[1]: *** [all] Error 2
>>> > make: *** [distribution] Error 2
>>> >
>>> >
>>> > Would it be possible for you to share your MkRules.local and
>>> Makefile.win
>>> > files?
>>>
>>>
>>> Hi Indrajit
>>>
>>> As somebody above already mentioned, the full build script as well as
>>> MkRules.local that we use for the CRAN releases of R for windows are
>>> available from https://github.com/rwinlib/base
>>>
>>> As is explained in the repository readme, if you have the required
>>> dependencies (rtools, miktex innosetup, strawberry perl) all you need
>>> to do is run the build-r-devel.bat script from the root of the
>>> repository.
>>>
>>> Once you got this to work, you can adapt it to your needs.
>>>
>>
>>
> --
Sent from Gmail Mobile

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Re: [Rd] R Compilation gets stuck on Windows 64

[Jeroen Ooms]

On Tue, Feb 13, 2018 at 2:18 PM, Indrajit Sen Gupta
 wrote:
> In the file MkRules.local.in, I see the line: USE_ATLAS = NO which I believe
> needs to be changed to YES. But how do I specify the BLAS file
> libopenblas_haswell-r0.2.20.a and its location?

I have never done this, but a good starting point is searching the R
source code for how this works:
https://github.com/wch/r-source/search?utf8=✓=USE_ATLAS

>From the extra/blas/Makefile.win file it looks like you may need to
rename libopenblas_haswell-r0.2.20.a to libatlas.a and point to this
directory via the variable ATLAS_PATH in your MkRules.local.in?

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Re: [Rd] R Compilation gets stuck on Windows 64

[Indrajit Sen Gupta]

In the file MkRules.local.in, I see the line: USE_ATLAS = NO which I
believe needs to be changed to YES. But how do I specify the BLAS file
*libopenblas_haswell-r0.2.20.a
*and its location?

Regards,
Indrajit

On Tue, Feb 13, 2018 at 6:41 PM, Indrajit Sen Gupta 
wrote:

> I was able to compile the R from the github by running build-r-devel.bat!
>
> Now need to see how to compile it with BLAS.
>
> Regard,
> Indrajit
>
> On Tue, Feb 13, 2018 at 5:45 PM, Jeroen Ooms  wrote:
>
>> On Tue, Feb 13, 2018 at 12:22 PM, Indrajit Sen Gupta
>>  wrote:
>> > Hi Avraham,
>> >
>> > I tried with the patched version. The same error message.
>> >
>> > gcc -std=gnu99 -m64 -shared -s -mwindows -o R.dll R.def console.o
>> dynload.o
>> > editor.o embeddedR.o extra.o malloc.o opt.o pager.o preferences.o
>> psignal.o
>> > rhome.o rt_complete.o rui.o run.o shext.o sys-win32.o system.o
>> dos_wglob.o
>> > dllversion.o ../main/libmain.a ../appl/libappl.a ../nmath/libnmath.a
>> > getline/gl.a ../extra/xdr/libxdr.a ../extra/intl/libintl.a
>> > ../extra/trio/libtrio.a ../extra/tzone/libtz.a ../extra/tre/libtre.a
>> > -fopenmp -L. -lgfortran -lquadmath -lRblas -L../../lib -lRgraphapp
>> -lRiconv
>> > -lcomctl32 -lversion -L"D:/R64/extsoft"/lib/x64 -lpcre -lz -lbz2 -llzma
>> > -L"D:/home/ICU"/lib/x64 -lsicuin -lsicuuc -lsicudt -lstdc++
>> > D:/Rtools/mingw_64/bin/../lib/gcc/x86_64-w64-mingw32/4.9.3/.
>> ./../../../x86_64-w64-mingw32/bin/ld.exe:
>> > cannot find -lRgraphapp
>> > collect2.exe: error: ld returned 1 exit status
>> > make[4]: *** [R.dll] Error 1
>> > make[3]: *** [../../bin/x64/R.dll] Error 2
>> > make[2]: *** [rbuild] Error 2
>> > make[1]: *** [all] Error 2
>> > make: *** [distribution] Error 2
>> >
>> >
>> > Would it be possible for you to share your MkRules.local and
>> Makefile.win
>> > files?
>>
>>
>> Hi Indrajit
>>
>> As somebody above already mentioned, the full build script as well as
>> MkRules.local that we use for the CRAN releases of R for windows are
>> available from https://github.com/rwinlib/base
>>
>> As is explained in the repository readme, if you have the required
>> dependencies (rtools, miktex innosetup, strawberry perl) all you need
>> to do is run the build-r-devel.bat script from the root of the
>> repository.
>>
>> Once you got this to work, you can adapt it to your needs.
>>
>
>

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Re: [Rd] R Compilation gets stuck on Windows 64

[Indrajit Sen Gupta]

I was able to compile the R from the github by running build-r-devel.bat!

Now need to see how to compile it with BLAS.

Regard,
Indrajit

On Tue, Feb 13, 2018 at 5:45 PM, Jeroen Ooms  wrote:

> On Tue, Feb 13, 2018 at 12:22 PM, Indrajit Sen Gupta
>  wrote:
> > Hi Avraham,
> >
> > I tried with the patched version. The same error message.
> >
> > gcc -std=gnu99 -m64 -shared -s -mwindows -o R.dll R.def console.o
> dynload.o
> > editor.o embeddedR.o extra.o malloc.o opt.o pager.o preferences.o
> psignal.o
> > rhome.o rt_complete.o rui.o run.o shext.o sys-win32.o system.o
> dos_wglob.o
> > dllversion.o ../main/libmain.a ../appl/libappl.a ../nmath/libnmath.a
> > getline/gl.a ../extra/xdr/libxdr.a ../extra/intl/libintl.a
> > ../extra/trio/libtrio.a ../extra/tzone/libtz.a ../extra/tre/libtre.a
> > -fopenmp -L. -lgfortran -lquadmath -lRblas -L../../lib -lRgraphapp
> -lRiconv
> > -lcomctl32 -lversion -L"D:/R64/extsoft"/lib/x64 -lpcre -lz -lbz2 -llzma
> > -L"D:/home/ICU"/lib/x64 -lsicuin -lsicuuc -lsicudt -lstdc++
> > D:/Rtools/mingw_64/bin/../lib/gcc/x86_64-w64-mingw32/4.9.3/.
> ./../../../x86_64-w64-mingw32/bin/ld.exe:
> > cannot find -lRgraphapp
> > collect2.exe: error: ld returned 1 exit status
> > make[4]: *** [R.dll] Error 1
> > make[3]: *** [../../bin/x64/R.dll] Error 2
> > make[2]: *** [rbuild] Error 2
> > make[1]: *** [all] Error 2
> > make: *** [distribution] Error 2
> >
> >
> > Would it be possible for you to share your MkRules.local and Makefile.win
> > files?
>
>
> Hi Indrajit
>
> As somebody above already mentioned, the full build script as well as
> MkRules.local that we use for the CRAN releases of R for windows are
> available from https://github.com/rwinlib/base
>
> As is explained in the repository readme, if you have the required
> dependencies (rtools, miktex innosetup, strawberry perl) all you need
> to do is run the build-r-devel.bat script from the root of the
> repository.
>
> Once you got this to work, you can adapt it to your needs.
>

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Re: [Rd] R Compilation gets stuck on Windows 64

[Jeroen Ooms]

On Tue, Feb 13, 2018 at 12:22 PM, Indrajit Sen Gupta
 wrote:
> Hi Avraham,
>
> I tried with the patched version. The same error message.
>
> gcc -std=gnu99 -m64 -shared -s -mwindows -o R.dll R.def console.o dynload.o
> editor.o embeddedR.o extra.o malloc.o opt.o pager.o preferences.o psignal.o
> rhome.o rt_complete.o rui.o run.o shext.o sys-win32.o system.o dos_wglob.o
> dllversion.o ../main/libmain.a ../appl/libappl.a ../nmath/libnmath.a
> getline/gl.a ../extra/xdr/libxdr.a ../extra/intl/libintl.a
> ../extra/trio/libtrio.a ../extra/tzone/libtz.a ../extra/tre/libtre.a
> -fopenmp -L. -lgfortran -lquadmath -lRblas -L../../lib -lRgraphapp -lRiconv
> -lcomctl32 -lversion -L"D:/R64/extsoft"/lib/x64 -lpcre -lz -lbz2 -llzma
> -L"D:/home/ICU"/lib/x64 -lsicuin -lsicuuc -lsicudt -lstdc++
> D:/Rtools/mingw_64/bin/../lib/gcc/x86_64-w64-mingw32/4.9.3/../../../../x86_64-w64-mingw32/bin/ld.exe:
> cannot find -lRgraphapp
> collect2.exe: error: ld returned 1 exit status
> make[4]: *** [R.dll] Error 1
> make[3]: *** [../../bin/x64/R.dll] Error 2
> make[2]: *** [rbuild] Error 2
> make[1]: *** [all] Error 2
> make: *** [distribution] Error 2
>
>
> Would it be possible for you to share your MkRules.local and Makefile.win
> files?


Hi Indrajit

As somebody above already mentioned, the full build script as well as
MkRules.local that we use for the CRAN releases of R for windows are
available from https://github.com/rwinlib/base

As is explained in the repository readme, if you have the required
dependencies (rtools, miktex innosetup, strawberry perl) all you need
to do is run the build-r-devel.bat script from the root of the
repository.

Once you got this to work, you can adapt it to your needs.

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Re: [Rd] R Compilation gets stuck on Windows 64

[Indrajit Sen Gupta]

Hi Avraham,

I tried with the patched version. The same error message.

gcc -std=gnu99 -m64 -shared -s -mwindows -o R.dll R.def console.o dynload.o
editor.o embeddedR.o extra.o malloc.o opt.o pager.o preferences.o psignal.o
rhome.o rt_complete.o rui.o run.o shext.o sys-win32.o system.o dos_wglob.o
dllversion.o ../main/libmain.a ../appl/libappl.a ../nmath/libnmath.a
getline/gl.a ../extra/xdr/libxdr.a ../extra/intl/libintl.a
../extra/trio/libtrio.a ../extra/tzone/libtz.a ../extra/tre/libtre.a
-fopenmp -L. -lgfortran -lquadmath -lRblas -L../../lib -lRgraphapp -lRiconv
-lcomctl32 -lversion -L"D:/R64/extsoft"/lib/x64 -lpcre -lz -lbz2 -llzma
-L"D:/home/ICU"/lib/x64 -lsicuin -lsicuuc -lsicudt -lstdc++
D:/Rtools/mingw_64/bin/../lib/gcc/x86_64-w64-mingw32/4.9.3/../../../../x86_64-w64-mingw32/bin/ld.exe:
cannot find -lRgraphapp
collect2.exe: error: ld returned 1 exit status
make[4]: *** [R.dll] Error 1
make[3]: *** [../../bin/x64/R.dll] Error 2
make[2]: *** [rbuild] Error 2
make[1]: *** [all] Error 2
make: *** [distribution] Error 2


Would it be possible for you to share your MkRules.local and Makefile.win
files?

Also as per your website, we don't need the line:

*TCL_VERSION = 86 *

in the file *Makeconf *inside *R_HOME/src/gnuwin32/fixed/etc*. Hence I am
commenting it. Also I noticed, just above this line (line 60), the
following line which specifies Rgraphapp:

*GRAPHAPP_LIB = -lRgraphapp*
# TCL_VERSION = 86
# was a reference to Rzlib.dll in R < 3.2.0
ZLIB_LIBS = -lz


This looks like the step which is causing the error. Anything I can try out
at this point?

Regards,
Indrajit


On Fri, Feb 9, 2018 at 9:58 PM, Avraham Adler 
wrote:

> On Fri, Feb 9, 2018 at 9:29 AM, Kenny Bell  wrote:
> > I suggest that you work off the build process in the  rwinlib repository
> so
> > you are starting from something that you know works and already
> incorporates
> > the set of dependencies you need.
>
> Hello, Kenny.
>
> For what it's worth I've been successfully building R+OpenBLAS on
> Windows64 since 2013, which I believe predates rwinlib on github, but
> I may be mistaken. Thus, I don't think I'm incorrect in saying that
> the instructions I provide are also "something that you know works" :)
> I did make the explicit assumption that people will successfully
> follow the instructions at R Installation & Administration. Perhaps
> that is too much to ask.
>
> Thanks,
>
> Avi
>

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Re: [Bioc-devel] Access to push to pacakges Polyester and Ballgown

[Jeff Leek]

HI Bioc Team

If you could please add Jack that would be great!

Jeff

On Mon, Feb 12, 2018 at 7:53 AM Jack Fu  wrote:

> Hi Bioc team,
>
> I'm currently maintaining the packages Ballgown and polyester. However,
> I haven't been able to access the new system since the change in system.
> I'm wondering if I would be able to be give access? I have included the
> maintainers on file for those packages as well.
>
> Best,
> Jack
>

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Re: [Rd] Fix minor typo in error message from grDevices

[Tomas Kalibera]

Fixed, thanks,
Tomas

On 02/12/2018 09:33 PM, John Blischak wrote:
> Hi,
>
> I fixed a minor typo in an error message from grDevices. Please see
> attached for a patch to revision 74246.
>
> Thanks,
>
> John
>
>
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Re: [Rd] Setting the path to Rtools for package compilation on Windows

[Jeroen Ooms]

On Tue, Feb 13, 2018 at 7:45 AM, Peter Langfelder
 wrote:
> Hi all,
>
> I'm trying to set up the Windows Rtools toolset for building packages
> with compiled code. I installed for Windows R-3.4.3 from CRAN and
> installed Rtools-3.4 in a custom location M:\R\R-3.4.3 and
> M:\R\Rtools-3.4
>
> Following the instructions, in shell, I set
> Path=M:\R\Rtools-3.4\bin;M:\R\Rtools-3.4\gcc-4.6.3\bin;M:\R\R-3.4.3\bin;...
> (the ... are other paths irrelevant for R/Rtools).

Thanks for your question. Your logs show that 'gcc' is not found. As
of R 3.3 you need to set the path to the compiler using the BINPREF
variable. This is because we ship two separate versions of gcc, one
targeting win32 and one targeting win64. I am not sure what your
rtools installation looks like, but could you try setting this
environment variable:

  BINPREF="M:/R/Rtools-3.4/mingw_$(WIN)/bin/"

I think this will do the job.

On Tue, Feb 13, 2018 at 10:21 AM, Tomas Kalibera
 wrote:
> Thanks for the report - this has been already reported as bug 17376, it is
> caused by scripts that build the Windows binaries and by now has been fixed
> in R-patched and R-devel snapshot builds. So as a solution that works now I
> would recommend using R-patched.

This issue is unrelated, I doubt your advice will solve anything. The
only thing that 17376 does is add c:/rtools/bin to the default path.
But this dir does not exist for this user, so it is ignored by windows
when searching the PATH.

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Re: [R-pkg-devel] new package? - Sports data from transfermarkt.com using rvest

[Kehl Dániel]

Dear Peter and Thierry,

thank you for your answers. I indeed contacted transfermarkt.com and write this 
just to finish up this conversation.

Here is part of their answer:

"thank you for getting in touch with us. Basically our data is copyrighted 
under German law by Transfermarkt, so there is no license whatsoever. 
Therefore, we�re also no friends of data scraping and tend to block bots more 
and more.
Rather we support the scientific community by providing data sets for single 
purposes in a structured process."

Seems like this is a polite way of saying: do not create an R package with this 
purpose. My first package is going to be something else. :(

Thanks and have a great day,
Daniel


[http://wweb.ktk.pte.hu/info/email-alairas/Oktat%C3%B3k/Dr.%20KEHL%20D%C3%A1niel/magyar/image001.png]



Dr. KEHL D�niel
adjunktus

[http://wweb.ktk.pte.hu/info/email-alairas/Oktat%C3%B3k/Dr.%20KEHL%20D%C3%A1niel/magyar/image002.png]
P�CSI TUDOM�NYEGYETEM K�ZGAZDAS�GTUDOM�NYI KAR
K�zgazdas�gtan �s �konometria Int�zet
H-7622 P�cs, R�k�czi �t 80. | www.ktk.pte.hu
+36 72 501 599/ 23144 | ke...@ktk.pte.hu

Felad�: Peter Meissner [retep.meiss...@gmail.com]
K�ldve: 2018. janu�r 24. 18:59
C�mzett: Thierry Onkelinx
M�solatot kap: Kehl D�niel; r-package-devel@r-project.org
T�rgy: Re: [R-pkg-devel] new package? - Sports data from transfermarkt.com 
using rvest

Hey,

I am not a laywer but their terms are quite explicitly prohibiting 
redistribution of their data without written consent.

Now you might build a package that does not collect, store and redistributes 
the data but only allows to access the data provided there 'live' via some 
convenience functions. But I don't really know if that argument actually is 
valid in any legal sense.

To be on the safe side, you probably should contact them.

Best, Peter


Am 24.01.2018 12:13 nachm. schrieb "Thierry Onkelinx" 
>:
Dear Daniel,

First of all you need to make sure that the licence of
transfermarkt.com allows the usage that you have 
intended. If that is
not clear from their website, then you should contact them rather than
us.

CRAN has several packages to assists in downloading data from online
sources. But the source has to allow that kind of usage.

Best regards,

ir. Thierry Onkelinx
Statisticus / Statistician

Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE
AND FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkel...@inbo.be
Havenlaan 88 bus 73, 1000 Brussel
www.inbo.be

///
To call in the statistician after the experiment is done may be no
more than asking him to perform a post-mortem examination: he may be
able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does
not ensure that a reasonable answer can be extracted from a given body
of data. ~ John Tukey
///




2018-01-23 16:27 GMT+01:00 Kehl D�niel 
>:
> Dear List members,
>
> maybe this is not the right place to ask, if that is the case, please forward 
> me to the right place.
> I developed some functions to download and transform football/soccer related 
> data from transfermarkt.com.
> There are plans to create my first package based on these functions and of 
> course develop them and add more later. As far as I know there is no API to 
> that page, so I am using the rvest package.
> My question is: is this an OK thing to do? Should I contact 
> transfermarkt.com? My german is not perfect (just 
> like my english), this is what I've found on thier webpage. Does that mean 
> one can not create a package related to that page? Or can't crawl at all? Or 
> just not allowed to sell the data? If it is allowed, can one post the package 
> on CRAN at the end?
>
> Please if any of you have experience in that or just show me where to ask, do 
> not hesitate!
>
> LEGAL NOTICE
> � Transfermarkt GmbH & Co. KG 2000-2018
>
> All rights reserved.
>
> Der Inhalt dieser Website ist urheberrechtlich gesch�tzt. Nachdruck, Aufnahme 
> in Online-Dienste, Internet und Vervielf�ltigung auf Datentr�ger wie CD-ROM, 
> DVD-ROM usw. d�rfen, auch auszugsweise, nur nach vorheriger schriftlicher 
> Zustimmung durch Transfermarkt erfolgen. Eine kommerzielle Weitervermarktung 
> des Inhalts ist untersagt.
>
> Transfermarkt haftet nicht f�r unverlangt eingesandte Inhalte, Manuskripte 
> und Fotos. F�r Inhalte externer 

Re: [Rd] Setting the path to Rtools for package compilation on Windows

[Tomas Kalibera]

Thanks for the report - this has been already reported as bug 17376, it 
is caused by scripts that build the Windows binaries and by now has been 
fixed in R-patched and R-devel snapshot builds. So as a solution that 
works now I would recommend using R-patched.


Tomas


On 02/13/2018 08:33 AM, Søren Højsgaard wrote:

I can confirm the behaviour that you report.

Usually I put Rtools in c:\programs\Rtools and modify the path
accordingly. Recently (don't recall for how long) I have encountered
the same problems as you have and I have resorted to moving Rtools to
c:\Rtools

I have no idea as how to proceed; perhaps it could be worth trying an
older version of Rtools (though that may cause other problems).

Regards
Søren


On Mon, 2018-02-12 at 22:45 -0800, Peter Langfelder wrote:

Hi all,

I'm trying to set up the Windows Rtools toolset for building packages
with compiled code. I installed for Windows R-3.4.3 from CRAN and
installed Rtools-3.4 in a custom location M:\R\R-3.4.3 and
M:\R\Rtools-3.4

Following the instructions, in shell, I set
Path=M:\R\Rtools-3.4\bin;M:\R\Rtools-3.4\gcc-4.6.3\bin;M:\R\R-
3.4.3\bin;...
(the ... are other paths irrelevant for R/Rtools).

When I run

M:\Work\RLibs>R.exe CMD INSTALL --build WGCNA

I get the following ouput:

In R CMD INSTALL
* installing to library 'M:/R/R-3.4.3/library'
* installing *source* package 'WGCNA' ...
** libs

*** arch - i386
c:/Rtools/mingw_32/bin/g++  -I"M:/R/R-3.4.3/include" -DNDEBUG
-O2 -Wall  -mtune=generic -c bucketApproxSort.cc
-o bucketApproxSort.o
c:/Rtools/mingw_32/bin/g++: not found
make: *** [bucketApproxSort.o] Error 127
Warning: running command 'make -f "Makevars.win" -f
"M:/R/R-3.4.3/etc/i386/Makeconf" -f "M:/R/R-3.4.3/share/make/winshli
b.mk" SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)'
SHLIB="WGCNA.dll" OBJECTS="bucketApproxSort.o corFun
ctions-common.o corFunctions-unified.o networkFunctions.o pivot.o
quantileC.o"' had status 2
ERROR: compilation failed for package 'WGCNA'
* removing 'M:/R/R-3.4.3/library/WGCNA'
* restoring previous 'M:/R/R-3.4.3/library/WGCNA'


Apparently the install is looking for Rtools in c:\Rtools. I am a
perpetual Windows newbie and would be really thankful for any
pointers
as to how to proceed.

Peter

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Re: [R-pkg-devel] Lapack: undefined symbol: zgbsv_

[Ralf Stubner]

On 13.02.2018 05:49, Baptiste Auguie wrote:
> On 13 February 2018 at 01:05, Dirk Eddelbuettel  > wrote:
> Maybe we are setting a more global "no advanced lapack" for Windows that
> assures success when we assume that the other system will always
> have it.
> 
> 
> it sounds plausible, but it would be nice to know for sure.

It is the case, c.f.
https://github.com/RcppCore/RcppArmadillo/blob/master/inst/include/RcppArmadilloConfig.h#L96-L106

> In
> particular, it doesn't explain why the external Lapack on linux appears
> to be missing these symbols (they're not very recent, as far as I can
> tell). I don't really know how to figure this out, but it seems to be key.

My understanding:

* On Windows internal LAPACK is used but it is not affected due to the
defines quoted above.
* At least Debian & Co but probably also other Linux distributions
compile R with external LAPACK and are not affected.
* CRAN (and probably r-hub) use R compiled with internal LAPACK and is
therefore affected.
* I do not understand why Mac OS is not affected. The FAQ [1] implies
that by default the internal BLAS/LAPACK is used. But then I do not see
the mentioned alternative libRblas.vecLib.dylib on a test system.

[1]
https://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html#Which-BLAS-is-used-and-how-can-it-be-changed_003f


> Or, be brutal, and set '#define ARMA_CRIPPLED_LAPACK 1' everywhere.  See
> lines 67 to 95 of RcppArmadillo's configure.ac :
> https://github.com/RcppCore/RcppArmadillo/blob/master/configure.ac#L67-L95
> 
> while this might solve the CRAN problem, it doesn't feel right to
> enforce the use of suboptimal routines throughout and on all platforms,
> including those that do in fact provide a full-fledged external Lapack. 

You could use this as a first step to get the package back into CRAN.
Later on you can try to only set the flag when an internal LAPACK is
detected, similar to the way RcppArmadillo does it. If my understanding
above is correct, the number of users with ARMA_CRIPPLED_LAPACK in your
package but not in RcppArmadillo will be quite small.

Greetings
Ralf

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R Institute GmbH
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