Submission of patch for Add r-abc

DoneSubmitted by Sahithi Yarlagadda.
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2 participants
  • Ricardo Wurmus
  • Sahithi Yarlagadda
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Sahithi Yarlagadda wrote on 21 Mar 2018 12:14
(address . guix-patches@gnu.org)(name . Ricardo Wurmus)(address . rekado@elephly.net)
071fa29f-107d-2097-586c-ce2f1eb91c23@swecha.net
Hi,
I am submitting a patch for r-abc. Please review.
-- RegardsSahithi
From 4b3b3eee4995616059d8a27489affc43cee26ea4 Mon Sep 17 00:00:00 2001From: Sahithi Yarlagadda <sahi@swecha.net>Date: Wed, 21 Mar 2018 16:30:18 +0530Subject: [PATCH] gnu: Add r-abc.
* gnu/packages/cran.scm (r-abc): New variable.--- gnu/packages/cran.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+)
Toggle diff (40 lines)diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scmindex ce09c22c5..6aecd0f8e 100644--- a/gnu/packages/cran.scm+++ b/gnu/packages/cran.scm@@ -3295,3 +3295,33 @@ Dependencies of the distribution of the specified variable (response variable) to other variables (explanatory variables) are derived and evaluated by the @dfn{Akaike Information Criterion} (AIC).") (license license:gpl2+)))++(define-public r-abc+ (package+ (name "r-abc")+ (version "2.1")+ (source+ (origin+ (method url-fetch)+ (uri (cran-uri "abc" version))+ (sha256+ (base32+ "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-abc-data" ,r-abc-data)+ ("r-locfit" ,r-locfit)+ ("r-mass" ,r-mass)+ ("r-nnet" ,r-nnet)+ ("r-quantreg" ,r-quantreg)))+ (home-page+ "http://cran.r-project.org/web/packages/abc")+ (synopsis+ "Tools for approximate bayesian computation (ABC)")+ (description+ "Implements several ABC algorithms for performing parameter estimation, +model selection, and goodness-of-fit. Cross-validation tools are also +available for measuring the accuracy of ABC estimates, and to calculate the +misclassification probabilities of different models.")+ (license license:gpl3+)))+-- 2.16.2
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Ricardo Wurmus wrote on 21 Mar 2018 22:27
(name . Sahithi Yarlagadda)(address . sahi@swecha.net)(address . 30894@debbugs.gnu.org)
87tvt9azl6.fsf@elephly.net
Hi Sahithi,
Toggle quote (2 lines)> I am submitting a patch for r-abc. Please review.
Thank you for the patch!
What follows is a short review that includes things I could changemyself before applying the patch, but for the sake of learning Iexplicitly point out in this message. I hope you don’t mind that I’mfocusing on what may seem like minor details.
Toggle quote (7 lines)> From 4b3b3eee4995616059d8a27489affc43cee26ea4 Mon Sep 17 00:00:00 2001> From: Sahithi Yarlagadda <sahi@swecha.net>> Date: Wed, 21 Mar 2018 16:30:18 +0530> Subject: [PATCH] gnu: Add r-abc.>> * gnu/packages/cran.scm (r-abc): New variable.
Nitpick: please don’t indent this line. The asterisk should be thefirst character in this line.
Toggle quote (22 lines)> +> +(define-public r-abc> + (package> + (name "r-abc")> + (version "2.1")> + (source> + (origin> + (method url-fetch)> + (uri (cran-uri "abc" version))> + (sha256> + (base32> + "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))> + (build-system r-build-system)> + (propagated-inputs> + `(("r-abc-data" ,r-abc-data)> + ("r-locfit" ,r-locfit)> + ("r-mass" ,r-mass)> + ("r-nnet" ,r-nnet)> + ("r-quantreg" ,r-quantreg)))> + (home-page> + "http://cran.r-project.org/web/packages/abc")
Please pull this onto the previous line and use “https”.
Toggle quote (3 lines)> + (synopsis> + "Tools for approximate bayesian computation (ABC)")
Please combine this line with the previous line.
Toggle quote (6 lines)> + (description> + "Implements several ABC algorithms for performing parameter estimation,> +model selection, and goodness-of-fit. Cross-validation tools are also> +available for measuring the accuracy of ABC estimates, and to calculate the> +misclassification probabilities of different models.")
Please use full sentences. For CRAN packages the official descriptionusually provides only a sentence fragment in place of the firstsentence. Please also use “@dfn{Approximate Bayesian Computation}(ABC)” the first time “ABC” is mentioned.
All thoughout the indentation is a bit off (that’s expected as theimporter is very simple and doesn’t know about the expectedindentation). If you’re using Emacs you can easily adjust it with M-C-q(also known as “indent-sexp”); otherwise please use“etc/indent-code.el”.
Have you built this package with Guix?
Finally, please rebase this patch so that it can be appliedindependently from the other patch you’ve sent, which cannot currentlybe applied due to problems in building the defined package. Rebasingthis patch ensures that it can be merged even if the other patch isstuck.
Thanks!
--Ricardo
GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAChttps://elephly.net
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Ricardo Wurmus wrote on 28 Mar 2018 21:44
Re: [bug#30894] Submission of patch for Add r-abc
(name . Sahithi Yarlagadda)(address . sahi@swecha.net)(address . 30894@debbugs.gnu.org)
87vadgdlyd.fsf@elephly.net
Hi Sahiti,
have you been able to look at my review below?Please let me know if anything is unclear.
~~ Ricardo
Ricardo Wurmus <rekado@elephly.net> writes:
Toggle quote (76 lines)> Hi Sahithi,>>> I am submitting a patch for r-abc. Please review.>> Thank you for the patch!>> What follows is a short review that includes things I could change> myself before applying the patch, but for the sake of learning I> explicitly point out in this message. I hope you don’t mind that I’m> focusing on what may seem like minor details.>>> From 4b3b3eee4995616059d8a27489affc43cee26ea4 Mon Sep 17 00:00:00 2001>> From: Sahithi Yarlagadda <sahi@swecha.net>>> Date: Wed, 21 Mar 2018 16:30:18 +0530>> Subject: [PATCH] gnu: Add r-abc.>>>> * gnu/packages/cran.scm (r-abc): New variable.>> Nitpick: please don’t indent this line. The asterisk should be the> first character in this line.>>> +>> +(define-public r-abc>> + (package>> + (name "r-abc")>> + (version "2.1")>> + (source>> + (origin>> + (method url-fetch)>> + (uri (cran-uri "abc" version))>> + (sha256>> + (base32>> + "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))>> + (build-system r-build-system)>> + (propagated-inputs>> + `(("r-abc-data" ,r-abc-data)>> + ("r-locfit" ,r-locfit)>> + ("r-mass" ,r-mass)>> + ("r-nnet" ,r-nnet)>> + ("r-quantreg" ,r-quantreg)))>> + (home-page>> + "http://cran.r-project.org/web/packages/abc")>> Please pull this onto the previous line and use “https”.>>> + (synopsis>> + "Tools for approximate bayesian computation (ABC)")>> Please combine this line with the previous line.>>> + (description>> + "Implements several ABC algorithms for performing parameter estimation,>> +model selection, and goodness-of-fit. Cross-validation tools are also>> +available for measuring the accuracy of ABC estimates, and to calculate the>> +misclassification probabilities of different models.")>> Please use full sentences. For CRAN packages the official description> usually provides only a sentence fragment in place of the first> sentence. Please also use “@dfn{Approximate Bayesian Computation}> (ABC)” the first time “ABC” is mentioned.>> All thoughout the indentation is a bit off (that’s expected as the> importer is very simple and doesn’t know about the expected> indentation). If you’re using Emacs you can easily adjust it with M-C-q> (also known as “indent-sexp”); otherwise please use> “etc/indent-code.el”.>> Have you built this package with Guix?>> Finally, please rebase this patch so that it can be applied> independently from the other patch you’ve sent, which cannot currently> be applied due to problems in building the defined package. Rebasing> this patch ensures that it can be merged even if the other patch is> stuck.>> Thanks!
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Ricardo Wurmus wrote on 28 Mar 2018 21:51
control message for bug #30894
(address . control@debbugs.gnu.org)
E1f1H6d-0006MD-Dw@debbugs.gnu.org
tags 30894 moreinfo
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Sahithi Yarlagadda wrote on 29 Mar 2018 12:15
Re: [bug#30894] Submission of patch for Add r-abc
(name . Ricardo Wurmus)(address . rekado@elephly.net)(address . 30894@debbugs.gnu.org)
6c9c531d-75a5-be08-2784-ebae3c3a432b@swecha.net
Hi Ricardo

I have a small doubt regarding the build. Let me explain the process iam doing the build.
1) Cloning the Source
2) Running guix environment guix
3) ./bootstrap
4) ./configure --localstatedir=/var
5) make
6) Make Changes to the cran.scm file
7) Build using  ./pre-inst-env guix build <package>
8) If build is success, format the patch and submit the patch
*When i am planning to write a different package description, i amfollowing this*
9) rebasing the patch
10) Pull for any changes
11) running the process from (2)

Am i doing the right way, I hope i have to compile everytime and thenmake changes each Package Description. Because when i tired to just makechanges and build on old one, i got many errors and warning saying the.go file is older than the .scm.

Please suggest me.

On Thursday 29 March 2018 01:14 AM, Ricardo Wurmus wrote:
Toggle quote (84 lines)> Hi Sahiti,>> have you been able to look at my review below?
> Please let me know if anything is unclear.>> ~~ Ricardo>> Ricardo Wurmus <rekado@elephly.net> writes:>>> Hi Sahithi,>>>>> I am submitting a patch for r-abc. Please review.>> Thank you for the patch!>>>> What follows is a short review that includes things I could change>> myself before applying the patch, but for the sake of learning I>> explicitly point out in this message. I hope you don’t mind that I’m>> focusing on what may seem like minor details.>>>>> From 4b3b3eee4995616059d8a27489affc43cee26ea4 Mon Sep 17 00:00:00 2001>>> From: Sahithi Yarlagadda <sahi@swecha.net>>>> Date: Wed, 21 Mar 2018 16:30:18 +0530>>> Subject: [PATCH] gnu: Add r-abc.>>>>>> * gnu/packages/cran.scm (r-abc): New variable.>> Nitpick: please don’t indent this line. The asterisk should be the>> first character in this line.>>>>> +>>> +(define-public r-abc>>> + (package>>> + (name "r-abc")>>> + (version "2.1")>>> + (source>>> + (origin>>> + (method url-fetch)>>> + (uri (cran-uri "abc" version))>>> + (sha256>>> + (base32>>> + "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))>>> + (build-system r-build-system)>>> + (propagated-inputs>>> + `(("r-abc-data" ,r-abc-data)>>> + ("r-locfit" ,r-locfit)>>> + ("r-mass" ,r-mass)>>> + ("r-nnet" ,r-nnet)>>> + ("r-quantreg" ,r-quantreg)))>>> + (home-page>>> + "http://cran.r-project.org/web/packages/abc")>> Please pull this onto the previous line and use “https”.>>>>> + (synopsis>>> + "Tools for approximate bayesian computation (ABC)")>> Please combine this line with the previous line.>>>>> + (description>>> + "Implements several ABC algorithms for performing parameter estimation,>>> +model selection, and goodness-of-fit. Cross-validation tools are also>>> +available for measuring the accuracy of ABC estimates, and to calculate the>>> +misclassification probabilities of different models.")>> Please use full sentences. For CRAN packages the official description>> usually provides only a sentence fragment in place of the first>> sentence. Please also use “@dfn{Approximate Bayesian Computation}>> (ABC)” the first time “ABC” is mentioned.>>>> All thoughout the indentation is a bit off (that’s expected as the>> importer is very simple and doesn’t know about the expected>> indentation). If you’re using Emacs you can easily adjust it with M-C-q>> (also known as “indent-sexp”); otherwise please use>> “etc/indent-code.el”.>>>> Have you built this package with Guix?>>>> Finally, please rebase this patch so that it can be applied>> independently from the other patch you’ve sent, which cannot currently>> be applied due to problems in building the defined package. Rebasing>> this patch ensures that it can be merged even if the other patch is>> stuck.>>>> Thanks!>>
-- RegardsSahithi
Attachment: file
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Ricardo Wurmus wrote on 29 Mar 2018 12:32
(name . Sahithi Yarlagadda)(address . sahi@swecha.net)(address . 30894@debbugs.gnu.org)
87lgebdveu.fsf@elephly.net
Hi Sahithi,
Toggle quote (8 lines)> 1) Cloning the Source>> 2) Running guix environment guix>> 3) ./bootstrap>> 4) ./configure --localstatedir=/var
You need to perform these steps only once.
Toggle quote (8 lines)> 5) make>> 6) Make Changes to the cran.scm file>> 7) Build using ./pre-inst-env guix build <package>>> 8) If build is success, format the patch and submit the patch
I suggest running make again after making changes to any file in theGuix source tree. This way you can avoid the “.go file is older thanthe .scm” messages.
Toggle quote (9 lines)> *When i am planning to write a different package description, i am> following this*>> 9) rebasing the patch>> 10) Pull for any changes>> 11) running the process from (2)
I’d do this instead:
git fetch origin # fetch any upstream changes git stash # hide my uncommitted local changes git rebase origin/master # rebase my local commits on top of upstream git stash pop # apply my uncommitted local changes make # compile .scm to .go
Note that you should be inside of a suitable environment when running“make”, so better do all of this after “guix environment guix”.
--Ricardo
GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAChttps://elephly.net
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Sahithi Yarlagadda wrote on 29 Mar 2018 12:50
(name . Ricardo Wurmus)(address . rekado@elephly.net)(address . 30894@debbugs.gnu.org)
cdefaf9b-5815-a400-97af-88f32fda656f@swecha.net
Thanks Ricardo
When i am building r-abc  I found errors with the following.
  (propagated-inputs     `(("r-abc-data" ,r-abc-data)

abc.data is the upstream name of abc-data. I am figuring out how to useit. I have searched for various package description to compare theusage, but in vain. Can u help me what attribute is to be given to makeit work.


On Thursday 29 March 2018 04:02 PM, Ricardo Wurmus wrote:
Toggle quote (50 lines)> Hi Sahithi,>>> 1) Cloning the Source>>>> 2) Running guix environment guix>>>> 3) ./bootstrap>>>> 4) ./configure --localstatedir=/var> You need to perform these steps only once.>>> 5) make>>>> 6) Make Changes to the cran.scm file>>>> 7) Build using ./pre-inst-env guix build <package>>>>> 8) If build is success, format the patch and submit the patch> I suggest running make again after making changes to any file in the> Guix source tree. This way you can avoid the “.go file is older than> the .scm” messages.>>> *When i am planning to write a different package description, i am>> following this*>>>> 9) rebasing the patch>>>> 10) Pull for any changes>>>> 11) running the process from (2)> I’d do this instead:>> git fetch origin # fetch any upstream changes> git stash # hide my uncommitted local changes> git rebase origin/master # rebase my local commits on top of upstream> git stash pop # apply my uncommitted local changes> make # compile .scm to .go>> Note that you should be inside of a suitable environment when running> “make”, so better do all of this after “guix environment guix”.>> --> Ricardo>> GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC> https://elephly.net>>>
-- RegardsSahithi
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Sahithi Yarlagadda wrote on 29 Mar 2018 13:00
(name . Ricardo Wurmus)(address . rekado@elephly.net)(address . 30894@debbugs.gnu.org)
53d2dd04-03cd-4069-5aee-e4ff3d1f865d@swecha.net
Hi
I am planning to do this.
I will submit the Package Description for r-abc-data. Which builds andcreate a derivative in gnu/store. Later i will send the abc packagedescription, where the build finds necessary data and does a successfulbuild.

On Thursday 29 March 2018 04:20 PM, Sahithi Yarlagadda wrote:
Toggle quote (66 lines)> Thanks Ricardo>> When i am building r-abc  I found errors with the following.>>   (propagated-inputs>      `(("r-abc-data" ,r-abc-data)>>> abc.data is the upstream name of abc-data. I am figuring out how to use> it. I have searched for various package description to compare the> usage, but in vain. Can u help me what attribute is to be given to make> it work.>>>> On Thursday 29 March 2018 04:02 PM, Ricardo Wurmus wrote:>> Hi Sahithi,>>>>> 1) Cloning the Source>>>>>> 2) Running guix environment guix>>>>>> 3) ./bootstrap>>>>>> 4) ./configure --localstatedir=/var>> You need to perform these steps only once.>>>>> 5) make>>>>>> 6) Make Changes to the cran.scm file>>>>>> 7) Build using ./pre-inst-env guix build <package>>>>>>> 8) If build is success, format the patch and submit the patch>> I suggest running make again after making changes to any file in the>> Guix source tree. This way you can avoid the “.go file is older than>> the .scm” messages.>>>>> *When i am planning to write a different package description, i am>>> following this*>>>>>> 9) rebasing the patch>>>>>> 10) Pull for any changes>>>>>> 11) running the process from (2)>> I’d do this instead:>>>> git fetch origin # fetch any upstream changes>> git stash # hide my uncommitted local changes>> git rebase origin/master # rebase my local commits on top of upstream>> git stash pop # apply my uncommitted local changes>> make # compile .scm to .go>>>> Note that you should be inside of a suitable environment when running>> “make”, so better do all of this after “guix environment guix”.>>>> -->> Ricardo>>>> GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC>> https://elephly.net>>>>>>
-- RegardsSahithi
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Sahithi Yarlagadda wrote on 29 Mar 2018 13:28
(name . Ricardo Wurmus)(address . rekado@elephly.net)(address . 30894@debbugs.gnu.org)
9fb9be96-8bc2-fd88-4528-0141cbdb323d@swecha.net
Hi
On Thursday 29 March 2018 04:30 PM, Sahithi Yarlagadda wrote:
Toggle quote (9 lines)> Hi>> I am planning to do this.>> I will submit the Package Description for r-abc-data. Which builds and> create a derivative in gnu/store. Later i will send the abc package> description, where the build finds necessary data and does a successful> build.
Submitted a Patch file for r-abc-data which is a dependency for r-abc
http://debbugs.gnu.org/cgi/bugreport.cgi?bug=30983

Then,Re-based the source
git fetch origin # fetch any upstream changes git stash # hide my uncommitted local changes git rebase origin/master # rebase my local commits on top of upstream git stash pop # apply my uncommitted local changes make # compile .scm to .go

I have done adding r-abc. And the build was success.
 ( I am still unsure whether i did it right. Fingers Crossed !!!! ...Waiting for your comment)
Its a great experience while learning with each contribution. EachPackage Description have a different things to look into carefully andcontribute.
Ricardo have been of great help in this process.
Created a Patch (I sense something's not right here!!!). Submitting for the review.


Toggle quote (68 lines)>> On Thursday 29 March 2018 04:20 PM, Sahithi Yarlagadda wrote:>> Thanks Ricardo>>>> When i am building r-abc  I found errors with the following.>>>>   (propagated-inputs>>      `(("r-abc-data" ,r-abc-data)>>>>>> abc.data is the upstream name of abc-data. I am figuring out how to use>> it. I have searched for various package description to compare the>> usage, but in vain. Can u help me what attribute is to be given to make>> it work.>>>>>>>> On Thursday 29 March 2018 04:02 PM, Ricardo Wurmus wrote:>>> Hi Sahithi,>>>>>>> 1) Cloning the Source>>>>>>>> 2) Running guix environment guix>>>>>>>> 3) ./bootstrap>>>>>>>> 4) ./configure --localstatedir=/var>>> You need to perform these steps only once.>>>>>>> 5) make>>>>>>>> 6) Make Changes to the cran.scm file>>>>>>>> 7) Build using ./pre-inst-env guix build <package>>>>>>>>> 8) If build is success, format the patch and submit the patch>>> I suggest running make again after making changes to any file in the>>> Guix source tree. This way you can avoid the “.go file is older than>>> the .scm” messages.>>>>>>> *When i am planning to write a different package description, i am>>>> following this*>>>>>>>> 9) rebasing the patch>>>>>>>> 10) Pull for any changes>>>>>>>> 11) running the process from (2)>>> I’d do this instead:>>>>>> git fetch origin # fetch any upstream changes>>> git stash # hide my uncommitted local changes>>> git rebase origin/master # rebase my local commits on top of upstream>>> git stash pop # apply my uncommitted local changes>>> make # compile .scm to .go>>>>>> Note that you should be inside of a suitable environment when running>>> “make”, so better do all of this after “guix environment guix”.>>>>>> -->>> Ricardo>>>>>> GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC>>> https://elephly.net>>>>>>>>>
-- RegardsSahithi
From 0f248126c47882a0d8b866787577a7335de0a735 Mon Sep 17 00:00:00 2001From: Sahithi Yarlagadda <sahi@swecha.net>Date: Thu, 29 Mar 2018 16:42:18 +0530Subject: [PATCH] gnu: Add r-abc.
* gnu/packages/cran.scm (r-abc): New variable.--- gnu/packages/cran.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+)
Toggle diff (39 lines)diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scmindex 8602a7d87..70551507a 100644--- a/gnu/packages/cran.scm+++ b/gnu/packages/cran.scm@@ -3593,3 +3593,32 @@ implements several @dfn{Approximate Bayesian Computation} (ABC) algorithms for performing parameter estimation, model selection, and goodness-of-fit.") (license license:gpl3))) +(define-public r-abc+ (package+ (name "r-abc")+ (version "2.1")+ (source+ (origin+ (method url-fetch)+ (uri (cran-uri "abc" version))+ (sha256+ (base32+ "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-abc-data" ,r-abc-data)+ ("r-locfit" ,r-locfit)+ ("r-mass" ,r-mass)+ ("r-nnet" ,r-nnet)+ ("r-quantreg" ,r-quantreg)))+ (home-page "https://cran.r-project.org/web/packages/abc")+ (synopsis "Tools for approximate bayesian computation (ABC)")+ (description+ "Implements several @dfn{Approximate Bayesian Computation} (ABC) +algorithms for performing parameter estimation, model selection, and +goodness-of-fit. Cross-validation tools are also available for +measuring the accuracy of ABC estimates, and to calculate the+misclassification probabilities of different models.")+ (license license:gpl3)))++-- 2.16.2
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Ricardo Wurmus wrote on 2 Apr 2018 23:26
(name . Sahithi Yarlagadda)(address . sahi@swecha.net)(address . 30894-done@debbugs.gnu.org)
87woxpcnbg.fsf@elephly.net
Hi Sahithi,
Toggle quote (2 lines)> I have done adding r-abc. And the build was success.
Excellent! I also built it without problems.
I couldn’t apply it cleanly after making modifications to r-abc-data,but that’s not your problem. I performed these minor changes:
* changed license from gpl3 to gpl3+* added a beginning to the description.
Pushed the patch to the master branch with commit 82c8e0ae0.
Thanks again!
~~ Ricardo
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