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Re: [outreach] Help trying to create R package
From: |
Laura Lazzati |
Subject: |
Re: [outreach] Help trying to create R package |
Date: |
Thu, 18 Oct 2018 14:26:50 -0300 |
On Thu, Oct 18, 2018 at 1:18 PM Laura Lazzati
<address@hidden> wrote:
>
> On Thu, Oct 18, 2018 at 12:40 PM Gábor Boskovits <address@hidden> wrote:
> >
> > Laura Lazzati <address@hidden> ezt írta (időpont: 2018.
> > okt. 18., Cs, 17:26):
> > >
> > > On Thu, Oct 18, 2018 at 12:15 PM Gábor Boskovits <address@hidden> wrote:
> > > >
> > > > Hi Laura,
> > > >
> > > > Laura Lazzati <address@hidden> ezt írta (időpont: 2018.
> > > > okt. 18., Cs, 16:49):
> > > > >
> > > > > On Thu, Oct 18, 2018 at 4:50 AM Gábor Boskovits <address@hidden>
> > > > > wrote:
> > > > > >
> > > > > > Wow, Björn, you were so fast again :)
> > > > > >
> > > > > > I just got around this right now.
> > > > > Again, thank both for being so kind :)
> > > > > >
> > > > > > Björn Höfling <address@hidden> ezt írta (időpont:
> > > > > > 2018. okt. 18., Cs, 8:54):
> > > > > > >
> > > > > > > Hi Laura,
> > > > > > >
> > > > > > > On Wed, 17 Oct 2018 22:36:02 -0300
> > > > > > > Laura Lazzati <address@hidden> wrote:
> > > > > > >
> > > > > > >
> > > > > > > > > https://www.gnu.org/software/guix/manual/en/html_node/Contributing.html#Contributing
> > > > > > > > I have already read this chapter, but I am messed up. I have
> > > > > > > > already
> > > > > > > > cloned from git, but I have some questions:
> > > > > > > > 1) Do I need to install everything from the git repo in my
> > > > > > > > distro?
> > > > > > >
> > > > > > > I'm not sure if I understand you right. You ask if you "need to
> > > > > > > install
> > > > > > > everything from the git in my distro?". I don't get that. Let me
> > > > > > > tell
> > > > > > > what I mean:
> > > > > > >
> > > > > > > You cloned that one, right?
> > > > > > >
> > > > > > > git clone https://git.savannah.gnu.org/git/guix.git
> > > > > > >
> > > > > > > That is the source code of Guix. I.e. when you do a
> > > > > > >
> > > > > > > guix package -i hello
> > > > > > >
> > > > > > > then you use the binary "guix" command that you installed in the
> > > > > > > beginning. And the repository you cloned is just the source code,
> > > > > > > there
> > > > > > > is nothing in there that you need to install.
> > > > > > >
> > > > > > >
> > > > > > > Maybe you ment the list of software that is written here:
> > > > > > >
> > > > > > > https://www.gnu.org/software/guix/manual/en/guix.html#Building-from-Git
> > > > > > >
> > > > > > > When building Guix from a checkout, the following packages are
> > > > > > > required in addition to those mentioned in the installation
> > > > > > > instructions (see Requirements).
> > > > > > >
> > > > > > > GNU Autoconf;
> > > > > > > GNU Automake;
> > > > > > > GNU Gettext;
> > > > > > > GNU Texinfo;
> > > > > > > Graphviz;
> > > > > > > GNU Help2man (optional).
> > > > > > >
> > > > > > > So, yeah. In order to compile Guix from source, you need all
> > > > > > > these.
> > > > > I was indeed trying to do this.
> > > > >
> > > > > > >
> > > > > > > But wait, read the next sentence. You have guix already
> > > > > > > installed. Guix
> > > > > > > provides a VERY nice command, `guix envirionment <PACKAGE>`. With
> > > > > > > that,
> > > > > > > Guix prepares an "environment" that can be directly used to build
> > > > > > > <PACKAGE>.
> > > > > > >
> > > > > > > So, if you enter:
> > > > > > >
> > > > > > > guix environment guix
> > > > > I have just did this :)
> > > > Great.
> > > > > > >
> > > > > > > then Guix will know best what software in which version it needs
> > > > > > > in
> > > > > > > order to build guix (in this case, itself, don't get trapped by
> > > > > > > that
> > > > > > > self-circularity :-))
> > > > > > >
> > > > > > > When you are in, you can just follow the next steps described:
> > > > > > >
> > > > > > > ./bootstrap
> > > > > This worked fine.
> > > > > > > ./configure --localstatedir=/var
> > > > >
> > > > > This did not, I am getting this error:
> > > > >
> > > > > configure: checking for guile 2.2
> > > > > configure: found guile 2.2
> > > > > checking for guile-2.2... /usr/bin/guile-2.2
> > > > > checking for Guile version >= 2.2... 2.2.3
> > > > > checking for guild-2.2... no
> > > > > checking for guile-config-2.2... no
> > > > > checking for guile-tools-2.2... no
> > > > > configure: error: 'guild' binary not found; please check your
> > > > > guile-2.x installation.
> > > > >
> > > >
> > > > I don't know what to make of this, but you could try guix environment
> > > > guix --ad-hoc guild.
> > > > Please see if that helps, if not then I will have a closer look at this.
> > > I restored everything to the snapshot where I ended cloning guix.
> > > I get this error when trying to run guix environme guix --ad-hoc guild:
> > > guix environment: error: guild: unknown package
> > >
> >
> > Oops, my bad, yes. I've checked this more thoroughly, on my system
> > guild is provided by guile, which should be provided by guile. Could you run
> > a which guild and a which guile inside the guix environment guix?
> I went back to the previous snapshot several times.
>
> I was cloning the guix and throwing guix environment guix without doing cd
> guix
> After several times, I realized that I had a warning in the output:
>
> building /gnu/store/ilscbls919b78vn9l7b2jb72jmalbxm8-profile.drv...
> warning: collision encountered:
> /gnu/store/b5x786d3h552j2zp4ppvlz9dkbiqy2ng-ld-wrapper-0/bin/ld
> /gnu/store/srmqh29dpm50j8kj1pbqg2rgh053wgyp-binutils-2.30/bin/ld
> warning: choosing
> /gnu/store/b5x786d3h552j2zp4ppvlz9dkbiqy2ng-ld-wrapper-0/bin/ld
> successfully built /gnu/store/ilscbls919b78vn9l7b2jb72jmalbxm8-profile.drv
> But I did not paid attention to that, echo $? was OK (0).
> And then ran everything as I stated, facing all that issues.
>
> Now I've cloned the repo again, removing previously the guix directory.
> did cd guix
> and ran guix environment guix
> Did not have that warning anymore, just the usual locale warning that
> happens all the time.
> ran ./bootstrap
>
> And in both cases (before restoring my VM state, and now) the result
> of the which commands are:
>
> /gnu/store/2w5kxhmkq4zkamsgx1b40vr3ii1z4dxb-profile/bin/guild
> and
> /gnu/store/2w5kxhmkq4zkamsgx1b40vr3ii1z4dxb-profile/bin/guile
>
> I don't know if this is relevant or not, and if I should run the
> .configure or not before you seing this.
I answer myself:
ran
$./configure --localstatedir=/var
And same output.
>
>
>
> >
> > > >
> > > > > Then ran
> > > > > $guix package -i guile
> > > > > Same error running configure.
> > > > > $guix package -s guild
> > > > > $guix package -i guildhall
> > > > > And my output of guix -I, however, is:
> > > > > hello 2.10 out
> > > > > /gnu/store/bihfrh609gkxb9dp7n96wlpigiv3krfy-hello-2.10
> > > > > recutils 1.7 out
> > > > > /gnu/store/6h02na6yz9smc7c7g62ss03kp4yhqpc1-recutils-1.7
> > > > > glibc-locales 2.27 out
> > > > > /gnu/store/s28fmfrq8r0c688x59cj0fcyh2pv87nj-glibc-locales-2.27
> > > > > glibc-utf8-locales 2.27 out
> > > > > /gnu/store/mbns811n696fl7g060cx6jqjh75mlj8i-glibc-utf8-locales-2.27
> > > > > nss-certs 3.36.1 out
> > > > > /gnu/store/h8qlwgwhg6jr0kp5ihy90cgb6h0q1fj9-nss-certs-3.36.1
> > > > > r-ade4 1.7-11 out
> > > > > /gnu/store/980xl9a58nd6f22wzwsmv9mkhv7pq3hh-r-ade4-1.7-11
> > > > > guile 2.2.4 out
> > > > > /gnu/store/p9wm67w3rfw3hlb9iljgvsfn84mz4w9d-guile-2.2.4
> > > > > guildhall 0-1.2fe2cc539 out
> > > > > /gnu/store/kd2mvhr18yphrkiqgavw0w0r0n5bfchn-guildhall-0-1.2fe2cc539
> > > > >
> > > > > Something weird is that in configure output I see there is a /usr/bin
> > > > > mentioned, so I went to that dir, ran
> > > > > $ ll | grep guile
> > > > > lrwxrwxrwx 1 root root 23 oct 10 22:55 guile ->
> > > > > /etc/alternatives/guile*
> > > > > lrwxrwxrwx 1 root root 43 jul 17 10:42 guile-2.2 ->
> > > > > ../lib/x86_64-linux-gnu/guile-2.2/bin/guile*
> > > > >
> > > > > And can't figure out why I have that links.
> > > > >
> > > > > > > make
> > > > > > >
> > > > > > > When that went all through well, you can install the "hello"
> > > > > > > application:
> > > > > > >
> > > > > > > ./pre-inst-env guix package -i hello
> > > > > > >
> > > > > > > The "./pre-inst-env" tells that you want to use the guix command
> > > > > > > that
> > > > > > > you just built, not the one that is somewhere else on your path.
> > > > > > >
> > > > > > > Now you just go on:
> > > > > > >
> > > > > > > > 2) How do I convert my template into a package? I can't figure
> > > > > > > > out
> > > > > > > > that part.
> > > > > > >
> > > > > > > You don't have to CONVERT. That template IS a package:
> > > > > > >
> > > > > > > > > (define-public r-aspi
> > > > > > > > > (package
> > > > > > > > > (name "r-aspi")
> > > > > > >
> > > > > > > What you do is you just open the file gnu/packages/r.scm and add
> > > > > > > your
> > > > > > > "(define... " at the end.
> > > > > > >
> > > > > > > Ehh, wait, there is no file r.scm. It is either cran.scm or
> > > > > > > bioinformatics.scm.
> > > > > > >
> > > > > > > Then you are done. Try to build it:
> > > > > > >
> > > > > > > ./pre-inst-env guix build r-aspi
> > > > > > >
> > > > > > > Björn
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > >
> > > > > > Thank you!
> > > > > > g_bor
> > > > >
> > > > > Regards :)
> > > > > Laura
> > > > Best regards,
> > > > g_bor
> Regards!
> Laur
- Re: [outreach] Help trying to create R package, (continued)
- Re: [outreach] Help trying to create R package, Laura Lazzati, 2018/10/17
- Re: [outreach] Help trying to create R package, Björn Höfling, 2018/10/18
- Re: [outreach] Help trying to create R package, Gábor Boskovits, 2018/10/18
- Re: [outreach] Help trying to create R package, Laura Lazzati, 2018/10/18
- Re: [outreach] Help trying to create R package, Gábor Boskovits, 2018/10/18
- Re: [outreach] Help trying to create R package, Laura Lazzati, 2018/10/18
- Re: [outreach] Help trying to create R package, Gábor Boskovits, 2018/10/18
- Re: [outreach] Help trying to create R package, Laura Lazzati, 2018/10/18
- Re: [outreach] Help trying to create R package,
Laura Lazzati <=
- Re: [outreach] Help trying to create R package, Björn Höfling, 2018/10/18
- Re: [outreach] Help trying to create R package, Ricardo Wurmus, 2018/10/18
- Re: [outreach] Help trying to create R package, Laura Lazzati, 2018/10/18
- Re: [outreach] Help trying to create R package, Laura Lazzati, 2018/10/18
- Re: [outreach] Help trying to create R package, Laura Lazzati, 2018/10/18
- Re: [outreach] Help trying to create R package, Gábor Boskovits, 2018/10/19
- Re: [outreach] Help trying to create R package, Ricardo Wurmus, 2018/10/19
- Re: [outreach] Help trying to create R package, Gábor Boskovits, 2018/10/19
- Re: [outreach] Help trying to create R package, Laura Lazzati, 2018/10/19
- Re: [outreach] Help trying to create R package, Gábor Boskovits, 2018/10/19