Re: [outreach] Help trying to create R package

[Laura Lazzati]

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.



>
> > >
> > > > 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