From mboxrd@z Thu Jan 1 00:00:00 1970 From: Laura Lazzati Subject: Re: [outreach] Help trying to create R package Date: Thu, 18 Oct 2018 13:18:06 -0300 Message-ID: References: <20181016074412.54757b18@alma-ubu> <20181016082350.75757e6b@alma-ubu> <20181017001851.71543cc9@alma-ubu> <20181017091750.1c408b8d@alma-ubu> <20181018085424.541e9287@alma-ubu> Mime-Version: 1.0 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:46849) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gDB0Y-0005jc-21 for guix-devel@gnu.org; Thu, 18 Oct 2018 12:18:52 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gDB0W-0000HB-Jh for guix-devel@gnu.org; Thu, 18 Oct 2018 12:18:46 -0400 Received: from mail-pf1-x434.google.com ([2607:f8b0:4864:20::434]:42338) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1gDB0W-0000GS-A4 for guix-devel@gnu.org; Thu, 18 Oct 2018 12:18:44 -0400 Received: by mail-pf1-x434.google.com with SMTP id f26-v6so15103619pfn.9 for ; Thu, 18 Oct 2018 09:18:44 -0700 (PDT) In-Reply-To: List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: =?UTF-8?Q?G=C3=A1bor_Boskovits?= Cc: Guix-devel , Ricardo Wurmus On Thu, Oct 18, 2018 at 12:40 PM G=C3=A1bor Boskovits = wrote: > > Laura Lazzati ezt =C3=ADrta (id=C5=91pont: 2= 018. > okt. 18., Cs, 17:26): > > > > On Thu, Oct 18, 2018 at 12:15 PM G=C3=A1bor Boskovits wrote: > > > > > > Hi Laura, > > > > > > Laura Lazzati ezt =C3=ADrta (id=C5=91pon= t: 2018. > > > okt. 18., Cs, 16:49): > > > > > > > > On Thu, Oct 18, 2018 at 4:50 AM G=C3=A1bor Boskovits wrote: > > > > > > > > > > Wow, Bj=C3=B6rn, you were so fast again :) > > > > > > > > > > I just got around this right now. > > > > Again, thank both for being so kind :) > > > > > > > > > > Bj=C3=B6rn H=C3=B6fling ezt = =C3=ADrta (id=C5=91pont: > > > > > 2018. okt. 18., Cs, 8:54): > > > > > > > > > > > > Hi Laura, > > > > > > > > > > > > On Wed, 17 Oct 2018 22:36:02 -0300 > > > > > > Laura Lazzati wrote: > > > > > > > > > > > > > > > > > > > > https://www.gnu.org/software/guix/manual/en/html_node/Contr= ibuting.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 di= stro? > > > > > > > > > > > > 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 m= e 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 th= e > > > > > > beginning. And the repository you cloned is just the source cod= e, 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 (s= ee 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 th= ese. > > > > I was indeed trying to do this. > > > > > > > > > > > > > > > > But wait, read the next sentence. You have guix already install= ed. Guix > > > > > > provides a VERY nice command, `guix envirionment `. Wi= th that, > > > > > > Guix prepares an "environment" that can be directly used to bui= ld > > > > > > . > > > > > > > > > > > > So, if you enter: > > > > > > > > > > > > guix environment guix > > > > I have just did this :) > > > Great. > > > > > > > > > > > > then Guix will know best what software in which version it need= s 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=3D/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 >=3D 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 th= is. > > 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/p9wm67w3rfw3hlb9iljgvsfn84mz4w9= d-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 comman= d 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 figur= e 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 ad= d 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 > > > > > > > > > > > > Bj=C3=B6rn > > > > > > > > > > > > > > > > > > > > > > > > > > > > Thank you! > > > > > g_bor > > > > > > > > Regards :) > > > > Laura > > > Best regards, > > > g_bor Regards! Laur