Bug#901356: r-cran-caret: new version pulls in loads of development packages
On 13 July 2018 at 09:10, Andreas Tille wrote: | Dirk, please make sure you will rebuild | | r-cran-rgl | r-cran-sn | | before Buster freeze. Sorry for the inconvenience. Done -- now that I am back from useR! in Australia. I appreciate the heads-up, and thanks of course also for the dh-r work. Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
Bug#901356: r-cran-caret: new version pulls in loads of development packages
Hi again, since I spotted an unrelated issue of dh-r when rebuilding r-bioc-dirichletmultinomial I went through the list of packages below. All team maintained packages are fixed now. Dirk, please make sure you will rebuild r-cran-rgl r-cran-sn before Buster freeze. Sorry for the inconvenience. Kind regards Andreas. On Thu, Jul 12, 2018 at 08:02:56AM +0200, Andreas Tille wrote: > Hi Rogério, > > On Wed, Jul 11, 2018 at 10:04:16PM -0300, Rogério Brito wrote: > > > The list of Depends / Recommends / Suggests is autogenerated by dh-r so > > > I need to check whether there is some bug there. > > > > I found other packages that seem to have some dubious dependencies on > > libgdal-dev (the previous versions didn't have such dependencies, but the > > new one does and it doesn't seem like the package should really depend on > > it): > > > > * r-cran-bbmle > > * r-cran-modeltools > > * r-cran-rgl > > * r-cran-sn > > > > Have I missed something? > > No, you are right. For some reason a libgdal-dev dependency was sneaked > into dh/R.pm. This was fixed here: > > > commit ef2aee944435e9027ee229e2332d79ba61f44836 > Author: Andreas Tille > Date: Wed Jun 13 13:12:05 2018 +0200 > > Do not replace random dependencies by libgdal-dev > > > Unfortunately r-* packages build before this date have quite some chance > that this dependency is injected. The actual packages are: > > udd=# select DISTINCT package from packages where package like 'r-%' and > depends like '%libgdal-dev%' and release = 'sid' order by package; >package > - > r-bioc-annotationdbi > r-bioc-dirichletmultinomial > r-bioc-genomeinfodb > r-bioc-genomicranges > r-bioc-graph > r-bioc-iranges > r-bioc-multtest > r-cran-bbmle > r-cran-lavaan > r-cran-mi > r-cran-modeltools > r-cran-rgl > r-cran-sn > r-cran-tmvtnorm > r-cran-truncdist > r-cran-vgam > r-other-nitpick > (17 Zeilen) > > > Most of the packages are "healed" automatically since I uploaded most of > the packages that were not part of the R migration to change the > maintainer field to R pkg team. If it is really disturbing to you I can > re-upload those 17 packages soon. At least we should make sure that they > will be fixed for Buster release. > > Thanks again for the heads up > > Andreas. > > -- > http://fam-tille.de > > -- http://fam-tille.de
Bug#901356: r-cran-caret: new version pulls in loads of development packages
Hi Rogério, On Wed, Jul 11, 2018 at 10:04:16PM -0300, Rogério Brito wrote: > > The list of Depends / Recommends / Suggests is autogenerated by dh-r so > > I need to check whether there is some bug there. > > I found other packages that seem to have some dubious dependencies on > libgdal-dev (the previous versions didn't have such dependencies, but the > new one does and it doesn't seem like the package should really depend on it): > > * r-cran-bbmle > * r-cran-modeltools > * r-cran-rgl > * r-cran-sn > > Have I missed something? No, you are right. For some reason a libgdal-dev dependency was sneaked into dh/R.pm. This was fixed here: commit ef2aee944435e9027ee229e2332d79ba61f44836 Author: Andreas Tille Date: Wed Jun 13 13:12:05 2018 +0200 Do not replace random dependencies by libgdal-dev Unfortunately r-* packages build before this date have quite some chance that this dependency is injected. The actual packages are: udd=# select DISTINCT package from packages where package like 'r-%' and depends like '%libgdal-dev%' and release = 'sid' order by package; package - r-bioc-annotationdbi r-bioc-dirichletmultinomial r-bioc-genomeinfodb r-bioc-genomicranges r-bioc-graph r-bioc-iranges r-bioc-multtest r-cran-bbmle r-cran-lavaan r-cran-mi r-cran-modeltools r-cran-rgl r-cran-sn r-cran-tmvtnorm r-cran-truncdist r-cran-vgam r-other-nitpick (17 Zeilen) Most of the packages are "healed" automatically since I uploaded most of the packages that were not part of the R migration to change the maintainer field to R pkg team. If it is really disturbing to you I can re-upload those 17 packages soon. At least we should make sure that they will be fixed for Buster release. Thanks again for the heads up Andreas. -- http://fam-tille.de
Bug#901356: r-cran-caret: new version pulls in loads of development packages
Hi, Andreas and other people.
I'm sending this to the list instead of filing other bugs, so that other
people can take a look and see if I am doing something wrong or not.
On Jun 12 2018, Andreas Tille wrote:
> On Mon, Jun 11, 2018 at 06:32:14PM -0300, Rogério Brito wrote:
> > In fact, looking more closely at the package relationships of r-cran-caret,
> > I see that it both Depends **and** also Suggests libgdal-dev, so, at least
> > one of thoses may be a mistake...
>
> The list of Depends / Recommends / Suggests is autogenerated by dh-r so
> I need to check whether there is some bug there.
I found other packages that seem to have some dubious dependencies on
libgdal-dev (the previous versions didn't have such dependencies, but the
new one does and it doesn't seem like the package should really depend on it):
* r-cran-bbmle
* r-cran-modeltools
* r-cran-rgl
* r-cran-sn
Have I missed something?
Thanks in advance,
Rogério.
--
Rogério Brito : rbrito@{ime.usp.br,gmail.com} : GPG key 4096R/BCFC
http://cynic.cc/blog/ : github.com/rbrito : profiles.google.com/rbrito
DebianQA: http://qa.debian.org/developer.php?login=rbrito%40ime.usp.br
Bug#901356: r-cran-caret: new version pulls in loads of development packages
Hi Rogério, On Mon, Jun 11, 2018 at 06:32:14PM -0300, Rogério Brito wrote: > I noticed that the new version of r-cran-caret depends on libgdal-dev, which > pulls in a lot of development packages and frustrates my plans of creating a > small live CD/DVD/USB of development tools for data analysis. I need to check this. > In fact, looking more closely at the package relationships of r-cran-caret, > I see that it both Depends **and** also Suggests libgdal-dev, so, at least > one of thoses may be a mistake... The list of Depends / Recommends / Suggests is autogenerated by dh-r so I need to check whether there is some bug there. > Similarly r-cran-testthat is listed both as a Recommends and as a > Suggests... (I may have missed other duplicate packages, if they exist). I think the reason for this is at least clear. I changed dh-r to add all packages that are needed to run the test suite of the package to Recommends. I think this makes sense to enable users checking the functionality on a default installation. Consequently I should have made sure that the packages which were upgraded to Recommends will be removed from the list of Suggests. That's surely a bug in dh-r which I'll tackle soon. > Can this be fixed with a new upload? We are currently in a transition to R 3.5. Thus no quick updates until this transition is finished but I try to do it quickly afterwards. Kind regards and thanks for your bug report Andreas. -- http://fam-tille.de
Bug#901356: r-cran-caret: new version pulls in loads of development packages
Package: r-cran-caret
Version: 6.0-80-1
Severity: normal
Hi.
Thanks for taking care of packaging R packages.
I noticed that the new version of r-cran-caret depends on libgdal-dev, which
pulls in a lot of development packages and frustrates my plans of creating a
small live CD/DVD/USB of development tools for data analysis.
In fact, looking more closely at the package relationships of r-cran-caret,
I see that it both Depends **and** also Suggests libgdal-dev, so, at least
one of thoses may be a mistake...
Similarly r-cran-testthat is listed both as a Recommends and as a
Suggests... (I may have missed other duplicate packages, if they exist).
Can this be fixed with a new upload?
Thanks,
Rogério Brito.
P.S: Please, ignore the dependencies listed below. They are for an outdated
version of the package.
-- System Information:
Debian Release: buster/sid
APT prefers testing
APT policy: (500, 'testing'), (200, 'unstable'), (150, 'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 4.16.0-1-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_US.utf-8, LC_CTYPE=pt_BR.utf-8 (charmap=UTF-8),
LANGUAGE=en_US.utf-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
Versions of packages r-cran-caret depends on:
ii libc62.27-3
ii libgcc1 1:8.1.0-5
ii libstdc++6 8.1.0-5
ii r-base-core [r-api-3.4] 3.4.4-1+b2
ii r-cran-foreach 1.4.4-1
ii r-cran-ggplot2 2.2.1-3
ii r-cran-lattice 0.20-35-1+b1
ii r-cran-modelmetrics 1.1.0-1+b1
ii r-cran-nlme 3.1.137-1
ii r-cran-plyr 1.8.4-1+b1
ii r-cran-recipes 0.1.2-1
ii r-cran-reshape2 1.4.3-1
ii r-cran-withr 2.1.2-2
r-cran-caret recommends no packages.
Versions of packages r-cran-caret suggests:
ii r-cran-bradleyterry2 1.0-8-1
ii r-cran-e1071 1.6-8-2+b1
pn r-cran-ellipse
pn r-cran-fastica
ii r-cran-gam1.15-1
ii r-cran-ipred 0.9-6-1
ii r-cran-kernlab0.9-26-1
ii r-cran-knitr 1.20-2
ii r-cran-mass 7.3-50-1
ii r-cran-mgcv 1.8-23-1
pn r-cran-mlbench
ii r-cran-nnet 7.3-12-2+b1
ii r-cran-randomforest 4.6-14-1
pn r-cran-testthat
-- no debconf information
--
Rogério Brito : rbrito@{ime.usp.br,gmail.com} : GPG key 4096R/BCFC
http://cynic.cc/blog/ : github.com/rbrito : profiles.google.com/rbrito
DebianQA: http://qa.debian.org/developer.php?login=rbrito%40ime.usp.br
