Bug 1074975 - R-3.1.0 is available
Summary: R-3.1.0 is available
Keywords:
Status: CLOSED ERRATA
Alias: None
Product: Fedora
Classification: Fedora
Component: R
Version: rawhide
Hardware: Unspecified
OS: Unspecified
unspecified
unspecified
Target Milestone: ---
Assignee: Tom "spot" Callaway
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard:
Depends On:
Blocks:
TreeView+ depends on / blocked
 
Reported: 2014-03-11 10:11 UTC by Upstream Release Monitoring
Modified: 2014-06-05 15:18 UTC (History)
7 users (show)

Fixed In Version: R-3.1.0-5.el6
Doc Type: Enhancement
Doc Text:
Clone Of:
Environment:
Last Closed: 2014-05-21 23:24:47 UTC
Type: ---
Embargoed:


Attachments (Terms of Use)

Description Upstream Release Monitoring 2014-03-11 10:11:09 UTC
Latest upstream release: 3.0.3
Current version/release in Fedora Rawhide: 3.0.2-7.fc21
URL: http://cran.rstudio.com/banner.shtml

Please consult the package updates policy before you issue an update to a stable branch: https://fedoraproject.org/wiki/Updates_Policy

More information about the service that created this bug can be found at:
https://fedoraproject.org/wiki/Upstream_release_monitoring

Comment 1 M. Edward (Ed) Borasky 2014-03-27 03:14:02 UTC
R 3.1 is due out April 10, 2014. Any chance we can get R 3.1 into Rawhide around then? I really don't want to wait for F21 to see a new R package.

Comment 2 Upstream Release Monitoring 2014-04-14 09:17:33 UTC
Latest upstream release: 3.1.0
Current version/release in Fedora Rawhide: 3.0.3-2.fc21
URL: http://cran.rstudio.com/banner.shtml

Please consult the package updates policy before you issue an update to a stable branch: https://fedoraproject.org/wiki/Updates_Policy

More information about the service that created this bug can be found at:
https://fedoraproject.org/wiki/Upstream_release_monitoring

Comment 3 E.N. 2014-04-23 09:00:09 UTC
Hello everybody,
Would someone know if there is any plan to make R-3.1.0 available in Fedora 20 ? Or do all F20 users have to built it on their own from sources ?

Comment 4 Tom "spot" Callaway 2014-04-23 16:05:41 UTC
I am working on it. It will come out for all active release targets when it is ready. It is currently failing in rawhide and I'm trying to figure out how to resolve that.

Comment 5 E.N. 2014-04-23 16:43:39 UTC
Thanks for replying, and best wishes.

Comment 6 M. Edward (Ed) Borasky 2014-04-23 17:25:09 UTC
(In reply to Tom "spot" Callaway from comment #4)
> I am working on it. It will come out for all active release targets when it
> is ready. It is currently failing in rawhide and I'm trying to figure out
> how to resolve that.

Can you describe the problem in more detail? I've built R from source many times over the years and it's usually very painless.

Comment 7 Tom "spot" Callaway 2014-04-23 17:54:13 UTC
(In reply to M. Edward (Ed) Borasky from comment #6)
> (In reply to Tom "spot" Callaway from comment #4)
> > I am working on it. It will come out for all active release targets when it
> > is ready. It is currently failing in rawhide and I'm trying to figure out
> > how to resolve that.
> 
> Can you describe the problem in more detail? I've built R from source many
> times over the years and it's usually very painless.

I've been building it for years and while you're right, it usually builds without issue, it is failing in the Matrix module on rawhide (not f20). You can see the build failure in this log:

http://kojipkgs.fedoraproject.org//work/tasks/5402/6765402/build.log

Loading required package: Matrix
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/builddir/build/BUILD/R-3.1.0/library/Matrix/libs/Matrix.so':
  /builddir/build/BUILD/R-3.1.0/library/Matrix/libs/Matrix.so: undefined symbol: cholmod_speye
Error : require(Matrix) is not TRUE

At this point, my best guess is that the new toolchain and new optflags in rawhide are causing Matrix to be miscompiled. I'm instantiating a rawhide VM so I can test this directly.

Comment 8 M. Edward (Ed) Borasky 2014-04-24 00:39:12 UTC
(In reply to Tom "spot" Callaway from comment #7)
> (In reply to M. Edward (Ed) Borasky from comment #6)
> > (In reply to Tom "spot" Callaway from comment #4)
> > > I am working on it. It will come out for all active release targets when it
> > > is ready. It is currently failing in rawhide and I'm trying to figure out
> > > how to resolve that.
> > 
> > Can you describe the problem in more detail? I've built R from source many
> > times over the years and it's usually very painless.
> 
> I've been building it for years and while you're right, it usually builds
> without issue, it is failing in the Matrix module on rawhide (not f20). You
> can see the build failure in this log:
> 
> http://kojipkgs.fedoraproject.org//work/tasks/5402/6765402/build.log
> 
> Loading required package: Matrix
> Error in dyn.load(file, DLLpath = DLLpath, ...) : 
>   unable to load shared object
> '/builddir/build/BUILD/R-3.1.0/library/Matrix/libs/Matrix.so':
>   /builddir/build/BUILD/R-3.1.0/library/Matrix/libs/Matrix.so: undefined
> symbol: cholmod_speye
> Error : require(Matrix) is not TRUE
> 
> At this point, my best guess is that the new toolchain and new optflags in
> rawhide are causing Matrix to be miscompiled. I'm instantiating a rawhide VM
> so I can test this directly.

Looks like it's compiling successfully but failing in the test load.

Comment 9 Tom "spot" Callaway 2014-04-24 15:49:06 UTC
The undefined symbol comes from the Matrix sources, so the only way it would be missing is if the Matrix.so object was miscompiled. Also, the fact that it works as is with the Fedora 20 environment makes me suspicious of the compiler & flags.

Comment 10 Fedora Update System 2014-04-30 21:05:39 UTC
rkward-0.6.1-7.fc20,rpy-2.3.10-1.fc20,R-3.1.0-4.fc20 has been submitted as an update for Fedora 20.
https://admin.fedoraproject.org/updates/rkward-0.6.1-7.fc20,rpy-2.3.10-1.fc20,R-3.1.0-4.fc20

Comment 11 Fedora Update System 2014-04-30 21:05:53 UTC
rkward-0.6.1-7.fc19,rpy-2.3.10-1.fc19,R-3.1.0-4.fc19 has been submitted as an update for Fedora 19.
https://admin.fedoraproject.org/updates/rkward-0.6.1-7.fc19,rpy-2.3.10-1.fc19,R-3.1.0-4.fc19

Comment 12 Fedora Update System 2014-04-30 21:06:01 UTC
R-3.1.0-4.el6 has been submitted as an update for Fedora EPEL 6.
https://admin.fedoraproject.org/updates/R-3.1.0-4.el6

Comment 13 Fedora Update System 2014-04-30 21:06:13 UTC
R-3.1.0-4.el5 has been submitted as an update for Fedora EPEL 5.
https://admin.fedoraproject.org/updates/R-3.1.0-4.el5

Comment 14 Fedora Update System 2014-05-01 06:59:02 UTC
Package rkward-0.6.1-7.fc19, rpy-2.3.10-1.fc19, R-3.1.0-4.fc19:
* should fix your issue,
* was pushed to the Fedora 19 testing repository,
* should be available at your local mirror within two days.
Update it with:
# su -c 'yum update --enablerepo=updates-testing rkward-0.6.1-7.fc19 rpy-2.3.10-1.fc19 R-3.1.0-4.fc19'
as soon as you are able to.
Please go to the following url:
https://admin.fedoraproject.org/updates/FEDORA-2014-5819/rkward-0.6.1-7.fc19,rpy-2.3.10-1.fc19,R-3.1.0-4.fc19
then log in and leave karma (feedback).

Comment 15 M. Edward (Ed) Borasky 2014-05-02 21:58:43 UTC
The R-core package appears to be missing the libRblas library:

# yum update 

[snip]

Error: Package: rstudio-0.98.806-1.x86_64 (@opt_RStudioRepo)
           Requires: libRblas.so()(64bit)
           Removing: R-core-3.0.2-1.fc20.x86_64 (@fedora)
               libRblas.so()(64bit)
           Updated By: R-core-3.1.0-4.fc20.x86_64 (updates-testing)
               Not found
Error: Package: rstudio-0.98.806-1.x86_64 (@opt_RStudioRepo)
           Requires: libRlapack.so()(64bit)
           Removing: R-core-3.0.2-1.fc20.x86_64 (@fedora)
               libRlapack.so()(64bit)
           Updated By: R-core-3.1.0-4.fc20.x86_64 (updates-testing)
               Not found
 You could try using --skip-broken to work around the problem
 You could try running: rpm -Va --nofiles --nodigest

Comment 16 Tom "spot" Callaway 2014-05-03 13:29:01 UTC
This is because we're building R with the system blas/lapack instead of their bundled copy (something we should have done a while ago).

rstudio just needs to be rebuilt.

Comment 17 M. Edward (Ed) Borasky 2014-05-03 19:56:50 UTC
(In reply to Tom "spot" Callaway from comment #16)
> This is because we're building R with the system blas/lapack instead of
> their bundled copy (something we should have done a while ago).
> 
> rstudio just needs to be rebuilt.

Yeah - I'll post an issue on their Github repo and see what happens. Meanwhile, if I have ATLAS installed, will R-3.1.0 find it?

Comment 18 Tom "spot" Callaway 2014-05-03 22:51:45 UTC
We built it against the lapack blas. I'm not an expert with atlas, but if that blas library is also named libblas.so.3, i think it _should_ work.

Comment 19 M. Edward (Ed) Borasky 2014-05-04 00:09:13 UTC
(In reply to Tom "spot" Callaway from comment #18)
> We built it against the lapack blas. I'm not an expert with atlas, but if
> that blas library is also named libblas.so.3, i think it _should_ work.

Nope - it's a huge hassle to link to ATLAS from R. The how-tos are buried in the documentation (http://cran.rstudio.com/doc/manuals/r-release/R-admin.html#BLAS) and there are other high-performance linear algebra libraries besides ATLAS. It's such a hassle that I either build the whole enchinlada (ATLAS, R and RStudio) from source or forget about ATLAS entirely.

Comment 20 E.N. 2014-05-06 19:40:21 UTC
(In reply to Tom "spot" Callaway from comment #16)
> This is because we're building R with the system blas/lapack instead of
> their bundled copy (something we should have done a while ago).
> 
> rstudio just needs to be rebuilt.

Hi Tom,

Many other R/Bioconductor packages behave the same way as the current RStudio release by linking to libraries in R instead of system's. I tried to explain what I got from your reply, but I'm a noob in packaging matters. Would be very acknowledged if you could intervene in this thread: <https://stat.ethz.ch/pipermail/bioc-devel/2014-May/005704.html>

Best regards,
Eric.

Comment 21 Fedora Update System 2014-05-10 13:56:09 UTC
R-3.1.0-5.el6 has been submitted as an update for Fedora EPEL 6.
https://admin.fedoraproject.org/updates/R-3.1.0-5.el6

Comment 22 Fedora Update System 2014-05-10 13:56:17 UTC
R-3.1.0-5.el5 has been submitted as an update for Fedora EPEL 5.
https://admin.fedoraproject.org/updates/R-3.1.0-5.el5

Comment 23 Fedora Update System 2014-05-10 13:56:36 UTC
nifti2dicom-0.4.7-3.fc20,cantor-4.12.5-3.fc20,R-qtl-1.29.2-2.fc20,R-msm-1.1.4-3.fc20,R-maanova-1.30.0-3.fc20,gammaray-2.0.0-3.fc20,InsightToolkit-4.4.2-2.fc20,rpy-2.3.10-1.fc20,rkward-0.6.1-7.fc20,R-preprocessCore-1.22.0-3.fc20,vtk-6.0.0-11.fc20,R-3.1.0-5.fc20 has been submitted as an update for Fedora 20.
https://admin.fedoraproject.org/updates/nifti2dicom-0.4.7-3.fc20,cantor-4.12.5-3.fc20,R-qtl-1.29.2-2.fc20,R-msm-1.1.4-3.fc20,R-maanova-1.30.0-3.fc20,gammaray-2.0.0-3.fc20,InsightToolkit-4.4.2-2.fc20,rpy-2.3.10-1.fc20,rkward-0.6.1-7.fc20,R-preprocessCore-1.22.0-3.fc20,vtk-6.0.0-11.fc20,R-3.1.0-5.fc20

Comment 24 Fedora Update System 2014-05-10 13:56:53 UTC
R-qtl-1.29.2-2.fc19,R-msm-1.1.4-2.fc19,R-maanova-1.30.0-2.fc19,R-preprocessCore-1.22.0-2.fc19,cantor-4.11.5-2.fc19,rpy-2.3.10-1.fc19,rkward-0.6.1-7.fc19,R-3.1.0-5.fc19 has been submitted as an update for Fedora 19.
https://admin.fedoraproject.org/updates/R-qtl-1.29.2-2.fc19,R-msm-1.1.4-2.fc19,R-maanova-1.30.0-2.fc19,R-preprocessCore-1.22.0-2.fc19,cantor-4.11.5-2.fc19,rpy-2.3.10-1.fc19,rkward-0.6.1-7.fc19,R-3.1.0-5.fc19

Comment 25 M. Edward (Ed) Borasky 2014-05-13 04:38:29 UTC
Latest updates:

1. RStudio has fixed their preview release to work without requiring libRblas and libRlapack. I don't know if they've backported the fix to their stable package, however. See https://support.rstudio.com/hc/communities/public/questions/201046993-Library-dependency-issue-on-Fedora-20- for the details.

2. The folks on the BioConductor list have run into some packages that need to be recompiled after an upgrade to R 3.1.0. So have I - some packages installed from source with R 3.0.2 linked to libRblas or libRlapack and will not load after the 3.0.2 -> 3.1.0 upgrade blows those libraries away. Here's the BioConductor list thread if you're interested: http://thread.gmane.org/gmane.science.biology.informatics.conductor.devel/5738

3. To be safe, after upgrading to 3.1.0 I am running a script to re-install all packages that were installed with an older version of R. It takes some time, but since I don't know which ones use the removed libraries I have to rebuild them all. Here's the code:

p <- rownames(subset(as.data.frame(installed.packages()), Built != '3.1.0'))
p
install.packages(p)

Comment 26 Tom "spot" Callaway 2014-05-13 14:32:28 UTC
Thanks for the info. I've rebuilt everything in the official Fedora repositories that depended on libRblas/libRlapack and made new updates (see previous comments).

Sorry for all the churn. :/ Hopefully this will be the last of the pain.

Comment 27 Fedora Update System 2014-05-21 23:24:47 UTC
R-qtl-1.29.2-2.fc19, R-msm-1.1.4-2.fc19, R-maanova-1.30.0-2.fc19, R-preprocessCore-1.22.0-2.fc19, cantor-4.11.5-2.fc19, rpy-2.3.10-1.fc19, rkward-0.6.1-7.fc19, R-3.1.0-5.fc19 has been pushed to the Fedora 19 stable repository.  If problems still persist, please make note of it in this bug report.

Comment 28 Fedora Update System 2014-05-21 23:32:21 UTC
nifti2dicom-0.4.7-3.fc20, cantor-4.12.5-3.fc20, R-qtl-1.29.2-2.fc20, R-msm-1.1.4-3.fc20, R-maanova-1.30.0-3.fc20, gammaray-2.0.0-3.fc20, InsightToolkit-4.4.2-2.fc20, rpy-2.3.10-1.fc20, rkward-0.6.1-7.fc20, R-preprocessCore-1.22.0-3.fc20, vtk-6.0.0-11.fc20, R-3.1.0-5.fc20 has been pushed to the Fedora 20 stable repository.  If problems still persist, please make note of it in this bug report.

Comment 29 Chris Schanzle 2014-05-23 13:07:34 UTC
yum update is failing on my systems with:

Error: Package: InsightToolkit-4.4.2-2.fc20.x86_64 (updates)
           Requires: libRblas.so()(64bit)
           Removing: R-core-3.0.2-1.fc20.x86_64 (@fedora)
               libRblas.so()(64bit)
           Updated By: R-core-3.1.0-5.fc20.x86_64 (updates)
               Not found
Error: Package: InsightToolkit-4.4.2-2.fc20.x86_64 (updates)
           Requires: libRlapack.so()(64bit)
           Removing: R-core-3.0.2-1.fc20.x86_64 (@fedora)
               libRlapack.so()(64bit)
           Updated By: R-core-3.1.0-5.fc20.x86_64 (updates)
               Not found

Comment 30 Tom "spot" Callaway 2014-05-23 15:34:21 UTC
I just pushed a new InsightToolkit update to resolve this in f20.

Comment 31 Erich Greene 2014-06-02 14:46:25 UTC
still failing; looks like package versions haven't changed since the 5/21 comment

Error: Package: nifti2dicom-0.4.7-3.fc20.x86_64 (@updates)
           Requires: libRblas.so()(64bit)
           Removing: R-core-3.0.2-1.fc20.x86_64 (@fedora)
               libRblas.so()(64bit)
           Updated By: R-core-3.1.0-5.fc20.x86_64 (updates)
               Not found
Error: Package: InsightToolkit-4.4.2-2.fc20.x86_64 (@updates)
           Requires: libRblas.so()(64bit)
           Removing: R-core-3.0.2-1.fc20.x86_64 (@fedora)
               libRblas.so()(64bit)
           Updated By: R-core-3.1.0-5.fc20.x86_64 (updates)
               Not found
Error: Package: nifti2dicom-0.4.7-3.fc20.x86_64 (@updates)
           Requires: libRlapack.so()(64bit)
           Removing: R-core-3.0.2-1.fc20.x86_64 (@fedora)
               libRlapack.so()(64bit)
           Updated By: R-core-3.1.0-5.fc20.x86_64 (updates)
               Not found
Error: Package: InsightToolkit-4.4.2-2.fc20.x86_64 (@updates)
           Requires: libRlapack.so()(64bit)
           Removing: R-core-3.0.2-1.fc20.x86_64 (@fedora)
               libRlapack.so()(64bit)
           Updated By: R-core-3.1.0-5.fc20.x86_64 (updates)
               Not found

Comment 32 Tom "spot" Callaway 2014-06-02 14:51:26 UTC
InsightToolkit-4.4.2-3.fc20 is in updates-testing.

Looks like nifti2dicom needs rebuilding too. :/ Lemme get on that.

Comment 33 Chris Schanzle 2014-06-03 12:32:13 UTC
Please push InsightToolkit out of Testing and into Stable.

Comment 34 Fedora Update System 2014-06-03 21:56:56 UTC
R-3.1.0-5.el5 has been pushed to the Fedora EPEL 5 stable repository.  If problems still persist, please make note of it in this bug report.

Comment 35 Fedora Update System 2014-06-03 21:57:14 UTC
R-3.1.0-5.el6 has been pushed to the Fedora EPEL 6 stable repository.  If problems still persist, please make note of it in this bug report.

Comment 36 Paul Stauffer 2014-06-05 13:49:23 UTC
Problem persists in EPEL 6 with R-qtl and R-msm:


Error: Package: R-qtl-1.29.2-1.el6.x86_64 (@epel/6.4)
           Requires: libRblas.so()(64bit)
           Removing: R-core-3.0.2-1.el6.x86_64 (@epel/6.4)
               libRblas.so()(64bit)
           Updated By: R-core-3.1.0-5.el6.x86_64 (epel)
               Not found
Error: Package: R-msm-1.1.4-1.el6.x86_64 (@epel/6.4)
           Requires: libRblas.so()(64bit)
           Removing: R-core-3.0.2-1.el6.x86_64 (@epel/6.4)
               libRblas.so()(64bit)
           Updated By: R-core-3.1.0-5.el6.x86_64 (epel)
               Not found
Error: Package: R-qtl-1.29.2-1.el6.x86_64 (@epel/6.4)
           Requires: libRlapack.so()(64bit)
           Removing: R-core-3.0.2-1.el6.x86_64 (@epel/6.4)
               libRlapack.so()(64bit)
           Updated By: R-core-3.1.0-5.el6.x86_64 (epel)
               Not found
Error: Package: R-msm-1.1.4-1.el6.x86_64 (@epel/6.4)
           Requires: libRlapack.so()(64bit)
           Removing: R-core-3.0.2-1.el6.x86_64 (@epel/6.4)
               libRlapack.so()(64bit)
           Updated By: R-core-3.1.0-5.el6.x86_64 (epel)
               Not found


Would it be preferable to open new bugs for each affected package, and include a reference to this bug in the new one?

Comment 37 Tom "spot" Callaway 2014-06-05 15:18:30 UTC
No need, these are (hopefully) the last of them and they're already pushing to updates:

https://admin.fedoraproject.org/updates/R-qtl-1.31.9-1.el6
https://admin.fedoraproject.org/updates/R-msm-1.1.4-1.el6.1


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