Bug 751003

Failed scratch build:
http://koji.fedoraproject.org/koji/taskinfo?taskID=3482130

The new version of R (2.14.0) will require a mass rebuild of all R modules and R dependent packages because of changes in how R handles NAMESPACE. As a result, I'm considering only updating to 2.14.0 in rawhide. Do you have a specific need for 2.14.0 in an older release (including f16)?

(In reply to comment #1)
> Failed scratch build:
> http://koji.fedoraproject.org/koji/taskinfo?taskID=3482130

It is just failing at the file-globing stage, so probably can be fixed relatively easily. BTW, R 2.14's documentation by default requires inconsolata font (TexLive 2010+ ?, or install stand-alone), unless you set - this is one of the error in the log:

R_RD4PDF="times,hyper" 

(the default is "times,inconsolata,hyper")

I filed a bug about inconsolata font not hooked up to tex a few months ago (it is shipped fedora but not used by Tex 2007). before of testing againg R-devel.

For some reason I am having problem building R 2.14 rpm's (failing at the compiling stage, not document-building stage) which is wierd, considering that I have been building R-devel every few days since a month or so ago.

(In reply to comment #3)
> (In reply to comment #1)
> > Failed scratch build:
> > http://koji.fedoraproject.org/koji/taskinfo?taskID=3482130
> 
> It is just failing at the file-globing stage, so probably can be fixed
> relatively easily. BTW, R 2.14's documentation by default requires inconsolata
> font (TexLive 2010+ ?, or install stand-alone), unless you set - this is one of
> the error in the log:
> 
> R_RD4PDF="times,hyper" 
> 
> (the default is "times,inconsolata,hyper")
> 
> I filed a bug about inconsolata font not hooked up to tex a few months ago (it
> is shipped fedora but not used by Tex 2007). before of testing againg R-devel.
> 
> For some reason I am having problem building R 2.14 rpm's (failing at the
> compiling stage, not document-building stage) which is wierd, considering that
> I have been building R-devel every few days since a month or so ago.

Try removing R entirely from your build system (or building in mock). I had to do that in order to get a 2.14.0 build to succeed on my Fedora system, otherwise the build would fail trying to load non-existent db files from the main system (as opposed to the buildroot).

Nevertheless, I have a 2.14.0 spec ready for rawhide that has built in a scratch build successfully, but I haven't kicked it off yet as an actual build because I need to come up with a plan for 2.14.0 deployment (even in Rawhide).

(In reply to comment #4)
<snipped>
> Try removing R entirely from your build system (or building in mock). I had to
> do that in order to get a 2.14.0 build to succeed on my Fedora system,
> otherwise the build would fail trying to load non-existent db files from the
> main system (as opposed to the buildroot).
> 
> Nevertheless, I have a 2.14.0 spec ready for rawhide that has built in a
> scratch build successfully, but I haven't kicked it off yet as an actual build
> because I need to come up with a plan for 2.14.0 deployment (even in Rawhide).

Okay, I'll try removing 2.13.2. This is certainly wierd: I have always had a system-wide R (whichever is up-to-date, taken from koji with a few extra switches), and every 6 months, I build R from git-svn every few days tracking the latest alpha/pre-releases (so that goes through soon-to-be-alpha, pre-, when it forks - and I continues onto early 2.15). My early 2.15 is still working okay.

Maybe the few   
echo 'R_LIBS_SITE=${R_LIBS_SITE-'"'/usr/local/lib/R/site-library:/usr/local/lib/R/library:%{_libdir}/R/library:%{_datadir}/
R/library'"'}' >> etc/Renviron.in

in the rpm.spec has some effect?

Here is the error:
----------------
make[4]: Entering directory `/usr/src/redhat/BUILD/R-2.14.0/src/library/compiler'
byte-compiling package 'compiler'
Warning in tools:::makeLazyLoading("compiler") :
  package seems to be using lazy loading already
make[4]: Leaving directory `/usr/src/redhat/BUILD/R-2.14.0/src/library/compiler'
make[3]: Leaving directory `/usr/src/redhat/BUILD/R-2.14.0/src/library/compiler'
make[3]: Entering directory `/usr/src/redhat/BUILD/R-2.14.0/src/library/base'
byte-compiling package 'base'
Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : 
  object 'tryCmpfun' not found
Calls: local ... makeLazyLoadDB -> lazyLoadDBinsertVariable -> .Call -> ::: -> get
Execution halted
make[3]: *** [../../../library/base/R/base.rdb] Error 1
make[3]: Leaving directory `/usr/src/redhat/BUILD/R-2.14.0/src/library/base'
make[2]: *** [R] Error 1
make[2]: Leaving directory `/usr/src/redhat/BUILD/R-2.14.0/src/library'
make[1]: *** [R] Error 1
make[1]: Leaving directory `/usr/src/redhat/BUILD/R-2.14.0/src'
make: *** [R] Error 1
error: Bad exit status from /var/tmp/rpm-tmp.eNVcMk (%build)
--------------------


I'll let you know about the R_RD2PDF tips. I needed it to check packages (I co-wrote a bioconductor package so that's reason why I use pre-release R every few days for a month every 6 months), but so far I haven't tried to build R's system-wide documentation with it yet.

(In reply to comment #4)
Thanks for the tips about removing the system-wide R first - indeed after I removed my system-wide R, I found a few recently created files in /usr/lib/R/library/compiler, so it looked like my 2.14 RPM-build was indeed playing with the system-wide R where it shouldn't. R_LIBS_SITE is possibly the culpit. (my early 2.15 in $HOME was updated/rebuilt as recent as yesterday).


I got to the final stage where it complains 3 file globs are not there - one is chinese-version documentation, the other is copyright notice, the third is an empty directory; so they are not important. These are the diff against 2.13.2, on fedora 15: 

-------------
> export R_RD4PDF="times,hyper"
455c459
< %lang(zh) %{_libdir}/R/library/compiler/po/zh*/
---
> #%lang(zh) %{_libdir}/R/library/compiler/po/zh*/
464c468
< %{_libdir}/R/library/datasets/R/
---
> #%{_libdir}/R/library/datasets/R/
787c791
< %{_libdir}/R/library/survival/COPYING
---
> #%{_libdir}/R/library/survival/COPYING
--------------

Might you I did bite the bullet and put inconsolata TeX support on a few days ago (TexLive2007 on fedora 15 is also missing the bulk of the CJK stuff...). YMMV; but it certainly looks like you need to do something about the inconsolata  situation on f17 one way or the other. (it is not too difficult - it is just need to put a dozen files in various places). I'll leave a comment on the inconsolata bug if you are interested.

*** Bug 751819 has been marked as a duplicate of this bug. ***

(In reply to comment #6)
> (In reply to comment #4)
> Thanks for the tips about removing the system-wide R first - indeed after I
> removed my system-wide R, I found a few recently created files in
> /usr/lib/R/library/compiler, so it looked like my 2.14 RPM-build was indeed
> playing with the system-wide R where it shouldn't. R_LIBS_SITE is possibly the
> culpit. (my early 2.15 in $HOME was updated/rebuilt as recent as yesterday).

Don't build software as root! Bad! *thwack* :)

> Might you I did bite the bullet and put inconsolata TeX support on a few days
> ago (TexLive2007 on fedora 15 is also missing the bulk of the CJK stuff...).
> YMMV; but it certainly looks like you need to do something about the
> inconsolata  situation on f17 one way or the other. (it is not too difficult -
> it is just need to put a dozen files in various places). I'll leave a comment
> on the inconsolata bug if you are interested.

I don't know what the "inconsolata" situation is.

So, I'm just going to bite the bullet and do 2.14.0 and mass rebuilds of all R dependent packages for EL4, EL5, EL6, f15, f16, and rawhide. (I'm starting with the EPEL branches since that is simpler.)

This is going to take a while, so please be patient.

(In reply to comment #8)

> I don't know what the "inconsolata" situation is.

Nevermind, I see it now. I'm working on a fix for Fedora's texlive-texmf, hackish, but should keep things going.

(In reply to comment #8)
> Don't build software as root! Bad! *thwack* :)

Yes, I am guilty... :-(.

> Nevermind, I see it now. I'm working on a fix for Fedora's texlive-texmf,
> hackish, but should keep things going.

I think if you do 

export R_RD4PDF="times,hyper"

You can also override the new default to get R 2.14's documentation to build with the older fonts - and for dependent R packages, you need to put this inside one of R's launch scripts, such as /usr/bin/R . (although I have bitten the bullet and put the extra inconsolata TeX support files on, and seeing as I am above to upgrade to f16 and going to going through some changes system-wide, put texlive 2010 on also..
https://bugzilla.redhat.com/show_bug.cgi?id=746626
https://bugzilla.redhat.com/show_bug.cgi?id=488651
)

I wrote a little too early the last time - R 2.14 also adds a few files, besides removing a few, compared, to 2.13.

So this is my full diff, or the relevant part (note new R-parallel)
----------------
8c8
< Version: 2.13.2
---
> Version: 2.14.0
80a81
> Provides: R-parallel = %{version}
247a249
> export R_RD4PDF="times,hyper"
264a269
> export R_RD4PDF="times,hyper"
429a435
> %{_libdir}/R/library/cluster/po/
455c461
< %lang(zh) %{_libdir}/R/library/compiler/po/zh*/
---
> #%lang(zh) %{_libdir}/R/library/compiler/po/zh*/
464c470,471
< %{_libdir}/R/library/datasets/R/
---
> %{_libdir}/R/library/datasets/NAMESPACE
> #%{_libdir}/R/library/datasets/R/
618a626,627
> %{_libdir}/R/library/Matrix/test-tools-1.R
> %{_libdir}/R/library/Matrix/test-tools-Matrix.R
686a696,697
> # parallel
> %{_libdir}/R/library/parallel/
787c798
< %{_libdir}/R/library/survival/COPYING
---
> #%{_libdir}/R/library/survival/COPYING
--------------------------

I have a 2.14.0 spec file done, I even have builds for the EPEL targets (they're not pushed to updates yet, since 2.14.0 requires a mass rebuild of R dependent components). 

We're going to have to add export R_RD4PDF="times,hyper" for EPEL targets, since they won't have inconsolata (and we have no way to add it, since the tex packages are in RHEL). For Fedora 15, 16, rawhide, I pushed an update yesterday with inconsolata support, so they won't need the workaround.

R-GenomicFeatures-1.6.1-1.fc15,R-biomaRt-2.10.0-1.fc15,R-rtracklayer-1.14.1-2.fc15,R-RCurl-1.7.0-2.fc15,R-Rcompression-0.93.2-3.fc15,R-affydata-1.11.15-2.fc15,R-BSgenome.Celegans.UCSC.ce2-1.3.17-2.fc15,R-hgu95av2probe-2.9.0-1.fc15,R-hgu95av2cdf-2.9.1-1.fc15,R-hgu133acdf-2.9.1-1.fc15,R-BSgenome-1.22.0-1.fc15,R-ROC-1.30.0-1.fc15,R-multtest-2.10.0-2.fc15,R-maanova-1.24.0-1.fc15,R-fibroEset-1.4.6-1.fc15,R-Biostrings-2.22.0-1.fc15,R-bigmemory-4.2.11-1.fc15,R-AnnotationDbi-1.16.0-2.fc15,R-affy-1.32.0-1.fc15,R-RM2-0.0-8.fc15,R-GenomicRanges-1.6.2-1.fc15,R-biglm-0.8-1.fc15,R-Biobase-2.14.0-2.fc15,R-XML-3.4.3-2.fc15,R-timeDate-2131.00-1.fc15,R-caTools-1.12-2.fc15,R-BufferedMatrixMethods-1.18.0-1.fc15,R-IRanges-1.12.1-1.fc15,R-tkWidgets-1.32.0-2.fc15,R-RSQLite-0.10.0-1.fc15,R-msm-1.1-1.fc15,R-lmtest-0.9.29-1.fc15,R-xtable-1.6.0-1.fc15,R-wavethresh-4.5-2.fc15,R-waveslim-1.6.4-2.fc15,R-statmod-1.4.13-1.fc15,R-sciplot-1.0.9-1.fc15,R-Rsolid-0.9.31-5.fc15,R-RScaLAPACK-0.6.1-8.fc15,scalapack-1.7.5-14.fc15,R-rlecuyer-0.3.1-3.fc15,R-qvalue-1.28.0-1.fc15,R-hdf5-1.6.9-13.fc15,R-GeneR-2.24.0-2.fc15,R-combinat-0.0.8-1.fc15,R-BufferedMatrix-1.18.0-2.fc15,R-bitops-1.0.4.1-6.fc15,R-widgetTools-1.32.0-2.fc15,R-DynDoc-1.32.0-2.fc15,R-preprocessCore-1.16.0-2.fc15,R-RUnit-0.4.26-3.fc15,R-affyio-1.22.0-1.fc15,R-acepack-1.3.3.0-1.fc15,R-abind-1.3.0-1.fc15,R-RODBC-1.3.3-1.fc15,R-qtl-1.21.2-2.fc15,R-nws-1.7.0.1-3.fc15,R-mvtnorm-0.9.9991-1.fc15,R-zoo-1.7.6-2.fc15,R-DBI-0.2.5-3.fc15,rpy-2.2.4-1.fc15,rkward-0.5.7-2.fc15.1,graphviz-2.26.3-6.fc15,R-2.14.0-3.fc15 has been submitted as an update for Fedora 15.
https://admin.fedoraproject.org/updates/R-GenomicFeatures-1.6.1-1.fc15,R-biomaRt-2.10.0-1.fc15,R-rtracklayer-1.14.1-2.fc15,R-RCurl-1.7.0-2.fc15,R-Rcompression-0.93.2-3.fc15,R-affydata-1.11.15-2.fc15,R-BSgenome.Celegans.UCSC.ce2-1.3.17-2.fc15,R-hgu95av2probe-2.9.0-1.fc15,R-hgu95av2cdf-2.9.1-1.fc15,R-hgu133acdf-2.9.1-1.fc15,R-BSgenome-1.22.0-1.fc15,R-ROC-1.30.0-1.fc15,R-multtest-2.10.0-2.fc15,R-maanova-1.24.0-1.fc15,R-fibroEset-1.4.6-1.fc15,R-Biostrings-2.22.0-1.fc15,R-bigmemory-4.2.11-1.fc15,R-AnnotationDbi-1.16.0-2.fc15,R-affy-1.32.0-1.fc15,R-RM2-0.0-8.fc15,R-GenomicRanges-1.6.2-1.fc15,R-biglm-0.8-1.fc15,R-Biobase-2.14.0-2.fc15,R-XML-3.4.3-2.fc15,R-timeDate-2131.00-1.fc15,R-caTools-1.12-2.fc15,R-BufferedMatrixMethods-1.18.0-1.fc15,R-IRanges-1.12.1-1.fc15,R-tkWidgets-1.32.0-2.fc15,R-RSQLite-0.10.0-1.fc15,R-msm-1.1-1.fc15,R-lmtest-0.9.29-1.fc15,R-xtable-1.6.0-1.fc15,R-wavethresh-4.5-2.fc15,R-waveslim-1.6.4-2.fc15,R-statmod-1.4.13-1.fc15,R-sciplot-1.0.9-1.fc15,R-Rsolid-0.9.31-5.fc15,R-RScaLAPACK-0.6.1-8.fc15,scalapack-1.7.5-14.fc15,R-rlecuyer-0.3.1-3.fc15,R-qvalue-1.28.0-1.fc15,R-hdf5-1.6.9-13.fc15,R-GeneR-2.24.0-2.fc15,R-combinat-0.0.8-1.fc15,R-BufferedMatrix-1.18.0-2.fc15,R-bitops-1.0.4.1-6.fc15,R-widgetTools-1.32.0-2.fc15,R-DynDoc-1.32.0-2.fc15,R-preprocessCore-1.16.0-2.fc15,R-RUnit-0.4.26-3.fc15,R-affyio-1.22.0-1.fc15,R-acepack-1.3.3.0-1.fc15,R-abind-1.3.0-1.fc15,R-RODBC-1.3.3-1.fc15,R-qtl-1.21.2-2.fc15,R-nws-1.7.0.1-3.fc15,R-mvtnorm-0.9.9991-1.fc15,R-zoo-1.7.6-2.fc15,R-DBI-0.2.5-3.fc15,rpy-2.2.4-1.fc15,rkward-0.5.7-2.fc15.1,graphviz-2.26.3-6.fc15,R-2.14.0-3.fc15

R-GenomicFeatures-1.6.1-1.fc16,R-biomaRt-2.10.0-1.fc16,R-rtracklayer-1.14.1-2.fc16,R-RCurl-1.7.0-2.fc16,R-Rcompression-0.93.2-3.fc16,R-affydata-1.11.15-2.fc16,R-BSgenome.Celegans.UCSC.ce2-1.3.17-2.fc16,R-hgu95av2probe-2.9.0-1.fc16,R-hgu95av2cdf-2.9.1-1.fc16,R-hgu133acdf-2.9.1-1.fc16,R-BSgenome-1.22.0-1.fc16,R-ROC-1.30.0-1.fc16,R-multtest-2.10.0-2.fc16,R-maanova-1.24.0-1.fc16,R-fibroEset-1.4.6-1.fc16,R-Biostrings-2.22.0-1.fc16,R-bigmemory-4.2.11-1.fc16,R-AnnotationDbi-1.16.0-2.fc16,R-affy-1.32.0-1.fc16,R-RM2-0.0-8.fc16,R-GenomicRanges-1.6.2-1.fc16,R-biglm-0.8-1.fc16,R-Biobase-2.14.0-2.fc16,R-XML-3.4.3-2.fc16,R-timeDate-2131.00-1.fc16,R-caTools-1.12-2.fc16,R-BufferedMatrixMethods-1.18.0-1.fc16,R-IRanges-1.12.1-1.fc16,R-tkWidgets-1.32.0-2.fc16,R-RSQLite-0.10.0-1.fc16,R-msm-1.1-1.fc16,R-lmtest-0.9.29-1.fc16,R-xtable-1.6.0-1.fc16,R-wavethresh-4.5-2.fc16,R-waveslim-1.6.4-2.fc16,R-statmod-1.4.13-1.fc16,R-sciplot-1.0.9-1.fc16,R-Rsolid-0.9.31-5.fc16,R-RScaLAPACK-0.6.1-8.fc16,scalapack-1.7.5-14.fc16,R-rlecuyer-0.3.1-3.fc16,R-qvalue-1.28.0-1.fc16,R-hdf5-1.6.9-13.fc16,R-GeneR-2.24.0-2.fc16,R-combinat-0.0.8-1.fc16,R-BufferedMatrix-1.18.0-2.fc16,R-bitops-1.0.4.1-6.fc16,R-widgetTools-1.32.0-2.fc16,R-DynDoc-1.32.0-2.fc16,R-preprocessCore-1.16.0-2.fc16,R-RUnit-0.4.26-3.fc16,R-affyio-1.22.0-1.fc16,R-acepack-1.3.3.0-1.fc16,R-abind-1.3.0-1.fc16,R-RODBC-1.3.3-1.fc16,R-qtl-1.21.2-2.fc16,R-nws-1.7.0.1-3.fc16,R-mvtnorm-0.9.9991-1.fc16,R-zoo-1.7.6-2.fc16,R-DBI-0.2.5-3.fc16,rpy-2.2.4-1.fc16,rkward-0.5.7-2.fc16,graphviz-2.28.0-10.fc16,R-2.14.0-3.fc16 has been submitted as an update for Fedora 16.
https://admin.fedoraproject.org/updates/R-GenomicFeatures-1.6.1-1.fc16,R-biomaRt-2.10.0-1.fc16,R-rtracklayer-1.14.1-2.fc16,R-RCurl-1.7.0-2.fc16,R-Rcompression-0.93.2-3.fc16,R-affydata-1.11.15-2.fc16,R-BSgenome.Celegans.UCSC.ce2-1.3.17-2.fc16,R-hgu95av2probe-2.9.0-1.fc16,R-hgu95av2cdf-2.9.1-1.fc16,R-hgu133acdf-2.9.1-1.fc16,R-BSgenome-1.22.0-1.fc16,R-ROC-1.30.0-1.fc16,R-multtest-2.10.0-2.fc16,R-maanova-1.24.0-1.fc16,R-fibroEset-1.4.6-1.fc16,R-Biostrings-2.22.0-1.fc16,R-bigmemory-4.2.11-1.fc16,R-AnnotationDbi-1.16.0-2.fc16,R-affy-1.32.0-1.fc16,R-RM2-0.0-8.fc16,R-GenomicRanges-1.6.2-1.fc16,R-biglm-0.8-1.fc16,R-Biobase-2.14.0-2.fc16,R-XML-3.4.3-2.fc16,R-timeDate-2131.00-1.fc16,R-caTools-1.12-2.fc16,R-BufferedMatrixMethods-1.18.0-1.fc16,R-IRanges-1.12.1-1.fc16,R-tkWidgets-1.32.0-2.fc16,R-RSQLite-0.10.0-1.fc16,R-msm-1.1-1.fc16,R-lmtest-0.9.29-1.fc16,R-xtable-1.6.0-1.fc16,R-wavethresh-4.5-2.fc16,R-waveslim-1.6.4-2.fc16,R-statmod-1.4.13-1.fc16,R-sciplot-1.0.9-1.fc16,R-Rsolid-0.9.31-5.fc16,R-RScaLAPACK-0.6.1-8.fc16,scalapack-1.7.5-14.fc16,R-rlecuyer-0.3.1-3.fc16,R-qvalue-1.28.0-1.fc16,R-hdf5-1.6.9-13.fc16,R-GeneR-2.24.0-2.fc16,R-combinat-0.0.8-1.fc16,R-BufferedMatrix-1.18.0-2.fc16,R-bitops-1.0.4.1-6.fc16,R-widgetTools-1.32.0-2.fc16,R-DynDoc-1.32.0-2.fc16,R-preprocessCore-1.16.0-2.fc16,R-RUnit-0.4.26-3.fc16,R-affyio-1.22.0-1.fc16,R-acepack-1.3.3.0-1.fc16,R-abind-1.3.0-1.fc16,R-RODBC-1.3.3-1.fc16,R-qtl-1.21.2-2.fc16,R-nws-1.7.0.1-3.fc16,R-mvtnorm-0.9.9991-1.fc16,R-zoo-1.7.6-2.fc16,R-DBI-0.2.5-3.fc16,rpy-2.2.4-1.fc16,rkward-0.5.7-2.fc16,graphviz-2.28.0-10.fc16,R-2.14.0-3.fc16

R-msm-1.1-1.el5,R-lmtest-0.9.29-1.el5,R-qtl-1.21.2-2.el5,R-nws-1.7.0.1-3.el5,R-mvtnorm-0.9.9991-1.el5,R-zoo-1.7.6-2.el5,R-DBI-0.2.5-3.el5,R-2.14.0-3.el5 has been submitted as an update for Fedora EPEL 5.
https://admin.fedoraproject.org/updates/R-msm-1.1-1.el5,R-lmtest-0.9.29-1.el5,R-qtl-1.21.2-2.el5,R-nws-1.7.0.1-3.el5,R-mvtnorm-0.9.9991-1.el5,R-zoo-1.7.6-2.el5,R-DBI-0.2.5-3.el5,R-2.14.0-3.el5

R-lmtest-0.9.29-1.el4,R-qtl-1.21.2-2.el4,R-nws-1.7.0.1-3.el4,R-zoo-1.7.6-2.el4,R-DBI-0.2.5-3.el4,R-2.14.0-3.el4 has been submitted as an update for Fedora EPEL 4.
https://admin.fedoraproject.org/updates/R-lmtest-0.9.29-1.el4,R-qtl-1.21.2-2.el4,R-nws-1.7.0.1-3.el4,R-zoo-1.7.6-2.el4,R-DBI-0.2.5-3.el4,R-2.14.0-3.el4

R-msm-1.1-1.el6,R-lmtest-0.9.29-1.el6,R-RODBC-1.3.3-1.el6,R-qtl-1.21.2-2.el6,R-nws-1.7.0.1-3.el6,R-mvtnorm-0.9.9991-1.el6,R-zoo-1.7.6-2.el6,R-DBI-0.2.5-3.el6,R-2.14.0-3.el6 has been submitted as an update for Fedora EPEL 6.
https://admin.fedoraproject.org/updates/R-msm-1.1-1.el6,R-lmtest-0.9.29-1.el6,R-RODBC-1.3.3-1.el6,R-qtl-1.21.2-2.el6,R-nws-1.7.0.1-3.el6,R-mvtnorm-0.9.9991-1.el6,R-zoo-1.7.6-2.el6,R-DBI-0.2.5-3.el6,R-2.14.0-3.el6

Package R-msm-1.1-1.el5, R-lmtest-0.9.29-1.el5, R-qtl-1.21.2-2.el5, R-nws-1.7.0.1-3.el5, R-mvtnorm-0.9.9991-1.el5, R-zoo-1.7.6-2.el5, R-DBI-0.2.5-3.el5, R-2.14.0-3.el5:
* should fix your issue,
* was pushed to the Fedora EPEL 5 testing repository,
* should be available at your local mirror within two days.
Update it with:
# su -c 'yum update --enablerepo=epel-testing R-msm-1.1-1.el5 R-lmtest-0.9.29-1.el5 R-qtl-1.21.2-2.el5 R-nws-1.7.0.1-3.el5 R-mvtnorm-0.9.9991-1.el5 R-zoo-1.7.6-2.el5 R-DBI-0.2.5-3.el5 R-2.14.0-3.el5'
as soon as you are able to.
Please go to the following url:
https://admin.fedoraproject.org/updates/FEDORA-EPEL-2011-4981
then log in and leave karma (feedback).

R-GenomicFeatures-1.6.1-1.fc15, R-biomaRt-2.10.0-1.fc15, R-rtracklayer-1.14.1-2.fc15, R-RCurl-1.7.0-2.fc15, R-Rcompression-0.93.2-3.fc15, R-affydata-1.11.15-2.fc15, R-BSgenome.Celegans.UCSC.ce2-1.3.17-2.fc15, R-hgu95av2probe-2.9.0-1.fc15, R-hgu95av2cdf-2.9.1-1.fc15, R-hgu133acdf-2.9.1-1.fc15, R-BSgenome-1.22.0-1.fc15, R-ROC-1.30.0-1.fc15, R-multtest-2.10.0-2.fc15, R-maanova-1.24.0-1.fc15, R-fibroEset-1.4.6-1.fc15, R-Biostrings-2.22.0-1.fc15, R-bigmemory-4.2.11-1.fc15, R-AnnotationDbi-1.16.0-2.fc15, R-affy-1.32.0-1.fc15, R-RM2-0.0-8.fc15, R-GenomicRanges-1.6.2-1.fc15, R-biglm-0.8-1.fc15, R-Biobase-2.14.0-2.fc15, R-XML-3.4.3-2.fc15, R-timeDate-2131.00-1.fc15, R-caTools-1.12-2.fc15, R-BufferedMatrixMethods-1.18.0-1.fc15, R-IRanges-1.12.1-1.fc15, R-tkWidgets-1.32.0-2.fc15, R-RSQLite-0.10.0-1.fc15, R-msm-1.1-1.fc15, R-lmtest-0.9.29-1.fc15, R-xtable-1.6.0-1.fc15, R-wavethresh-4.5-2.fc15, R-waveslim-1.6.4-2.fc15, R-statmod-1.4.13-1.fc15, R-sciplot-1.0.9-1.fc15, R-Rsolid-0.9.31-5.fc15, R-RScaLAPACK-0.6.1-8.fc15, scalapack-1.7.5-14.fc15, R-rlecuyer-0.3.1-3.fc15, R-qvalue-1.28.0-1.fc15, R-hdf5-1.6.9-13.fc15, R-GeneR-2.24.0-2.fc15, R-combinat-0.0.8-1.fc15, R-BufferedMatrix-1.18.0-2.fc15, R-bitops-1.0.4.1-6.fc15, R-widgetTools-1.32.0-2.fc15, R-DynDoc-1.32.0-2.fc15, R-preprocessCore-1.16.0-2.fc15, R-RUnit-0.4.26-3.fc15, R-affyio-1.22.0-1.fc15, R-acepack-1.3.3.0-1.fc15, R-abind-1.3.0-1.fc15, R-RODBC-1.3.3-1.fc15, R-qtl-1.21.2-2.fc15, R-nws-1.7.0.1-3.fc15, R-mvtnorm-0.9.9991-1.fc15, R-zoo-1.7.6-2.fc15, R-DBI-0.2.5-3.fc15, rpy-2.2.4-1.fc15, rkward-0.5.7-2.fc15.1, graphviz-2.26.3-6.fc15, R-2.14.0-3.fc15 has been pushed to the Fedora 15 stable repository.  If problems still persist, please make note of it in this bug report.

R-GenomicFeatures-1.6.1-1.fc16, R-biomaRt-2.10.0-1.fc16, R-rtracklayer-1.14.1-2.fc16, R-RCurl-1.7.0-2.fc16, R-Rcompression-0.93.2-3.fc16, R-affydata-1.11.15-2.fc16, R-BSgenome.Celegans.UCSC.ce2-1.3.17-2.fc16, R-hgu95av2probe-2.9.0-1.fc16, R-hgu95av2cdf-2.9.1-1.fc16, R-hgu133acdf-2.9.1-1.fc16, R-BSgenome-1.22.0-1.fc16, R-ROC-1.30.0-1.fc16, R-multtest-2.10.0-2.fc16, R-maanova-1.24.0-1.fc16, R-fibroEset-1.4.6-1.fc16, R-Biostrings-2.22.0-1.fc16, R-bigmemory-4.2.11-1.fc16, R-AnnotationDbi-1.16.0-2.fc16, R-affy-1.32.0-1.fc16, R-RM2-0.0-8.fc16, R-GenomicRanges-1.6.2-1.fc16, R-biglm-0.8-1.fc16, R-Biobase-2.14.0-2.fc16, R-XML-3.4.3-2.fc16, R-timeDate-2131.00-1.fc16, R-caTools-1.12-2.fc16, R-BufferedMatrixMethods-1.18.0-1.fc16, R-IRanges-1.12.1-1.fc16, R-tkWidgets-1.32.0-2.fc16, R-RSQLite-0.10.0-1.fc16, R-msm-1.1-1.fc16, R-lmtest-0.9.29-1.fc16, R-xtable-1.6.0-1.fc16, R-wavethresh-4.5-2.fc16, R-waveslim-1.6.4-2.fc16, R-statmod-1.4.13-1.fc16, R-sciplot-1.0.9-1.fc16, R-Rsolid-0.9.31-5.fc16, R-RScaLAPACK-0.6.1-8.fc16, scalapack-1.7.5-14.fc16, R-rlecuyer-0.3.1-3.fc16, R-qvalue-1.28.0-1.fc16, R-hdf5-1.6.9-13.fc16, R-GeneR-2.24.0-2.fc16, R-combinat-0.0.8-1.fc16, R-BufferedMatrix-1.18.0-2.fc16, R-bitops-1.0.4.1-6.fc16, R-widgetTools-1.32.0-2.fc16, R-DynDoc-1.32.0-2.fc16, R-preprocessCore-1.16.0-2.fc16, R-RUnit-0.4.26-3.fc16, R-affyio-1.22.0-1.fc16, R-acepack-1.3.3.0-1.fc16, R-abind-1.3.0-1.fc16, R-RODBC-1.3.3-1.fc16, R-qtl-1.21.2-2.fc16, R-nws-1.7.0.1-3.fc16, R-mvtnorm-0.9.9991-1.fc16, R-zoo-1.7.6-2.fc16, R-DBI-0.2.5-3.fc16, rpy-2.2.4-1.fc16, rkward-0.5.7-2.fc16, graphviz-2.28.0-10.fc16, R-2.14.0-3.fc16 has been pushed to the Fedora 16 stable repository.  If problems still persist, please make note of it in this bug report.

R-msm-1.1-1.el5, R-lmtest-0.9.29-1.el5, R-qtl-1.21.2-2.el5, R-nws-1.7.0.1-3.el5, R-mvtnorm-0.9.9991-1.el5, R-zoo-1.7.6-2.el5, R-DBI-0.2.5-3.el5, R-2.14.0-3.el5 has been pushed to the Fedora EPEL 5 stable repository.  If problems still persist, please make note of it in this bug report.

R-msm-1.1-1.el6, R-lmtest-0.9.29-1.el6, R-RODBC-1.3.3-1.el6, R-qtl-1.21.2-2.el6, R-nws-1.7.0.1-3.el6, R-mvtnorm-0.9.9991-1.el6, R-zoo-1.7.6-2.el6, R-DBI-0.2.5-3.el6, R-2.14.0-3.el6 has been pushed to the Fedora EPEL 6 stable repository.  If problems still persist, please make note of it in this bug report.

R-lmtest-0.9.29-1.el4, R-qtl-1.21.2-2.el4, R-nws-1.7.0.1-3.el4, R-zoo-1.7.6-2.el4, R-DBI-0.2.5-3.el4, R-2.14.0-3.el4 has been pushed to the Fedora EPEL 4 stable repository.  If problems still persist, please make note of it in this bug report.