[Bioc-devel] Failed to locate any version of JAGS version 4
Zhi Yang
zy@ng895 @end|ng |rom gm@||@com
Fri Oct 15 06:25:56 CEST 2021
Many thanks to Hervé and Martin. Two of my packages now passed multiple
platform build/check.
Regards,
Zhi Yang
On Wed, Oct 13, 2021 at 10:18 AM Hervé Pagès <hpages.on.github using gmail.com>
wrote:
> Update: I defined the JAGS_HOME environment variable on riesling1 as
> suggested off-list by Martin (thanks Martin), so now rjags can be loaded
> again. This should solve the problem for CNVrd2, HiLDA, infercnv, and
> MADSEQ.
>
> I did the same on tokay2 (Windows server for the 3.13 builds) where the
> recent update to rjags also broke the 4 Bioconductor packages above.
> While I was on it, I updated JAGS from JAGS-4.2.0 to the latest version
> (JAGS-4.3.0) on tokay2. So now we have the same version on riesling1 and
> tokay2.
>
> Cheers,
> H.
>
>
> On 12/10/2021 13:29, Zhi Yang wrote:
> > Thank you so much, Herve! It makes sense to me now. I imported R2jags in
> > my package, which depends on rjags.
> >
> > Regards,
> > Zhi Yang
> >
> >
> >
> >
> > On Tue, Oct 12, 2021 at 1:14 PM Hervé Pagès <hpages.on.github using gmail.com
> > <mailto:hpages.on.github using gmail.com>> wrote:
> >
> > Hmm.. so a new version of rjags (4-11) got published on CRAN on Sept
> 24:
> >
> > https://cran.r-project.org/package=rjags
> > <https://cran.r-project.org/package=rjags>
> >
> > and for some reason they modified the code they use in their onLoad()
> > hook to find JAGS on Windows. They were using in rjags 4-10:
> >
> > readRegistry("SOFTWARE\\JAGS", hive="HLM", maxdepth=2,
> > view="32-bit")
> >
> >
> > which was working fine on our Windows server riesling1 (and AFAIK
> also
> > on the CRAN Windows build machine), but in rjags 4-11 they use:
> >
> > readRegistry("SOFTWARE\\JAGS", hive="HLM", maxdepth=2,
> > view="64-bit")
> >
> >
> >
> > which fails on riesling1 with:
> >
> > Error in readRegistry("SOFTWARE\\JAGS", hive = "HLM", maxdepth
> > = 2,
> > view = "64-bit") :
> >
> > Registry key 'SOFTWARE\JAGS' not found
> >
> >
> > I've reinstalled JAGS-4.3.0 on riesling1 but that doesn't change
> > anything.
> >
> > Unfortunately this breaks all packages that depend on rjags:
> >
> > - https://bioconductor.org/checkResults/3.14/bioc-LATEST/CNVrd2/
> > <https://bioconductor.org/checkResults/3.14/bioc-LATEST/CNVrd2/>
> > - https://bioconductor.org/checkResults/3.14/bioc-LATEST/HiLDA/
> > <https://bioconductor.org/checkResults/3.14/bioc-LATEST/HiLDA/>
> > -
> > https://bioconductor.org/checkResults/3.14/bioc-LATEST/infercnv/
> > <https://bioconductor.org/checkResults/3.14/bioc-LATEST/infercnv/>
> > - https://bioconductor.org/checkResults/3.14/bioc-LATEST/MADSEQ/
> > <https://bioconductor.org/checkResults/3.14/bioc-LATEST/MADSEQ/>
> >
> > Help appreciated.
> >
> > BTW your package HiLDA is one of them so I wonder why rjags is not
> > listed in the Imports field.
> >
> > Best,
> > H.
> >
> >
> > On 11/10/2021 21:24, Zhi Yang wrote:
> > > Hello everyone,
> > >
> > > I encountered a problem with two of my Bioconductor packages
> > built on the
> > > windows server for the next release. Specifically, it couldn't
> > locate any
> > > version of JAGS version 4. Has anyone experienced the same issue
> with
> > > importing or depending on rjags? Thank you!
> > >
> > > ** using staged installation
> > > ** libs
> > > "C:/rtools40/mingw32/bin/"g++ -std=gnu++11
> > > -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG
> > > -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'
> > > -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2
> > > -mstackrealign -c EMalgorithm.cpp -o EMalgorithm.o
> > > "C:/rtools40/mingw32/bin/"g++ -std=gnu++11
> > > -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG
> > > -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'
> > > -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2
> > > -mstackrealign -c RcppExports.cpp -o RcppExports.o
> > > "C:/rtools40/mingw32/bin/"g++ -std=gnu++11
> > > -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG
> > > -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'
> > > -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2
> > > -mstackrealign -c checkBoundary.cpp -o checkBoundary.o
> > > "C:/rtools40/mingw32/bin/"g++ -std=gnu++11
> > > -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG
> > > -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'
> > > -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2
> > > -mstackrealign -c convertFromToVector.cpp -o
> convertFromToVector.o
> > > C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s
> -static-libgcc -o
> > > HiLDA.dll tmp.def EMalgorithm.o RcppExports.o checkBoundary.o
> > > convertFromToVector.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib
> > > -LD:/biocbuild/bbs-3.14-bioc/R/bin/i386 -lR
> > > installing to
> >
> D:/biocbuild/bbs-3.14-bioc/meat/HiLDA.buildbin-libdir/00LOCK-HiLDA/00new/HiLDA/libs/i386
> > > ** R
> > > ** inst
> > > ** byte-compile and prepare package for lazy loading
> > > Error: .onLoad failed in loadNamespace() for 'rjags', details:
> > > call: fun(libname, pkgname)
> > > error: Failed to locate any version of JAGS version 4
> > >
> > > The rjags package is just an interface to the JAGS library
> > > Make sure you have installed JAGS-4.x.y.exe (for any x >=0, y>=0)
> > > fromhttp://www.sourceforge.net/projects/mcmc-jags/files
> > <http://www.sourceforge.net/projects/mcmc-jags/files>
> > > Execution halted
> > > ERROR: lazy loading failed for package 'HiLDA'
> > > * removing
> > 'D:/biocbuild/bbs-3.14-bioc/meat/HiLDA.buildbin-libdir/HiLDA'
> > >
> > >
> > > Regards,
> > > Zhi Yang
> > >
> > > [[alternative HTML version deleted]]
> > >
> > > _______________________________________________
> > > Bioc-devel using r-project.org <mailto:Bioc-devel using r-project.org>
> > mailing list
> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > <https://stat.ethz.ch/mailman/listinfo/bioc-devel>
> > >
> >
> > --
> > Hervé Pagès
> >
> > Bioconductor Core Team
> > hpages.on.github using gmail.com <mailto:hpages.on.github using gmail.com>
> >
>
> --
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.github using gmail.com
>
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