[Bioc-devel] Failed to locate any version of JAGS version 4

[Zhi Yang]

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>
wrote:

> Hmm.. so a new version of rjags (4-11) got published on CRAN on Sept 24:
>
>    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/HiLDA/
>    - https://bioconductor.org/checkResults/3.14/bioc-LATEST/infercnv/
>    - 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
> > 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 mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
> --
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.github using gmail.com
>

	[[alternative HTML version deleted]]