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

[Hervé Pagès]

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>
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>      >
> 
>     -- 
>     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