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.git...@gmail.com
<mailto:hpages.on.git...@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@r-project.org <mailto:Bioc-devel@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.git...@gmail.com <mailto:hpages.on.git...@gmail.com>
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
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