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
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