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.git...@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.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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel