Re: [Bioc-devel] Failed to locate any version of JAGS version 4
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
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 > <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
&
Re: [Bioc-devel] Failed to locate any version of JAGS version 4
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
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@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
> --
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.git...@gmail.com
>
[[alternative HTML version deleted]]
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[Bioc-devel] Failed to locate any version of JAGS version 4
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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
