Venkatesh Prasad Ranganath
2020-Jun-17 19:49 UTC
[R] Installation of mclust package v5.4.6 on R v4.0.1 on Ubuntu v20.04 hangs
Hey Bert, Since the process stalls during byte-compilation and package preparation, I am thinking the issue is likely due to R and not the Ubuntu platform. If you think otherwise, then can you please say you think so? Also, is there a way to trace/debug the package build process? The same action via "R CMD INSTALL --no-byte-compile" and "R CMD INSTALL --no-staged-install" also results in a hang (except the absence of "byte-compile and" in the output when --no-byte-compile option is specified). Cheers, Venkatesh-Prasad Ranganath On Wed, Jun 17, 2020 at 1:40 PM Bert Gunter <bgunter.4567 at gmail.com> wrote:> Probably better posted on R-sig-debian. > > Bert Gunter > > "The trouble with having an open mind is that people keep coming along and > sticking things into it." > -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) > > > On Wed, Jun 17, 2020 at 11:33 AM Venkatesh Prasad Ranganath < > rvprasad at cis.ksu.edu> wrote: > >> Hey All, >> >> When I execute 'Rscript -e "install.packages('mclust')"` with R 4.0.1 on >> Ubuntu 20.04, the process hangs during package preparation. Any idea how >> to fix or debug this issue? >> >> Venkatesh-Prasad Ranganath >> >> ----------------------------------------- >> ENV: R v4.0.1, GCC v9, Ubuntu v20.04 >> CMD: Rscript -e "install.packages('mclust')" >> OUTPUT: >> Installing package into ?/usr/local/lib/R/site-library? >> (as ?lib? is unspecified) >> trying URL 'https://cloud.r-project.org/src/contrib/mclust_5.4.6.tar.gz' >> Content type 'application/x-gzip' length 2877519 bytes (2.7 MB) >> =================================================>> downloaded 2.7 MB >> >> * installing *source* package ?mclust? ... >> ** package ?mclust? successfully unpacked and MD5 sums checked >> ** using staged installation >> ** libs >> gfortran -fno-optimize-sibling-calls -fpic -g -O2 >> -fdebug-prefix-map=/build/r-base-dEscXG/r-base-4.0.1=. >> -fstack-protector-strong -c dmvnorm.f -o dmvnorm.o >> gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 >> -fdebug-prefix-map=/build/r-base-dEscXG/r-base-4.0.1=. >> -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time >> -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o >> gfortran -fno-optimize-sibling-calls -fpic -g -O2 >> -fdebug-prefix-map=/build/r-base-dEscXG/r-base-4.0.1=. >> -fstack-protector-strong -c mclust.f -o mclust.o >> gfortran -fno-optimize-sibling-calls -fpic -g -O2 >> -fdebug-prefix-map=/build/r-base-dEscXG/r-base-4.0.1=. >> -fstack-protector-strong -c mclustaddson.f -o mclustaddson.o >> gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions >> -Wl,-z,relro -o mclust.so dmvnorm.o init.o mclust.o mclustaddson.o >> -llapack >> -lblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath >> -L/usr/lib/R/lib >> -lR >> installing to >> /usr/local/lib/R/site-library/00LOCK-mclust/00new/mclust/libs >> ** R >> ** data >> *** moving datasets to lazyload DB >> ** inst >> ** byte-compile and prepare package for lazy loading >> >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. >> >[[alternative HTML version deleted]]
Venkatesh Prasad Ranganath
2020-Jun-17 20:47 UTC
[R] Installation of mclust package v5.4.6 on R v4.0.1 on Ubuntu v20.04 hangs
Hey Jeff, Thanks for confirming the package could be built and installed on Ubuntu 18.04. I will pose the question to the SIG. Cheers, Venkatesh-Prasad Ranganath http://rvprasad.com On Wed, Jun 17, 2020 at 3:39 PM Jeff Newmiller <jdnewmil at dcn.davis.ca.us> wrote:> Please (re)read the Posting guide, which says that this mailing list is > for questions about the R language and not about compiling issues, and > then go to r-sig-debian to look for more expertise. > > FYI I don't have Ubuntu 20.04, but I had no trouble installing mclust > 5.4.6 with R4.0.1 on Ubuntu 18.04, so your problem is a specific > interaction with your OS (or how you have your OS configured). > > > sessionInfo() > R version 4.0.1 (2020-06-06) > Platform: x86_64-pc-linux-gnu (64-bit) > Running under: Ubuntu 18.04.4 LTS > > Matrix products: default > BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1 > LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1 > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] mclust_5.4.6 > > loaded via a namespace (and not attached): > [1] compiler_4.0.1 tools_4.0.1 > > > > On Wed, 17 Jun 2020, Venkatesh Prasad Ranganath wrote: > > > Hey Bert, > > > > Since the process stalls during byte-compilation and package > preparation, I > > am thinking the issue is likely due to R and not the Ubuntu platform. If > > you think otherwise, then can you please say you think so? Also, is > there > > a way to trace/debug the package build process? > > > > The same action via "R CMD INSTALL --no-byte-compile" and "R CMD INSTALL > > --no-staged-install" also results in a hang (except the absence of > > "byte-compile and" in the output when --no-byte-compile option is > > specified). > > > > Cheers, > > > > Venkatesh-Prasad Ranganath > > > > > > > > On Wed, Jun 17, 2020 at 1:40 PM Bert Gunter <bgunter.4567 at gmail.com> > wrote: > > > >> Probably better posted on R-sig-debian. > >> > >> Bert Gunter > >> > >> "The trouble with having an open mind is that people keep coming along > and > >> sticking things into it." > >> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) > >> > >> > >> On Wed, Jun 17, 2020 at 11:33 AM Venkatesh Prasad Ranganath < > >> rvprasad at cis.ksu.edu> wrote: > >> > >>> Hey All, > >>> > >>> When I execute 'Rscript -e "install.packages('mclust')"` with R 4.0.1 > on > >>> Ubuntu 20.04, the process hangs during package preparation. Any idea > how > >>> to fix or debug this issue? > >>> > >>> Venkatesh-Prasad Ranganath > >>> > >>> ----------------------------------------- > >>> ENV: R v4.0.1, GCC v9, Ubuntu v20.04 > >>> CMD: Rscript -e "install.packages('mclust')" > >>> OUTPUT: > >>> Installing package into ?/usr/local/lib/R/site-library? > >>> (as ?lib? is unspecified) > >>> trying URL ' > https://cloud.r-project.org/src/contrib/mclust_5.4.6.tar.gz' > >>> Content type 'application/x-gzip' length 2877519 bytes (2.7 MB) > >>> =================================================> >>> downloaded 2.7 MB > >>> > >>> * installing *source* package ?mclust? ... > >>> ** package ?mclust? successfully unpacked and MD5 sums checked > >>> ** using staged installation > >>> ** libs > >>> gfortran -fno-optimize-sibling-calls -fpic -g -O2 > >>> -fdebug-prefix-map=/build/r-base-dEscXG/r-base-4.0.1=. > >>> -fstack-protector-strong -c dmvnorm.f -o dmvnorm.o > >>> gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 > >>> -fdebug-prefix-map=/build/r-base-dEscXG/r-base-4.0.1=. > >>> -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time > >>> -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o > >>> gfortran -fno-optimize-sibling-calls -fpic -g -O2 > >>> -fdebug-prefix-map=/build/r-base-dEscXG/r-base-4.0.1=. > >>> -fstack-protector-strong -c mclust.f -o mclust.o > >>> gfortran -fno-optimize-sibling-calls -fpic -g -O2 > >>> -fdebug-prefix-map=/build/r-base-dEscXG/r-base-4.0.1=. > >>> -fstack-protector-strong -c mclustaddson.f -o mclustaddson.o > >>> gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions > >>> -Wl,-z,relro -o mclust.so dmvnorm.o init.o mclust.o mclustaddson.o > >>> -llapack > >>> -lblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath > >>> -L/usr/lib/R/lib > >>> -lR > >>> installing to > >>> /usr/local/lib/R/site-library/00LOCK-mclust/00new/mclust/libs > >>> ** R > >>> ** data > >>> *** moving datasets to lazyload DB > >>> ** inst > >>> ** byte-compile and prepare package for lazy loading > >>> > >>> [[alternative HTML version deleted]] > >>> > >>> ______________________________________________ > >>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > >>> https://stat.ethz.ch/mailman/listinfo/r-help > >>> PLEASE do read the posting guide > >>> http://www.R-project.org/posting-guide.html > >>> and provide commented, minimal, self-contained, reproducible code. > >>> > >> > > > > [[alternative HTML version deleted]] > > > > ______________________________________________ > > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. > > > > --------------------------------------------------------------------------- > Jeff Newmiller The ..... ..... Go Live... > DCN:<jdnewmil at dcn.davis.ca.us> Basics: ##.#. ##.#. Live > Go... > Live: OO#.. Dead: OO#.. Playing > Research Engineer (Solar/Batteries O.O#. #.O#. with > /Software/Embedded Controllers) .OO#. .OO#. rocks...1k > --------------------------------------------------------------------------- >[[alternative HTML version deleted]]
Jeff Newmiller
2020-Jun-17 20:47 UTC
[R] Installation of mclust package v5.4.6 on R v4.0.1 on Ubuntu v20.04 hangs
Please (re)read the Posting guide, which says that this mailing list is for questions about the R language and not about compiling issues, and then go to r-sig-debian to look for more expertise. FYI I don't have Ubuntu 20.04, but I had no trouble installing mclust 5.4.6 with R4.0.1 on Ubuntu 18.04, so your problem is a specific interaction with your OS (or how you have your OS configured).> sessionInfo()R version 4.0.1 (2020-06-06) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.4 LTS Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] mclust_5.4.6 loaded via a namespace (and not attached): [1] compiler_4.0.1 tools_4.0.1>On Wed, 17 Jun 2020, Venkatesh Prasad Ranganath wrote:> Hey Bert, > > Since the process stalls during byte-compilation and package preparation, I > am thinking the issue is likely due to R and not the Ubuntu platform. If > you think otherwise, then can you please say you think so? Also, is there > a way to trace/debug the package build process? > > The same action via "R CMD INSTALL --no-byte-compile" and "R CMD INSTALL > --no-staged-install" also results in a hang (except the absence of > "byte-compile and" in the output when --no-byte-compile option is > specified). > > Cheers, > > Venkatesh-Prasad Ranganath > > > > On Wed, Jun 17, 2020 at 1:40 PM Bert Gunter <bgunter.4567 at gmail.com> wrote: > >> Probably better posted on R-sig-debian. >> >> Bert Gunter >> >> "The trouble with having an open mind is that people keep coming along and >> sticking things into it." >> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) >> >> >> On Wed, Jun 17, 2020 at 11:33 AM Venkatesh Prasad Ranganath < >> rvprasad at cis.ksu.edu> wrote: >> >>> Hey All, >>> >>> When I execute 'Rscript -e "install.packages('mclust')"` with R 4.0.1 on >>> Ubuntu 20.04, the process hangs during package preparation. Any idea how >>> to fix or debug this issue? >>> >>> Venkatesh-Prasad Ranganath >>> >>> ----------------------------------------- >>> ENV: R v4.0.1, GCC v9, Ubuntu v20.04 >>> CMD: Rscript -e "install.packages('mclust')" >>> OUTPUT: >>> Installing package into ?/usr/local/lib/R/site-library? >>> (as ?lib? is unspecified) >>> trying URL 'https://cloud.r-project.org/src/contrib/mclust_5.4.6.tar.gz' >>> Content type 'application/x-gzip' length 2877519 bytes (2.7 MB) >>> =================================================>>> downloaded 2.7 MB >>> >>> * installing *source* package ?mclust? ... >>> ** package ?mclust? successfully unpacked and MD5 sums checked >>> ** using staged installation >>> ** libs >>> gfortran -fno-optimize-sibling-calls -fpic -g -O2 >>> -fdebug-prefix-map=/build/r-base-dEscXG/r-base-4.0.1=. >>> -fstack-protector-strong -c dmvnorm.f -o dmvnorm.o >>> gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 >>> -fdebug-prefix-map=/build/r-base-dEscXG/r-base-4.0.1=. >>> -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time >>> -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o >>> gfortran -fno-optimize-sibling-calls -fpic -g -O2 >>> -fdebug-prefix-map=/build/r-base-dEscXG/r-base-4.0.1=. >>> -fstack-protector-strong -c mclust.f -o mclust.o >>> gfortran -fno-optimize-sibling-calls -fpic -g -O2 >>> -fdebug-prefix-map=/build/r-base-dEscXG/r-base-4.0.1=. >>> -fstack-protector-strong -c mclustaddson.f -o mclustaddson.o >>> gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions >>> -Wl,-z,relro -o mclust.so dmvnorm.o init.o mclust.o mclustaddson.o >>> -llapack >>> -lblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath >>> -L/usr/lib/R/lib >>> -lR >>> installing to >>> /usr/local/lib/R/site-library/00LOCK-mclust/00new/mclust/libs >>> ** R >>> ** data >>> *** moving datasets to lazyload DB >>> ** inst >>> ** byte-compile and prepare package for lazy loading >>> >>> [[alternative HTML version deleted]] >>> >>> ______________________________________________ >>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >>> https://stat.ethz.ch/mailman/listinfo/r-help >>> PLEASE do read the posting guide >>> http://www.R-project.org/posting-guide.html >>> and provide commented, minimal, self-contained, reproducible code. >>> >> > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >--------------------------------------------------------------------------- Jeff Newmiller The ..... ..... Go Live... DCN:<jdnewmil at dcn.davis.ca.us> Basics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/Batteries O.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k
Bert Gunter
2020-Jun-17 21:41 UTC
[R] Installation of mclust package v5.4.6 on R v4.0.1 on Ubuntu v20.04 hangs
I would think that it is how interacts with the OS on Ubuntu, which is what the SIG is about and where also relevant expertise is likely to be found. But I claim no such expertise and you are certainly free to reject my suggestion as useless. Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Wed, Jun 17, 2020 at 12:50 PM Venkatesh Prasad Ranganath < rvprasad at cis.ksu.edu> wrote:> Hey Bert, > > Since the process stalls during byte-compilation and package preparation, > I am thinking the issue is likely due to R and not the Ubuntu platform. If > you think otherwise, then can you please say you think so? Also, is there > a way to trace/debug the package build process? > > The same action via "R CMD INSTALL --no-byte-compile" and "R CMD INSTALL > --no-staged-install" also results in a hang (except the absence of > "byte-compile and" in the output when --no-byte-compile option is > specified). > > Cheers, > > Venkatesh-Prasad Ranganath > > > > On Wed, Jun 17, 2020 at 1:40 PM Bert Gunter <bgunter.4567 at gmail.com> > wrote: > >> Probably better posted on R-sig-debian. >> >> Bert Gunter >> >> "The trouble with having an open mind is that people keep coming along >> and sticking things into it." >> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) >> >> >> On Wed, Jun 17, 2020 at 11:33 AM Venkatesh Prasad Ranganath < >> rvprasad at cis.ksu.edu> wrote: >> >>> Hey All, >>> >>> When I execute 'Rscript -e "install.packages('mclust')"` with R 4.0.1 on >>> Ubuntu 20.04, the process hangs during package preparation. Any idea how >>> to fix or debug this issue? >>> >>> Venkatesh-Prasad Ranganath >>> >>> ----------------------------------------- >>> ENV: R v4.0.1, GCC v9, Ubuntu v20.04 >>> CMD: Rscript -e "install.packages('mclust')" >>> OUTPUT: >>> Installing package into ?/usr/local/lib/R/site-library? >>> (as ?lib? is unspecified) >>> trying URL 'https://cloud.r-project.org/src/contrib/mclust_5.4.6.tar.gz' >>> Content type 'application/x-gzip' length 2877519 bytes (2.7 MB) >>> =================================================>>> downloaded 2.7 MB >>> >>> * installing *source* package ?mclust? ... >>> ** package ?mclust? successfully unpacked and MD5 sums checked >>> ** using staged installation >>> ** libs >>> gfortran -fno-optimize-sibling-calls -fpic -g -O2 >>> -fdebug-prefix-map=/build/r-base-dEscXG/r-base-4.0.1=. >>> -fstack-protector-strong -c dmvnorm.f -o dmvnorm.o >>> gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 >>> -fdebug-prefix-map=/build/r-base-dEscXG/r-base-4.0.1=. >>> -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time >>> -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o >>> gfortran -fno-optimize-sibling-calls -fpic -g -O2 >>> -fdebug-prefix-map=/build/r-base-dEscXG/r-base-4.0.1=. >>> -fstack-protector-strong -c mclust.f -o mclust.o >>> gfortran -fno-optimize-sibling-calls -fpic -g -O2 >>> -fdebug-prefix-map=/build/r-base-dEscXG/r-base-4.0.1=. >>> -fstack-protector-strong -c mclustaddson.f -o mclustaddson.o >>> gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions >>> -Wl,-z,relro -o mclust.so dmvnorm.o init.o mclust.o mclustaddson.o >>> -llapack >>> -lblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath >>> -L/usr/lib/R/lib >>> -lR >>> installing to >>> /usr/local/lib/R/site-library/00LOCK-mclust/00new/mclust/libs >>> ** R >>> ** data >>> *** moving datasets to lazyload DB >>> ** inst >>> ** byte-compile and prepare package for lazy loading >>> >>> [[alternative HTML version deleted]] >>> >>> ______________________________________________ >>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >>> https://stat.ethz.ch/mailman/listinfo/r-help >>> PLEASE do read the posting guide >>> http://www.R-project.org/posting-guide.html >>> and provide commented, minimal, self-contained, reproducible code. >>> >>[[alternative HTML version deleted]]