[R] Installation of mclust package v5.4.6 on R v4.0.1 on Ubuntu v20.04 hangs
Venkatesh Prasad Ranganath
rvpr@@@d @end|ng |rom c|@@k@u@edu
Wed Jun 17 22:47:16 CEST 2020
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 using 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 using 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 using 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 using 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 using 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.
> >
>
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