[R] Installation of mclust package v5.4.6 on R v4.0.1 on Ubuntu v20.04 hangs

[Jeff Newmiller]

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]]
>>>
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>>
>
> 	[[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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