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

[Bert Gunter]

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 using 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 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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>>

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