R help - Jun 2020 - Installation of mclust package v5.4.6 on R v4.0.1 on Ubuntu v20.04 hangs

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]]

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]]

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]]