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.4...@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 <
> rvpra...@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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>> 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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