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

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

Venkatesh Prasad Ranganath
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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Re: Installation of mclust package v5.4.6 on R v4.0.1 on Ubuntu v20.04 hangs

Bert Gunter-2
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 <
[hidden email]> 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]]
>
> ______________________________________________
> [hidden email] 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]]

______________________________________________
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Re: Installation of mclust package v5.4.6 on R v4.0.1 on Ubuntu v20.04 hangs

Venkatesh Prasad Ranganath
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 <[hidden email]> 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 <
> [hidden email]> 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]]
>>
>> ______________________________________________
>> [hidden email] 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]]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: 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 <[hidden email]> 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 <
>> [hidden email]> 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]]
>>>
>>> ______________________________________________
>>> [hidden email] 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]]
>
> ______________________________________________
> [hidden email] 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.
>

---------------------------------------------------------------------------
Jeff Newmiller                        The     .....       .....  Go Live...
DCN:<[hidden email]>        Basics: ##.#.       ##.#.  Live Go...
                                       Live:   OO#.. Dead: OO#..  Playing
Research Engineer (Solar/Batteries            O.O#.       #.O#.  with
/Software/Embedded Controllers)               .OO#.       .OO#.  rocks...1k

______________________________________________
[hidden email] 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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Re: Installation of mclust package v5.4.6 on R v4.0.1 on Ubuntu v20.04 hangs

Venkatesh Prasad Ranganath
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 <[hidden email]>
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 <[hidden email]>
> 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 <
> >> [hidden email]> 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]]
> >>>
> >>> ______________________________________________
> >>> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
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Re: Installation of mclust package v5.4.6 on R v4.0.1 on Ubuntu v20.04 hangs

Bert Gunter-2
In reply to this post by Venkatesh Prasad Ranganath
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 <
[hidden email]> 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 <[hidden email]>
> 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 <
>> [hidden email]> 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
>>>
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>>>
>>> ______________________________________________
>>> [hidden email] 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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