[R-sig-Debian] mclust package installation is preparing for lazy loading and never finishes

[Michael Rutter]

On 6/4/20 8:43 AM, mcomas using ima.udg.edu wrote:
> Hi,
> 
> After loading R 4.0.0 on Ubuntu 20.04.
> 
>      R version 4.0.0 (2020-04-24) -- "Arbor Day"
>      Copyright (C) 2020 The R Foundation for Statistical Computing
>      Platform: x86_64-pc-linux-gnu (64-bit)
> 
>      R is free software and comes with ABSOLUTELY NO WARRANTY.
>      You are welcome to redistribute it under certain conditions.
>      Type 'license()' or 'licence()' for distribution details.
> 
>      Natural language support but running in an English locale
> 
>      R is a collaborative project with many contributors.
>      Type 'contributors()' for more information and
>      'citation()' on how to cite R or R packages in publications.
> 
>      Type 'demo()' for some demos, 'help()' for on-line help, or
>      'help.start()' for an HTML browser interface to help.
>      Type 'q()' to quit R.
> 
> and with the following session information:
> 
>      > sessionInfo()
>      R version 4.0.0 (2020-04-24)
>      Platform: x86_64-pc-linux-gnu (64-bit)
>      Running under: Ubuntu 20.04 LTS
> 
>      Matrix products: default
>      BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
>      LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3
> 
>      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
> 
>      loaded via a namespace (and not attached):
>      [1] compiler_4.0.0
> 
> I try to install package `mclust`. R gets stuck when preparing for lazy 
> loading:
> 
>      > install.packages('mclust')
>      Installing package into ‘/home/marc/R/x86_64-pc-linux-gnu-library/4.0’
>      (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-Do_dS_/r-base-4.0.0=. 
> -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-Do_dS_/r-base-4.0.0=. 
> -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-Do_dS_/r-base-4.0.0=. 
> -fstack-protector-strong  -c
> mclust.f -o mclust.o
>      gfortran -fno-optimize-sibling-calls  -fpic  -g -O2
> -fdebug-prefix-map=/build/r-base-Do_dS_/r-base-4.0.0=. 
> -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
> /home/marc/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-mclust/00new/mclust/libs 
> 
>      ** R
>      ** data
>      *** moving datasets to lazyload DB
>      ** inst
>      ** byte-compile and prepare package for lazy loading
> 
> I have wait for all night, but the installation is still stuck at the 
> same point. Does
> anybody know how to solve this?
> 

It does build, as the c2d4u4.0 PPA 
(https://launchpad.net/~c2d4u.team/+archive/ubuntu/c2d4u4.0+) has the 
package.  So one option is to install the package from there.

If you upgraded to R 4.0 from 3.5, make sure you re-install all your old 
packages against 4.0.  You can look over the buildlog (if you have a 
launchpad account) for mclust on c2d4u4.0 here:

https://launchpad.net/~c2d4u.team/+archive/ubuntu/c2d4u4.0+/+build/19271073/+files/buildlog_ubuntu-focal-amd64.mclust_5.4.6-1cran1.2004.0_BUILDING.txt.gz

That might give you some ideas where the hang-up is.  I suspect this is 
unique to the combination of packages you have installed on your machine.

Michael