R SIG Debian - Jun 2020 - mclust package installation is preparing for lazy loading and never finishes

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?

I have installed different packages with no problems. Here a complete  
list of packages
already installed at my library directory:

     marc at hera:~/R/x86_64-pc-linux-gnu-library/4.0$ ls
     askpass     DEoptimR   generics     later       pkgbuild        
readxl       tibble
     assertthat  desc       ggplot2      lazyeval    pkgconfig       
rematch      tictoc
     backports   deSolve    glue         lifecycle   pkgload         
remotes      tidyr
     base64enc   digest     gridExtra    lspline     plotly          
reprex       tidyselect
     BH          diptest    gtable       lubridate   plyr            
reshape2     tidyverse
     blob        dplyr      gtools       magrittr    praise          
rlang        tinytex
     broom       egg        haven        markdown    prettyunits     
rmarkdown    utf8
     callr       ellipsis   hexbin       mime        processx        
robustbase   uuid
     cellranger  evaluate   highr        modelr      progress        
rprojroot    vctrs
     cli         fansi      hms          modeltools  promises       rstudioapi
viridisLite
     clipr       farver     htmltools    mstate      ps              
rvest        webshot
     coda.base   flexmix    htmlwidgets  muhaz       purrr           
scales       whisker
     colorspace  flexsurv   httr         munsell     qpdf            
selectr      withr
     crayon      flextable  isoband      mvtnorm     quadprog        
spatial      xfun
     crosstalk   forcats    jsonlite     nlme        R6              
stringi      xml2
     curl        foreign    kableExtra   officer     RColorBrewer    
stringr      yaml
     data.table  fs         kernlab      openssl     Rcpp            
sys          zip
     DBI         gdata      knitr        pdftools    RcppArmadillo  systemfonts
     dbplyr      gdtools    labeling     pillar      readr          testthat

On 6/4/20 8:43 AM, mcomas at 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

Well there is a known issue stemming from the libopenblas0-pthread package on
Ubuntu 20.04.  A fix is forthcoming. This issue has manifested itself via
other packages too -- as soon as something calls into lapack/blas an infinite
loop or lock starts.

In the meantime you could try another BLAS package.

Of course, it could be something else altogether too...

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org