[R] Package installation help: Stuck at "** byte-compile and prepare package for lazy loading"

[Henrik Bengtsson]

I just tried on an up-to-date CentOS 7 with R 4.1.1 built from source
using gcc 8.3.1 (from SCL devtoolset-8; so not the default gcc 4.8.5),
and it works there.  If of any help, here's the output when installing
to user's personal package library:

> chooseCRANmirror(ind = 1)
> install.packages("forensim")
Installing package into
‘/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/forensim_4.3.tar.gz'
Content type 'application/x-gzip' length 84232 bytes (82 KB)
==================================================
downloaded 82 KB

* installing *source* package ‘forensim’ ...
** package ‘forensim’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -I"/software/c4/cbi/software/R-4.1.1-gcc8/lib64/R/include"
-DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c auxilary.c -o
auxilary.o
gcc -I"/software/c4/cbi/software/R-4.1.1-gcc8/lib64/R/include"
-DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c recursFinal.c -o
recursFinal.o
gcc -shared -L/software/c4/cbi/software/R-4.1.1-gcc8/lib64/R/lib
-L/usr/local/lib64 -o forensim.so auxilary.o recursFinal.o
-L/software/c4/cbi/software/R-4.1.1-gcc8/lib64/R/lib -lR
installing to /c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/00LOCK-forensim/00new/forensim/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (forensim)

The downloaded source packages are in
    ‘/scratch/henrik/RtmpYFlQyS/downloaded_packages’

You could also try to install it via 'R CMD INSTALL' and try with
different options disabled to maybe narrow in on what's going on.

My $.02

/Henrik

On Wed, Sep 29, 2021 at 6:37 PM Brodie, Kent via R-help
<r-help using r-project.org> wrote:
>
> Hey everyone!  So, I've been asked by one of our researchers to install "all" cran packages on one of our servers.    Yeah, it's a bit much (and clearly, not everything will install correctly due to various missing tidbits), but it will go a long way to having to constantly respond to install requests of various packages.  OK, fine.
>
> Anyway, I have tried this, and things proceed nicely for several hours until the process gets completely and absolutely stuck.   I have tried several things, for example trying newer versions of R, and even repeating the process on a CentOS 8 server instead of where my stuff is now (CentOS 7).
>
> While re-trying one of my newer attempts at this, I decided to focus on the very first place where it hangs.   It dies on package "forensim".    It's a slightly older package, and I don't see anything particularly special about it.    The text below is where it hangs.    The install "R" process doing this is whizzing at 100%,  but no progress, no output, no errors.  Nothing in the system logs.
>
> On new "R" installs, with either operating system (CentOS 7, CentOS 8) and even different versions of "R" (up to including 4.1.1), I get the same result when just attempting to install this ONE package.    (and my guess, there's more packages out there that may bite me the same way).
>
> I am seeking any recommendations on how I can get past this?   A debug option?  A timeout of sorts so things will  move along to the next package when attempting to install a ton, or...?   I'm of course willing to try anything.   It's stupidly frustrating.    I'd be OK if it errored out and moved on.   But it...  hangs.
>
> Here's the latter part of the install attempt of this one package.     This latest attempt has been stuck on that last line now for 5 hours and counting.
>
> * DONE (tkrplot)
> Making 'packages.html' ... done
> * installing *source* package 'forensim' ...
> ** package 'forensim' successfully unpacked and MD5 sums checked
> ** using staged installation
> ** libs
> gcc -m64 -I"/usr/include/R" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c auxilary.c -o auxilary.o
> gcc -m64 -I"/usr/include/R" -DNDEBUG   -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c recursFinal.c -o recursFinal.o
> gcc -m64 -shared -L/usr/lib64/R/lib -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o forensim.so auxilary.o recursFinal.o -L/usr/lib64/R/lib -lR
> installing to /usr/lib64/R/library/00LOCK-forensim/00new/forensim/libs
> ** R
> ** data
> ** inst
> ** byte-compile and prepare package for lazy loading
>
>
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