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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