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@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 > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org 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. ______________________________________________ R-help@r-project.org 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.