Brodie, Kent
2021-Sep-29 21:11 UTC
[R] Package installation help: Stuck at "** byte-compile and prepare package for lazy loading"
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]]
Henrik Bengtsson
2021-Sep-30 02:42 UTC
[R] Package installation help: Stuck at "** byte-compile and prepare package for lazy loading"
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 at 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 at 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.