I just tried installing forensim on R-devel/Ubuntu 20.04/WSL-2.0 without an
X server (hence DISPLAY was not set). Loading tktcl gives a warning that
Tk is not available because DISPLAY is not set. The installation hung
after the byte-compile message:
installing to
/home/bill/R-devel/R-build/site-library/00LOCK-tkrplot/00new/tkrplot/libs
** R
** byte-compile and prepare package for lazy loading
Warning message:
no DISPLAY variable so Tk is not available
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Warning: no DISPLAY variable so Tk is not available
Warning: loading Rplot failed
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: no DISPLAY variable so Tk is not available
Warning: loading Rplot failed
** testing if installed package keeps a record of temporary installation
path
* DONE (tkrplot)
* installing *source* package ‘forensim’ ...
** package ‘forensim’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -I"/home/bill/R-devel/R-build/include" -DNDEBUG -I/usr/local/include
-fpic -g -c auxilary.c -o auxilary.o
gcc -I"/home/bill/R-devel/R-build/include" -DNDEBUG -I/usr/local/include
-fpic -g -c recursFinal.c -o recursFinal.o
gcc -shared -L/usr/local/lib -o forensim.so auxilary.o recursFinal.o
installing to
/home/bill/R-devel/R-build/site-library/00LOCK-forensim/00new/forensim/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
[hang]
gdb gives a traceback that I think indicates that the package is trying to
plot something via tcltk at this point:
Attaching to process 9310
[New LWP 9315]
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
0x00007fe20a50f560 in ?? () from /usr/lib/x86_64-linux-gnu/libtcl8.6.so
(gdb) where
#0 0x00007fe20a50f560 in ?? () from /usr/lib/x86_64-linux-gnu/libtcl8.6.so
#1 0x00007fe20a50f5f2 in TclNRRunCallbacks () from
/usr/lib/x86_64-linux-gnu/libtcl8.6.so
#2 0x00007fe20a5e4cd9 in Tcl_PkgRequireProc () from
/usr/lib/x86_64-linux-gnu/libtcl8.6.so
#3 0x00007fe20a5e4b06 in Tcl_PkgRequireEx () from
/usr/lib/x86_64-linux-gnu/libtcl8.6.so
#4 0x00007fe20a976be8 in Rplot_Init (interp=0x55ae6437a6c0) at
tcltkimg.c:465
#5 0x00007fe20a5d1ee3 in ?? () from /usr/lib/x86_64-linux-gnu/libtcl8.6.so
#6 0x00007fe20a50f5f2 in TclNRRunCallbacks () from
/usr/lib/x86_64-linux-gnu/libtcl8.6.so
#7 0x00007fe20b04d7f0 in dotTclObjv (args=0x55ae6489d210) at
/mnt/c/R/R-svn/trunk/src/library/tcltk/src/tcltk.c:250
#8 0x000055ae611cd5a8 in do_External (call=0x55ae6440a270,
op=0x55ae61fe1338, args=0x55ae6489d210, env=0x55ae6489d3d0)
at /mnt/c/R/R-svn/trunk/src/main/dotcode.c:576
#9 0x000055ae6122a0b3 in bcEval (body=0x55ae6440a190, rho=0x55ae6489d3d0,
useCache=TRUE)
at /mnt/c/R/R-svn/trunk/src/main/eval.c:7128
#10 0x000055ae6121644a in Rf_eval (e=0x55ae6440a190, rho=0x55ae6489d3d0) at
/mnt/c/R/R-svn/trunk/src/main/eval.c:740
#11 0x000055ae61215fda in forcePromise (e=0x55ae6489d398) at
/mnt/c/R/R-svn/trunk/src/main/eval.c:568
#12 0x000055ae61220b80 in FORCE_PROMISE (value=0x55ae6489d398,
symbol=0x55ae62282a08, rho=0x55ae6489d248,
keepmiss=FALSE) at /mnt/c/R/R-svn/trunk/src/main/eval.c:5149
#13 0x000055ae61220d2f in getvar (symbol=0x55ae62282a08,
rho=0x55ae6489d248, dd=FALSE, keepmiss=FALSE,
vcache=0x7fe20b2ec1f0, sidx=1) at
/mnt/c/R/R-svn/trunk/src/main/eval.c:5190
Henrik, can you reproduce this if you undefine DISPLAY?
-Bill
On Wed, Sep 29, 2021 at 7:48 PM Henrik Bengtsson <henrik.bengts...@gmail.com>
wrote:
> 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.
>
[[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.
