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rstudio / renv

renv: Project environments for R.
https://rstudio.github.io/renv/
MIT License
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Running renv::restore() during Docker build fails. #1767

Closed gordongrabert closed 11 months ago

gordongrabert commented 11 months ago

Hi,

when I use renv::restore() within a Docker build, the following problem has recently occurred. The download of the packages works fine but from the point of installation the following problem occurs.

`RUN Rscript -e 'renv::restore()'

12 964.7 # Installing packages --------------------------------------------------------

12 964.8 - Installing lattice ... buffer overflow detected : terminated

12 974.1 Aborted (core dumped)

12 ERROR: executor failed running [/bin/sh -c Rscript -e 'renv::restore()']: exit code: 134

This problem did not occur 1 1/2 months ago.
When I install the packages with install.packages("") it works without any issues.

kevinushey commented 11 months ago

Sorry, but I'm going to need more details / a reproducible example to be able to help diagnose.

I found this potentially related issue:

https://github.com/NixOS/nixpkgs/issues/123209

so my best guess is that the issue might be resolved by updating R, or by adjusting your compiler settings.

gordongrabert commented 11 months ago

Hi,

I have created a repository with a Dockerfile and a renv.lock file. I copied the renv.lock file from a current project of mine. I am working on a Shiny app and I need a large number of packages for this project.

Here is the link to the repo

For the docker build I used this command: docker build --platform linux/amd64 .

kevinushey commented 11 months ago

Thanks; I was able to reproduce locally. Oddly, the error doesn't occur if lattice is the only package included in the lockfile, and I'm also not able to reproduce on real hardware (it seems to only happen in docker).

I'm going to see if there's any hope of getting a gdb backtrace for when this error occurs...

kevinushey commented 11 months ago

Okay, here's the stack trace:

564.4 Thread 1 "R" received signal SIGABRT, Aborted.
564.4 0x00007f4655f099fc in pthread_kill () from /lib/x86_64-linux-gnu/libc.so.6
564.4 #0  0x00007f4655f099fc in pthread_kill () from /lib/x86_64-linux-gnu/libc.so.6
564.4 #1  0x00007f4655eb5476 in raise () from /lib/x86_64-linux-gnu/libc.so.6
564.4 #2  0x00007f4655e9b7f3 in abort () from /lib/x86_64-linux-gnu/libc.so.6
564.4 #3  0x00007f4655efc676 in ?? () from /lib/x86_64-linux-gnu/libc.so.6
564.4 #4  0x00007f4655fa978a in __fortify_fail () from /lib/x86_64-linux-gnu/libc.so.6
564.4 #5  0x00007f4655fa8106 in __chk_fail () from /lib/x86_64-linux-gnu/libc.so.6
564.4 #6  0x00007f4655fa96cb in __fdelt_warn () from /lib/x86_64-linux-gnu/libc.so.6
564.4 #7  0x00007f4548763eba in R_SockConnect (port=<optimized out>, host=<optimized out>, timeout=timeout@entry=60) at Rsock.c:440
564.4 #8  0x00007f4548768397 in sock_open (con=0x564879db8890) at sockconn.c:89
564.5 #9  0x00007f4656175d0f in checked_open (ncon=<optimized out>, ncon@entry=3) at connections.c:1471
564.5 #10 0x00007f465617bc48 in do_sockconn (call=<optimized out>, op=<optimized out>, args=<optimized out>, env=<optimized out>) at connections.c:3562
564.5 #11 0x00007f46561de935 in bcEval (body=<optimized out>, rho=<optimized out>, useCache=<optimized out>) at eval.c:7446
564.5 #12 0x00007f46561f93d0 in Rf_eval (e=0x564846f397e0, rho=rho@entry=0x5648493934e0) at eval.c:1013
564.5 #13 0x00007f46561fb466 in R_execClosure (call=call@entry=0x564846f3a378, newrho=newrho@entry=0x5648493934e0, sysparent=<optimized out>, rho=rho@entry=0x564849393080, arglist=arglist@entry=0x5648493930f0, op=op@entry=0x564846f39b60) at eval.c:2187
564.5 #14 0x00007f46561fc295 in Rf_applyClosure (call=call@entry=0x564846f3a378, op=op@entry=0x564846f39b60, arglist=arglist@entry=0x5648493930f0, rho=rho@entry=0x564849393080, suppliedvars=<optimized out>) at eval.c:2113
564.5 #15 0x00007f46561ea3cd in bcEval (body=<optimized out>, rho=<optimized out>, useCache=<optimized out>) at eval.c:7414
564.5 #16 0x00007f46561f93d0 in Rf_eval (e=0x564846f3a420, rho=rho@entry=0x564849393080) at eval.c:1013
564.5 #17 0x00007f46561fb466 in R_execClosure (call=call@entry=0x564846ec6bf0, newrho=newrho@entry=0x564849393080, sysparent=<optimized out>, rho=rho@entry=0x564849392948, arglist=arglist@entry=0x564849392f68, op=op@entry=0x564846f3a8b8) at eval.c:2187
564.5 #18 0x00007f46561fc295 in Rf_applyClosure (call=call@entry=0x564846ec6bf0, op=op@entry=0x564846f3a8b8, arglist=arglist@entry=0x564849392f68, rho=rho@entry=0x564849392948, suppliedvars=<optimized out>) at eval.c:2113
564.5 #19 0x00007f46561ea3cd in bcEval (body=<optimized out>, rho=<optimized out>, useCache=<optimized out>) at eval.c:7414
564.5 #20 0x00007f46561f93d0 in Rf_eval (e=0x564846ec7050, rho=rho@entry=0x564849392948) at eval.c:1013
564.5 #21 0x00007f46561fb466 in R_execClosure (call=call@entry=0x564846ec56a8, newrho=newrho@entry=0x564849392948, sysparent=<optimized out>, rho=rho@entry=0x564848f29028, arglist=arglist@entry=0x564849392830, op=op@entry=0x564846ec7440) at eval.c:2187
564.5 #22 0x00007f46561fc295 in Rf_applyClosure (call=call@entry=0x564846ec56a8, op=op@entry=0x564846ec7440, arglist=arglist@entry=0x564849392830, rho=rho@entry=0x564848f29028, suppliedvars=<optimized out>) at eval.c:2113
564.5 #23 0x00007f46561ea3cd in bcEval (body=<optimized out>, rho=<optimized out>, useCache=<optimized out>) at eval.c:7414
564.5 #24 0x00007f46561f93d0 in Rf_eval (e=0x564846ec55c8, rho=0x564848f29028) at eval.c:1013
564.5 #25 0x00007f46561f9d84 in forcePromise (e=e@entry=0x564848f29060) at eval.c:833
564.5 #26 0x00007f46561fa068 in FORCE_PROMISE (keepmiss=FALSE, rho=0x564848f29220, symbol=0x564844cc9458, value=0x564848f29060) at eval.c:5467
564.5 #27 getvar (symbol=0x564844cc9458, rho=0x564848f29220, dd=<optimized out>, keepmiss=FALSE, vcache=<optimized out>, sidx=<optimized out>) at eval.c:5508
564.5 #28 0x00007f46561e5412 in bcEval (body=<optimized out>, rho=<optimized out>, useCache=<optimized out>) at eval.c:7198
564.5 #29 0x00007f46561f93d0 in Rf_eval (e=0x56484502d088, rho=0x564848f29220) at eval.c:1013
564.5 #30 0x00007f46561f9d84 in forcePromise (e=e@entry=0x564848f29610) at eval.c:833
564.5 #31 0x00007f46561fa068 in FORCE_PROMISE (keepmiss=FALSE, rho=0x564849391e58, symbol=0x564844cc9458, value=0x564848f29610) at eval.c:5467
564.5 #32 getvar (symbol=0x564844cc9458, rho=0x564849391e58, dd=<optimized out>, keepmiss=FALSE, vcache=<optimized out>, sidx=<optimized out>) at eval.c:5508
564.5 #33 0x00007f46561e5412 in bcEval (body=<optimized out>, rho=<optimized out>, useCache=<optimized out>) at eval.c:7198
564.5 #34 0x00007f46561f93d0 in Rf_eval (e=0x5648450267f8, rho=0x564849391e58) at eval.c:1013
564.5 #35 0x00007f46561f9d84 in forcePromise (e=e@entry=0x564849391f00) at eval.c:833
564.5 #36 0x00007f46561fa068 in FORCE_PROMISE (keepmiss=FALSE, rho=0x564849392210, symbol=0x564844cc9458, value=0x564849391f00) at eval.c:5467
564.5 #37 getvar (symbol=0x564844cc9458, rho=0x564849392210, dd=<optimized out>, keepmiss=FALSE, vcache=<optimized out>, sidx=<optimized out>) at eval.c:5508
564.5 #38 0x00007f46561e5412 in bcEval (body=<optimized out>, rho=<optimized out>, useCache=<optimized out>) at eval.c:7198
564.5 #39 0x00007f46561f93d0 in Rf_eval (e=0x56484502d3d0, rho=0x564849392210) at eval.c:1013
564.5 #40 0x00007f46561f9d84 in forcePromise (e=e@entry=0x5648493922b8) at eval.c:833
564.5 #41 0x00007f46561fa068 in FORCE_PROMISE (keepmiss=FALSE, rho=0x564849392558, symbol=0x564844cc9458, value=0x5648493922b8) at eval.c:5467
564.5 #42 getvar (symbol=0x564844cc9458, rho=0x564849392558, dd=<optimized out>, keepmiss=FALSE, vcache=<optimized out>, sidx=<optimized out>) at eval.c:5508
564.5 #43 0x00007f46561e5412 in bcEval (body=<optimized out>, rho=<optimized out>, useCache=<optimized out>) at eval.c:7198
564.5 #44 0x00007f46561f93d0 in Rf_eval (e=0x56484502d750, rho=rho@entry=0x564849392558) at eval.c:1013
564.5 #45 0x00007f46561fb466 in R_execClosure (call=call@entry=0x564845025e20, newrho=newrho@entry=0x564849392558, sysparent=<optimized out>, rho=rho@entry=0x564849392210, arglist=arglist@entry=0x5648493922f0, op=op@entry=0x564849392248) at eval.c:2187
564.5 #46 0x00007f46561fc295 in Rf_applyClosure (call=call@entry=0x564845025e20, op=op@entry=0x564849392248, arglist=arglist@entry=0x5648493922f0, rho=rho@entry=0x564849392210, suppliedvars=<optimized out>) at eval.c:2113
564.5 #47 0x00007f46561ea3cd in bcEval (body=<optimized out>, rho=<optimized out>, useCache=<optimized out>) at eval.c:7414
564.5 #48 0x00007f46561f93d0 in Rf_eval (e=0x564845026520, rho=rho@entry=0x564849392210) at eval.c:1013
564.5 #49 0x00007f46561fb466 in R_execClosure (call=call@entry=0x564845026d70, newrho=newrho@entry=0x564849392210, sysparent=<optimized out>, rho=rho@entry=0x564849391e58, arglist=arglist@entry=0x564849391fa8, op=op@entry=0x564848f292c8) at eval.c:2187
564.5 #50 0x00007f46561fc295 in Rf_applyClosure (call=call@entry=0x564845026d70, op=op@entry=0x564848f292c8, arglist=arglist@entry=0x564849391fa8, rho=rho@entry=0x564849391e58, suppliedvars=<optimized out>) at eval.c:2113
564.5 #51 0x00007f46561ea3cd in bcEval (body=<optimized out>, rho=<optimized out>, useCache=<optimized out>) at eval.c:7414
564.5 #52 0x00007f46561f93d0 in Rf_eval (e=0x5648450277f0, rho=rho@entry=0x564849391e58) at eval.c:1013
564.5 #53 0x00007f46561fb466 in R_execClosure (call=call@entry=0x5648450279e8, newrho=newrho@entry=0x564849391e58, sysparent=<optimized out>, rho=rho@entry=0x564848f29220, arglist=arglist@entry=0x564848f29648, op=op@entry=0x564848f29258) at eval.c:2187
564.5 #54 0x00007f46561fc295 in Rf_applyClosure (call=call@entry=0x5648450279e8, op=op@entry=0x564848f29258, arglist=arglist@entry=0x564848f29648, rho=rho@entry=0x564848f29220, suppliedvars=<optimized out>) at eval.c:2113
564.5 #55 0x00007f46561ea3cd in bcEval (body=<optimized out>, rho=<optimized out>, useCache=<optimized out>) at eval.c:7414
564.5 #56 0x00007f46561f93d0 in Rf_eval (e=0x56484501abc8, rho=rho@entry=0x564848f29220) at eval.c:1013
564.5 #57 0x00007f46561fb466 in R_execClosure (call=call@entry=0x564846ec5718, newrho=newrho@entry=0x564848f29220, sysparent=<optimized out>, rho=rho@entry=0x564848f29028, arglist=arglist@entry=0x564848f29098, op=op@entry=0x56484501ad18) at eval.c:2187
564.5 #58 0x00007f46561fc295 in Rf_applyClosure (call=call@entry=0x564846ec5718, op=op@entry=0x56484501ad18, arglist=arglist@entry=0x564848f29098, rho=rho@entry=0x564848f29028, suppliedvars=<optimized out>) at eval.c:2113
564.5 #59 0x00007f46561ea3cd in bcEval (body=<optimized out>, rho=<optimized out>, useCache=<optimized out>) at eval.c:7414
564.5 #60 0x00007f46561f93d0 in Rf_eval (e=0x564846ec57c0, rho=rho@entry=0x564848f29028) at eval.c:1013
564.5 #61 0x00007f46561fb466 in R_execClosure (call=call@entry=0x564846eaa2e8, newrho=newrho@entry=0x564848f29028, sysparent=<optimized out>, rho=rho@entry=0x5648491c28d8, arglist=arglist@entry=0x564848f28f10, op=op@entry=0x564846ec5bb0) at eval.c:2187
564.5 #62 0x00007f46561fc295 in Rf_applyClosure (call=call@entry=0x564846eaa2e8, op=op@entry=0x564846ec5bb0, arglist=arglist@entry=0x564848f28f10, rho=rho@entry=0x5648491c28d8, suppliedvars=<optimized out>) at eval.c:2113
564.5 #63 0x00007f46561ea3cd in bcEval (body=<optimized out>, rho=<optimized out>, useCache=<optimized out>) at eval.c:7414
564.5 #64 0x00007f46561f93d0 in Rf_eval (e=0x564846ea79b8, rho=rho@entry=0x5648491c28d8) at eval.c:1013
564.5 #65 0x00007f46561fb466 in R_execClosure (call=call@entry=0x564846ea8518, newrho=newrho@entry=0x5648491c28d8, sysparent=<optimized out>, rho=rho@entry=0x5648491c27c0, arglist=arglist@entry=0x5648491c2868, op=op@entry=0x564846ea7ef8) at eval.c:2187
564.5 #66 0x00007f46561fc295 in Rf_applyClosure (call=call@entry=0x564846ea8518, op=op@entry=0x564846ea7ef8, arglist=arglist@entry=0x5648491c2868, rho=rho@entry=0x5648491c27c0, suppliedvars=<optimized out>) at eval.c:2113
564.5 #67 0x00007f46561ea3cd in bcEval (body=<optimized out>, rho=<optimized out>, useCache=<optimized out>) at eval.c:7414
564.5 #68 0x00007f46561f93d0 in Rf_eval (e=0x564846ea85c0, rho=rho@entry=0x5648491c27c0) at eval.c:1013
564.5 #69 0x00007f46561fb466 in R_execClosure (call=call@entry=0x564848d53b60, newrho=newrho@entry=0x5648491c27c0, sysparent=<optimized out>, rho=rho@entry=0x56484904a700, arglist=arglist@entry=0x5648491c2718, op=op@entry=0x564846ea8a20) at eval.c:2187
564.5 #70 0x00007f46561fc295 in Rf_applyClosure (call=call@entry=0x564848d53b60, op=op@entry=0x564846ea8a20, arglist=arglist@entry=0x5648491c2718, rho=rho@entry=0x56484904a700, suppliedvars=<optimized out>) at eval.c:2113
564.5 #71 0x00007f46561ea3cd in bcEval (body=<optimized out>, rho=<optimized out>, useCache=<optimized out>) at eval.c:7414
564.5 #72 0x00007f46561f93d0 in Rf_eval (e=0x564848d510e0, rho=rho@entry=0x56484904a700) at eval.c:1013
564.5 #73 0x00007f46561fb466 in R_execClosure (call=call@entry=0x564848cd55c8, newrho=newrho@entry=0x56484904a700, sysparent=<optimized out>, rho=rho@entry=0x564849ca5440, arglist=arglist@entry=0x56484904a498, op=op@entry=0x564848d51540) at eval.c:2187
564.5 #74 0x00007f46561fc295 in Rf_applyClosure (call=call@entry=0x564848cd55c8, op=op@entry=0x564848d51540, arglist=arglist@entry=0x56484904a498, rho=rho@entry=0x564849ca5440, suppliedvars=<optimized out>) at eval.c:2113
564.5 #75 0x00007f46561ea3cd in bcEval (body=<optimized out>, rho=<optimized out>, useCache=<optimized out>) at eval.c:7414
564.5 #76 0x00007f46561f93d0 in Rf_eval (e=0x564848cd2d40, rho=rho@entry=0x564849ca5440) at eval.c:1013
564.5 #77 0x00007f46561fb466 in R_execClosure (call=call@entry=0x564848b551f8, newrho=newrho@entry=0x564849ca5440, sysparent=<optimized out>, rho=rho@entry=0x5648481e6078, arglist=arglist@entry=0x564849ca52f0, op=op@entry=0x564848cd3130) at eval.c:2187
564.5 #78 0x00007f46561fc295 in Rf_applyClosure (call=call@entry=0x564848b551f8, op=op@entry=0x564848cd3130, arglist=arglist@entry=0x564849ca52f0, rho=rho@entry=0x5648481e6078, suppliedvars=<optimized out>) at eval.c:2113
564.5 #79 0x00007f46561ea3cd in bcEval (body=<optimized out>, rho=<optimized out>, useCache=<optimized out>) at eval.c:7414
564.5 #80 0x00007f46561f93d0 in Rf_eval (e=0x564848b56fb8, rho=rho@entry=0x5648481e6078) at eval.c:1013
564.5 #81 0x00007f46561fb466 in R_execClosure (call=call@entry=0x564848b53c78, newrho=newrho@entry=0x5648481e6078, sysparent=<optimized out>, rho=rho@entry=0x5648481e5c50, arglist=arglist@entry=0x5648481e6008, op=op@entry=0x564848b53508) at eval.c:2187
564.5 #82 0x00007f46561fc295 in Rf_applyClosure (call=call@entry=0x564848b53c78, op=op@entry=0x564848b53508, arglist=arglist@entry=0x5648481e6008, rho=rho@entry=0x5648481e5c50, suppliedvars=<optimized out>) at eval.c:2113
564.5 #83 0x00007f46561ea3cd in bcEval (body=<optimized out>, rho=<optimized out>, useCache=<optimized out>) at eval.c:7414
564.5 #84 0x00007f46561f93d0 in Rf_eval (e=0x564848b53b98, rho=0x5648481e5c50) at eval.c:1013
564.5 #85 0x00007f46561f9d84 in forcePromise (e=e@entry=0x5648481e5eb8) at eval.c:833
564.5 #86 0x00007f46561fa068 in FORCE_PROMISE (keepmiss=FALSE, rho=0x5648481e5f98, symbol=0x564847687868, value=0x5648481e5eb8) at eval.c:5467
564.5 #87 getvar (symbol=0x564847687868, rho=0x5648481e5f98, dd=<optimized out>, keepmiss=FALSE, vcache=<optimized out>, sidx=<optimized out>) at eval.c:5508
564.5 #88 0x00007f46561e5412 in bcEval (body=<optimized out>, rho=<optimized out>, useCache=<optimized out>) at eval.c:7198
564.5 #89 0x00007f46561f93d0 in Rf_eval (e=0x564844e7f500, rho=rho@entry=0x5648481e5f98) at eval.c:1013
564.5 #90 0x00007f46561fb466 in R_execClosure (call=call@entry=0x564848b53d20, newrho=newrho@entry=0x5648481e5f98, sysparent=<optimized out>, rho=rho@entry=0x5648481e5c50, arglist=arglist@entry=0x5648481e5e80, op=op@entry=0x564847e63710) at eval.c:2187
564.5 #91 0x00007f46561fc295 in Rf_applyClosure (call=call@entry=0x564848b53d20, op=op@entry=0x564847e63710, arglist=arglist@entry=0x5648481e5e80, rho=rho@entry=0x5648481e5c50, suppliedvars=<optimized out>) at eval.c:2113
564.5 #92 0x00007f46561ea3cd in bcEval (body=<optimized out>, rho=<optimized out>, useCache=<optimized out>) at eval.c:7414
564.5 #93 0x00007f46561f93d0 in Rf_eval (e=0x564848b54378, rho=rho@entry=0x5648481e5c50) at eval.c:1013
564.5 #94 0x00007f46561fb466 in R_execClosure (call=call@entry=0x564848b178b0, newrho=newrho@entry=0x5648481e5c50, sysparent=<optimized out>, rho=rho@entry=0x5648489ad9b0, arglist=arglist@entry=0x5648481e5be0, op=op@entry=0x564848b546f8) at eval.c:2187
564.5 #95 0x00007f46561fc295 in Rf_applyClosure (call=call@entry=0x564848b178b0, op=op@entry=0x564848b546f8, arglist=arglist@entry=0x5648481e5be0, rho=rho@entry=0x5648489ad9b0, suppliedvars=<optimized out>) at eval.c:2113
564.5 #96 0x00007f46561ea3cd in bcEval (body=<optimized out>, rho=<optimized out>, useCache=<optimized out>) at eval.c:7414
564.5 #97 0x00007f46561f93d0 in Rf_eval (e=0x564848b17ed0, rho=rho@entry=0x5648489ad9b0) at eval.c:1013
564.5 #98 0x00007f46561fb466 in R_execClosure (call=call@entry=0x564848b0f808, newrho=newrho@entry=0x5648489ad9b0, sysparent=<optimized out>, rho=rho@entry=0x5648490522d8, arglist=arglist@entry=0x5648489ad940, op=op@entry=0x564848b18250) at eval.c:2187
564.5 #99 0x00007f46561fc295 in Rf_applyClosure (call=call@entry=0x564848b0f808, op=op@entry=0x564848b18250, arglist=arglist@entry=0x5648489ad940, rho=rho@entry=0x5648490522d8, suppliedvars=<optimized out>) at eval.c:2113
564.5 #100 0x00007f46561ea3cd in bcEval (body=<optimized out>, rho=<optimized out>, useCache=<optimized out>) at eval.c:7414
564.5 #101 0x00007f46561f93d0 in Rf_eval (e=0x564848b0fbf8, rho=rho@entry=0x5648490522d8) at eval.c:1013
564.5 #102 0x00007f46561fb466 in R_execClosure (call=call@entry=0x564846536a38, newrho=newrho@entry=0x5648490522d8, sysparent=<optimized out>, rho=rho@entry=0x564847887938, arglist=arglist@entry=0x564849052268, op=op@entry=0x564848b0ffb0) at eval.c:2187
564.5 #103 0x00007f46561fc295 in Rf_applyClosure (call=call@entry=0x564846536a38, op=op@entry=0x564848b0ffb0, arglist=arglist@entry=0x564849052268, rho=rho@entry=0x564847887938, suppliedvars=<optimized out>) at eval.c:2113
564.5 #104 0x00007f46561ea3cd in bcEval (body=<optimized out>, rho=<optimized out>, useCache=<optimized out>) at eval.c:7414
564.5 #105 0x00007f46561f93d0 in Rf_eval (e=0x564846533c00, rho=rho@entry=0x564847887938) at eval.c:1013
564.5 #106 0x00007f46561fb466 in R_execClosure (call=call@entry=0x56484567fdd0, newrho=newrho@entry=0x564847887938, sysparent=<optimized out>, rho=rho@entry=0x564845684ea8, arglist=arglist@entry=0x564847887c80, op=op@entry=0x564846534098) at eval.c:2187
564.5 #107 0x00007f46561fc295 in Rf_applyClosure (call=call@entry=0x56484567fdd0, op=op@entry=0x564846534098, arglist=arglist@entry=0x564847887c80, rho=rho@entry=0x564845684ea8, suppliedvars=<optimized out>) at eval.c:2113
564.5 #108 0x00007f46561ea3cd in bcEval (body=<optimized out>, rho=<optimized out>, useCache=<optimized out>) at eval.c:7414
564.5 #109 0x00007f46561f93d0 in Rf_eval (e=0x564845677c10, rho=rho@entry=0x564845684ea8) at eval.c:1013
564.5 #110 0x00007f46561fb466 in R_execClosure (call=call@entry=0x564846cfdf68, newrho=newrho@entry=0x564845684ea8, sysparent=<optimized out>, rho=rho@entry=0x564844c96068, arglist=arglist@entry=0x564844c5e8c0, op=op@entry=0x5648456781f8) at eval.c:2187
564.5 #111 0x00007f46561fc295 in Rf_applyClosure (call=call@entry=0x564846cfdf68, op=op@entry=0x5648456781f8, arglist=arglist@entry=0x564844c5e8c0, rho=rho@entry=0x564844c96068, suppliedvars=<optimized out>) at eval.c:2113
564.5 #112 0x00007f46561f94fc in Rf_eval (e=e@entry=0x564846cfdf68, rho=rho@entry=0x564844c96068) at eval.c:1140
564.5 #113 0x00007f465622f3ea in Rf_ReplIteration (rho=rho@entry=0x564844c96068, savestack=savestack@entry=0, browselevel=browselevel@entry=0, state=state@entry=0x7fffc868ee50) at main.c:262
564.5 #114 0x00007f465622f780 in R_ReplConsole (rho=0x564844c96068, savestack=savestack@entry=0, browselevel=browselevel@entry=0) at main.c:314
564.5 #115 0x00007f465622f840 in run_Rmainloop () at main.c:1200
564.5 #116 0x00007f465622f896 in Rf_mainloop () at main.c:1207
564.5 #117 0x000056484490f09f in main (ac=<optimized out>, av=<optimized out>) at Rmain.c:29

The crash is apparently happening when R attempts to open a socket. Not much renv can do about this...

kevinushey commented 11 months ago

As a workaround, you can probably disable the renv watchdog, e.g.

RENV_WATCHDOG_ENABLED = FALSE

in the project's .Renviron file, or set as an environment variable through some other means.

kevinushey commented 11 months ago

Did the above workaround help?

Lukas-Novak commented 11 months ago

Dear Kevin @kevinushey , I am experiencing the same issue. I tried to add RENV_WATCHDOG_ENABLED into Dockerfie, but it did not help. My Dockerfile and docker-compose.yml files are uploaded here. The full log of my issue is as follows:

=> => extracting sha256:b37163a14abc6a871550c37f1d3b5cdea4fea0f43fe8758b26c578d1ad4a 0.0s => [rstudio internal] load build context 30.5s => => transferring context: 1.89GB 30.5s => [rstudio 2/9] RUN apt-get update && apt-get install -y libgmp3-dev libm 237.7s => [rstudio 3/9] COPY . /home/rstudio 9.7s => [rstudio 4/9] WORKDIR /home/rstudio 0.0s => [rstudio 5/9] RUN R -e "install.packages('remotes',dependencies=TRUE, version = 848.7s => [rstudio 6/9] RUN Rscript -e "remotes::install_github('rstudio/renv@1.0.3')" 3.4s => [rstudio 7/9] RUN Rscript -e "install.packages('renv')" 15.5s => [rstudio 8/9] RUN R -e "renv::consent(provided = TRUE)" 2.4s => ERROR [rstudio 9/9] RUN Rscript -e "renv::restore()" 406.8s

[rstudio 9/9] RUN Rscript -e "renv::restore()": 2.453 - One or more packages recorded in the lockfile are not installed. 2.453 - Use renv::status() for more details. 2.456 [1] "Package file exists" 3.755 The following package(s) will be updated: 3.755 3.755 # Bioconductor --------------------------------------------------------------- 3.755 - BiocParallel [ -> 1.36.0] 3.755 - BiocVersion [ -> 3.18.1] 3.755 - mixOmics [ -> 6.26.0] 3.755 3.755 # CRAN ----------------------------------------------------------------------- 3.755 - bslib [0.6.1 -> 0.6.0] 3.755 - fansi [1.0.5 -> 1.0.4] 3.755 - jsonlite [1.8.8 -> 1.8.7] 3.755 - KernSmooth [2.23-20 -> 2.23-22] 3.755 - Matrix [1.5-4 -> 1.6-1.1] 3.755 - sass [0.4.8 -> 0.4.7] 3.755 - stringi [1.8.2 -> 1.7.12] 3.755 - stringr [1.5.1 -> 1.5.0] 3.755 - testthat [3.2.1 -> 3.2.0] 3.755 - utf8 [1.2.4 -> 1.2.3] 3.755 - vctrs [0.6.5 -> 0.6.3] 3.755 - xfun [0.41 -> 0.40] 3.755 - abind [ -> 1.4-5] 3.755 - afex [ -> 1.3-0] 3.755 - backports [ -> 1.4.1] 3.755 - bayestestR [ -> 0.13.1] 3.755 - BH [ -> 1.81.0-1] 3.755 - bigD [ -> 0.2.0] 3.755 - bit [ -> 4.0.5] 3.755 - bit64 [ -> 4.0.5] 3.755 - bitops [ -> 1.0-7] 3.755 - blob [ -> 1.2.4] 3.755 - bookdown [ -> 0.36] 3.755 - broom [ -> 1.0.5] 3.755 - broom.helpers [ -> 1.14.0] 3.755 - broom.mixed [ -> 0.2.9.4] 3.755 - car [ -> 3.1-2] 3.755 - carData [ -> 3.0-5] 3.755 - caret [ -> 6.0-94] 3.755 - cellranger [ -> 1.1.0] 3.755 - clipr [ -> 0.8.0] 3.755 - clock [ -> 0.7.0] 3.755 - coda [ -> 0.19-4] 3.755 - colorspace [ -> 2.1-0] 3.755 - commonmark [ -> 1.9.0] 3.755 - conflicted [ -> 1.2.0] 3.755 - corpcor [ -> 1.6.10] 3.755 - correlation [ -> 0.8.4] 3.755 - corrplot [ -> 0.92] 3.755 - corx [ -> 1.0.7.2] 3.755 - cowplot [ -> 1.1.1] 3.755 - cpp11 [ -> 0.4.6] 3.755 - crul [ -> 1.4.0] 3.755 - data.table [ -> 1.14.8] 3.755 - datawizard [ -> 0.9.0] 3.755 - DBI [ -> 1.1.3] 3.755 - dbplyr [ -> 2.4.0] 3.755 - DescTools [ -> 0.99.50] 3.755 - diagram [ -> 1.6.5] 3.755 - diptest [ -> 0.76-0] 3.755 - dplyr [ -> 1.1.3] 3.755 - dtplyr [ -> 1.3.1] 3.755 - e1071 [ -> 1.7-13] 3.755 - effectsize [ -> 0.8.6] 3.755 - ellipse [ -> 0.5.0] 3.755 - emmeans [ -> 1.8.9] 3.755 - estimability [ -> 1.4.1] 3.755 - Exact [ -> 3.2] 3.755 - expm [ -> 0.999-7] 3.755 - farver [ -> 2.1.1] 3.755 - flextable [ -> 0.9.3] 3.755 - fontBitstreamVera [ -> 0.1.1] 3.755 - fontLiberation [ -> 0.1.0] 3.755 - fontquiver [ -> 0.2.1] 3.755 - forcats [ -> 1.0.0] 3.755 - foreach [ -> 1.5.2] 3.755 - formatR [ -> 1.14] 3.755 - ftExtra [ -> 0.6.1] 3.755 - furrr [ -> 0.3.1] 3.755 - futile.logger [ -> 1.4.3] 3.755 - futile.options [ -> 1.0.1] 3.755 - future [ -> 1.33.0] 3.755 - future.apply [ -> 1.11.0] 3.755 - gargle [ -> 1.5.2] 3.755 - gdtools [ -> 0.3.4] 3.755 - generics [ -> 0.1.3] 3.755 - gfonts [ -> 0.2.0] 3.755 - ggcorrplot [ -> 0.1.4.1] 3.755 - ggeffects [ -> 1.3.2] 3.755 - ggplot2 [ -> 3.4.4] 3.755 - ggpubr [ -> 0.6.0] 3.755 - ggrepel [ -> 0.9.4] 3.755 - ggridges [ -> 0.5.4] 3.755 - ggsci [ -> 3.0.0] 3.755 - ggsignif [ -> 0.6.4] 3.755 - gld [ -> 2.6.6] 3.755 - globals [ -> 0.16.2] 3.755 - googledrive [ -> 2.1.1] 3.755 - googlesheets4 [ -> 1.1.1] 3.755 - gower [ -> 1.0.1] 3.755 - GPArotation [ -> 2023.11-1] 3.755 - gridExtra [ -> 2.3] 3.755 - gt [ -> 0.10.0] 3.755 - gtable [ -> 0.3.4] 3.755 - gtsummary [ -> 1.7.2] 3.755 - hardhat [ -> 1.3.0] 3.755 - haven [ -> 2.5.3] 3.755 - here [ -> 1.0.1] 3.755 - hms [ -> 1.1.3] 3.755 - htmlwidgets [ -> 1.6.3] 3.755 - httpcode [ -> 0.3.0] 3.755 - httpuv [ -> 1.6.12] 3.755 - ids [ -> 1.0.1] 3.755 - igraph [ -> 1.5.1] 3.755 - insight [ -> 0.19.6] 3.755 - ipred [ -> 0.9-14] 3.755 - isoband [ -> 0.2.7] 3.755 - iterators [ -> 1.0.14] 3.755 - janitor [ -> 2.2.0] 3.755 - juicyjuice [ -> 0.1.0] 3.755 - kableExtra [ -> 1.3.4] 3.755 - labeling [ -> 0.4.3] 3.755 - labelled [ -> 2.12.0] 3.755 - lambda.r [ -> 1.2.4] 3.755 - later [ -> 1.3.1] 3.755 - lava [ -> 1.7.3] 3.755 - listenv [ -> 0.9.0] 3.755 - lme4 [ -> 1.1-34] 3.755 - lmerTest [ -> 3.1-3] 3.755 - lmom [ -> 3.0] 3.755 - lubridate [ -> 1.9.3] 3.755 - markdown [ -> 1.11] 3.755 - MatrixModels [ -> 0.5-3] 3.755 - matrixStats [ -> 1.1.0] 3.755 - minqa [ -> 1.2.6] 3.755 - ModelMetrics [ -> 1.2.2.2] 3.755 - modelr [ -> 0.1.11] 3.755 - moments [ -> 0.14.1] 3.755 - multcompView [ -> 0.1-9] 3.755 - MuMIn [ -> 1.47.5] 3.755 - munsell [ -> 0.5.0] 3.755 - mvtnorm [ -> 1.2-3] 3.755 - nloptr [ -> 2.0.3] 3.755 - numDeriv [ -> 2016.8-1.1] 3.755 - officedown [ -> 0.3.1] 3.755 - officer [ -> 0.6.3] 3.755 - paletteer [ -> 1.5.0] 3.755 - pander [ -> 0.6.5] 3.755 - papaja [ -> 0.1.2] 3.755 - parallelly [ -> 1.36.0] 3.755 - parameters [ -> 0.21.3] 3.755 - pbkrtest [ -> 0.5.2] 3.755 - performance [ -> 0.10.8] 3.755 - pls [ -> 2.8-2] 3.755 - plyr [ -> 1.8.9] 3.755 - png [ -> 0.1-8] 3.755 - polynom [ -> 1.4-1] 3.755 - ppcor [ -> 1.1] 3.755 - prismatic [ -> 1.1.1] 3.755 - pROC [ -> 1.18.5] 3.755 - prodlim [ -> 2023.08.28] 3.755 - progress [ -> 1.2.2] 3.755 - progressr [ -> 0.14.0] 3.755 - promises [ -> 1.2.1] 3.755 - proxy [ -> 0.4-27] 3.755 - purrr [ -> 1.0.2] 3.755 - pwr [ -> 1.3-0] 3.755 - quantreg [ -> 5.97] 3.755 - ragg [ -> 1.2.5] 3.755 - rARPACK [ -> 0.11-0] 3.755 - RColorBrewer [ -> 1.1-3] 3.755 - Rcpp [ -> 1.0.11] 3.755 - RcppEigen [ -> 0.3.3.9.4] 3.755 - RcppTOML [ -> 0.2.2] 3.755 - reactable [ -> 0.4.4] 3.755 - reactR [ -> 0.5.0] 3.755 - readr [ -> 2.1.4] 3.755 - readxl [ -> 1.4.3] 3.755 - recipes [ -> 1.0.8] 3.755 - rematch [ -> 2.0.0] 3.755 - reprex [ -> 2.0.2] 3.755 - reshape [ -> 0.8.9] 3.755 - reshape2 [ -> 1.4.4] 3.755 - rmdpartials [ -> 0.5.8] 3.755 - Rmpfr [ -> 0.9-4] 3.755 - rootSolve [ -> 1.8.2.4] 3.755 - RSpectra [ -> 0.16-1] 3.755 - rstatix [ -> 0.7.2] 3.755 - rstudioapi [ -> 0.15.0] 3.755 - rvest [ -> 1.0.3] 3.755 - rvg [ -> 0.3.3] 3.755 - scales [ -> 1.2.1] 3.755 - selectr [ -> 0.4-2] 3.755 - shape [ -> 1.4.6] 3.755 - shiny [ -> 1.8.0] 3.755 - sjlabelled [ -> 1.2.0] 3.755 - sjmisc [ -> 2.8.9] 3.755 - sjPlot [ -> 2.8.15] 3.755 - sjstats [ -> 0.18.2] 3.755 - snakecase [ -> 0.11.1] 3.755 - snow [ -> 0.4-4] 3.755 - sourcetools [ -> 0.1.7-1] 3.755 - SparseM [ -> 1.81] 3.755 - SQUAREM [ -> 2021.1] 3.755 - SuppDists [ -> 1.1-9.7] 3.755 - svglite [ -> 2.1.2] 3.755 - systemfonts [ -> 1.0.4] 3.755 - textshaping [ -> 0.3.7] 3.755 - tidyr [ -> 1.3.0] 3.755 - tidyselect [ -> 1.2.0] 3.755 - tidyverse [ -> 2.0.0] 3.755 - timechange [ -> 0.2.0] 3.755 - timeDate [ -> 4022.108] 3.755 - tinylabels [ -> 0.2.4] 3.755 - triebeard [ -> 0.4.1] 3.755 - tzdb [ -> 0.4.0] 3.755 - urltools [ -> 1.7.3] 3.755 - uuid [ -> 1.1-1] 3.755 - V8 [ -> 4.4.0] 3.755 - viridisLite [ -> 0.4.2] 3.755 - vroom [ -> 1.6.4] 3.755 - webshot [ -> 0.5.5] 3.755 - WRS2 [ -> 1.1-5] 3.755 - xml2 [ -> 1.3.5] 3.755 - xtable [ -> 1.8-4] 3.755 - zeallot [ -> 0.1.0] 3.755 - zip [ -> 2.3.0] 3.755 3.755 # GitHub --------------------------------------------------------------------- 3.755 - label4MRI [ -> yunshiuan/label4MRI@HEAD] 3.755 - reticulate [ -> rstudio/reticulate@HEAD] 3.755 - rmdfiltr [ -> crsh/rmdfiltr@HEAD] 3.755 3.755 # GitLab --------------------------------------------------------------------- 3.755 - ufs [ -> r-packages/ufs@HEAD] 3.755 3.755 # Local ---------------------------------------------------------------------- 3.755 - equatiomatic [ -> 0.3.1] 3.755 3.755 # RSPM ----------------------------------------------------------------------- 3.755 - assertthat [ -> 0.2.1] 3.755 - BayesFactor [ -> 0.9.12-4.6] 3.755 - BWStest [ -> 0.2.3] 3.755 - contfrac [ -> 1.1-12] 3.755 - deSolve [ -> 1.40] 3.755 - elliptic [ -> 1.4-0] 3.755 - ggside [ -> 0.2.2] 3.755 - ggstatsplot [ -> 0.12.1] 3.755 - gmp [ -> 0.7-3] 3.755 - hypergeo [ -> 1.2-13] 3.755 - kSamples [ -> 1.2-10] 3.755 - openxlsx [ -> 4.2.5] 3.755 - patchwork [ -> 1.1.3] 3.755 - pbapply [ -> 1.4-2] 3.755 - PMCMRplus [ -> 1.9.9] 3.755 - QuantPsyc [ -> 1.5] 3.755 - Routliers [ -> 0.0.0.3] 3.755 - statsExpressions [* -> 1.5.2] 3.755 3.797 # Downloading packages ------------------------------------------------------- 12.81 - Downloading xfun from CRAN ... OK [132.4 Kb in 0.23s] 18.15 - Downloading bslib from CRAN ... OK [5.8 Mb in 2.1s] 25.82 - Downloading jsonlite from CRAN ... OK [1 Mb in 0.37s] 31.44 - Downloading sass from CRAN ... OK [2.9 Mb in 1.2s] 38.13 - Downloading vctrs from CRAN ... OK [944.7 Kb in 0.36s] 44.82 - Downloading fansi from CRAN ... OK [470.8 Kb in 0.27s] 50.12 - Downloading stringr from CRAN ... OK [171.6 Kb in 0.31s] 56.32 - Downloading stringi from CRAN ... OK [7.3 Mb in 2.7s] 65.61 - Downloading utf8 from CRAN ... OK [235.8 Kb in 0.17s] 71.06 - Downloading testthat from CRAN ... OK [722.2 Kb in 0.28s] 76.96 - Downloading Matrix from CRAN ... OK [2 Mb in 1.0s] 78.10 - Downloading KernSmooth from CRAN ... OK [25.4 Kb in 0.35s] 78.49 - Downloading BH from CRAN ... OK [13.3 Mb in 5.0s] 85.07 - Downloading BWStest from RSPM ... OK [363.1 Kb in 0.43s] 85.60 - Downloading Rcpp from CRAN ... OK [2.9 Mb in 1.2s] 86.98 - Downloading BayesFactor from RSPM ... OK [1.7 Mb in 0.87s] 93.57 - Downloading pbapply from RSPM ... OK [14.7 Kb in 0.31s] 101.1 - Downloading mvtnorm from CRAN ... OK [647.9 Kb in 1.3s] 102.6 - Downloading MatrixModels from CRAN ... OK [24.2 Kb in 0.46s] 103.3 - Downloading hypergeo from RSPM ... OK [198.9 Kb in 0.77s] 104.4 - Downloading elliptic from RSPM ... OK [1 Mb in 1.0s] 105.8 - Downloading contfrac from RSPM ... OK [5.5 Kb in 0.5s] 106.5 - Downloading deSolve from RSPM ... OK [1.9 Mb in 1.4s] 108.2 - Downloading coda from CRAN ... OK [72.5 Kb in 0.75s] 109.1 - Downloading RcppEigen from CRAN ... OK [1.4 Mb in 0.75s] 110.1 - Downloading BiocParallel from Bioconductor ... OK [973.7 Kb in 0.57s] 110.9 - Downloading futile.logger from CRAN ... OK [17 Kb in 0.47s] 111.5 - Downloading lambda.r from CRAN ... OK [25.1 Kb in 0.41s] 112.1 - Downloading formatR from CRAN ... OK [93.8 Kb in 0.38s] 112.6 - Downloading futile.options from CRAN ... OK [3.8 Kb in 0.41s] 113.0 - Downloading snow from CRAN ... OK [20 Kb in 0.31s] 120.5 - Downloading cpp11 from CRAN ... OK [293.8 Kb in 0.44s] 121.0 - Downloading BiocVersion from Bioconductor ... OK [973 bytes in 0.28s] 121.4 - Downloading DBI from CRAN ... OK [713.1 Kb in 0.61s] 127.5 - Downloading DescTools from CRAN ... OK [2.5 Mb in 1.1s] 135.9 - Downloading expm from CRAN ... OK [133.6 Kb in 0.42s] 136.4 - Downloading rstudioapi from CRAN ... OK [113 Kb in 0.62s] 137.2 - Downloading Exact from CRAN ... OK [45.1 Kb in 0.32s] 137.8 - Downloading rootSolve from CRAN ... OK [492.3 Kb in 0.67s] 138.6 - Downloading gld from CRAN ... OK [53.5 Kb in 0.52s] 146.1 - Downloading e1071 from CRAN ... OK [306.8 Kb in 0.47s] 146.7 - Downloading proxy from CRAN ... OK [72.9 Kb in 0.17s] 147.0 - Downloading lmom from CRAN ... OK [341.6 Kb in 0.33s] 147.4 - Downloading data.table from CRAN ... OK [5.1 Mb in 2.0s] 149.7 - Downloading readxl from CRAN ... OK [2 Mb in 0.87s] 150.9 - Downloading cellranger from CRAN ... OK [62.4 Kb in 0.3s] 151.4 - Downloading rematch from CRAN ... OK [4.7 Kb in 0.41s] 161.1 - Downloading progress from CRAN ... OK [28.8 Kb in 0.15s] 161.4 - Downloading hms from CRAN ... OK [42.4 Kb in 0.27s] 161.7 - Downloading GPArotation from CRAN ... OK [301.1 Kb in 0.43s] 162.2 - Downloading ModelMetrics from CRAN ... OK [16.7 Kb in 0.23s] 162.5 - Downloading MuMIn from CRAN ... OK [178.7 Kb in 0.31s] 168.5 - Downloading insight from CRAN ... OK [917.2 Kb in 0.59s] 169.1 - Downloading PMCMRplus from RSPM ... OK [258.3 Kb in 0.36s] 169.5 - Downloading multcompView from CRAN ... OK [36.5 Kb in 0.31s] 169.9 - Downloading gmp from RSPM ... OK [163.5 Kb in 0.31s] 170.3 - Downloading Rmpfr from CRAN ... OK [604.2 Kb in 0.41s] 170.8 - Downloading SuppDists from CRAN ... OK [138.5 Kb in 0.31s] 171.1 - Downloading kSamples from RSPM ... OK [74.5 Kb in 0.43s] 176.7 - Downloading QuantPsyc from RSPM ... OK [47.6 Kb in 0.31s] 177.0 - Downloading RColorBrewer from CRAN ... OK [11.4 Kb in 0.25s] 177.3 - Downloading RSpectra from CRAN ... OK [124.1 Kb in 0.14s] 177.5 - Downloading RcppTOML from CRAN ... OK [137.9 Kb in 0.41s] 178.0 - Downloading Routliers from RSPM ... OK [113.3 Kb in 0.41s] 178.4 - Downloading ggplot2 from CRAN ... OK [3 Mb in 1.1s] 179.8 - Downloading gtable from CRAN ... OK [127.1 Kb in 0.26s] 180.1 - Downloading isoband from CRAN ... OK [1.5 Mb in 0.58s] 187.1 - Downloading scales from CRAN ... OK [264.3 Kb in 0.32s] 187.5 - Downloading farver from CRAN ... OK [1.2 Mb in 0.47s] 188.1 - Downloading labeling from CRAN ... OK [9.9 Kb in 0.11s] 188.4 - Downloading munsell from CRAN ... OK [178.4 Kb in 0.16s] 188.6 - Downloading colorspace from CRAN ... OK [2 Mb in 0.86s] 189.7 - Downloading viridisLite from CRAN ... OK [1.2 Mb in 0.55s] 190.3 - Downloading SQUAREM from CRAN ... OK [235.9 Kb in 0.31s] 190.6 - Downloading SparseM from CRAN ... OK [717.9 Kb in 0.41s] 195.9 - Downloading V8 from CRAN ... 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failed to solve: process "/bin/sh -c Rscript -e \"renv::restore()\"" did not complete successfully: exit code: 134

kevinushey commented 11 months ago

https://github.com/Lukas-Novak/neuroanatomical_bases_of_empathy/blob/main/Dockerfile#L89-L90

Does it make a difference if you set those environment variables before trying to run renv::restore()?

Lukas-Novak commented 11 months ago

@kevinushey Yes it does! Placing environmental variable: RENV_WATCHDOG_ENABLED before renv::restore() resolved my issue, many thanks for your help!!!

kevinushey commented 11 months ago

I've figured out the underlying issue; there's a bug in R where sockets are leaked if a call to download.file() fails in some cases. I've pushed a couple of mitigations to the development version of renv, but there are a couple ways to work around this: