Ryan Novosielski
2020-Jun-14 02:16 UTC
[R] R 4.0.1 built with Intel Composer 19.1.1, error in R CMD make check on CentOS 7.7
Hi there,
Built R 4.0.1 with the Intel Composer 19.1.1. Build seems to go fine. I built it
like this:
module purge
module load intel/19.1.1
module list
export CC=icc
export CXX=icpc
export F77=ifort
export FC=ifort
export AR=xiar
export LD=xild
export CFLAGS="-O3 -ipo -qopenmp -axAVX,CORE-AVX2,CORE-AVX512"
export F77FLAGS="-O3 -ipo -qopenmp -axAVX,CORE-AVX2,CORE-AVX512"
export FFLAGS="-O3 -ipo -qopenmp -axAVX,CORE-AVX2,CORE-AVX512"
export CXXFLAGS="-O3 -ipo -qopenmp -axAVX,CORE-AVX2,CORE-AVX512"
export MKL="-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5
-lpthread"
VERSION=4.0.1
/scratch/novosirj/install-files/R-${VERSION}/configure
--with-blas="$MKL" --with-lapack
--prefix=/opt/sw/packages/intel-19_1/R-Project/${VERSION} && \
make -j32 && make check && make -j32 install
However, the ?make check" phase fails at this part:
Testing examples for package ?parallel?
make[2]: Leaving directory
`/mnt/scratch/novosirj/R-4.0.1-intel-19.1-build/tests/Examples'
make[1]: Leaving directory
`/mnt/scratch/novosirj/R-4.0.1-intel-19.1-build/tests'
make[1]: Entering directory
`/mnt/scratch/novosirj/R-4.0.1-intel-19.1-build/tests'
running strict specific tests
make[2]: Entering directory
`/mnt/scratch/novosirj/R-4.0.1-intel-19.1-build/tests'
running code in
'/scratch/novosirj/install-files/R-4.0.1/tests/eval-etc.R' ... OK
comparing 'eval-etc.Rout' to
'/scratch/novosirj/install-files/R-4.0.1/tests/eval-etc.Rout.save' ...
OK
running code in
'/scratch/novosirj/install-files/R-4.0.1/tests/simple-true.R' ... OK
comparing 'simple-true.Rout' to
'/scratch/novosirj/install-files/R-4.0.1/tests/simple-true.Rout.save'
... OK
running code in
'/scratch/novosirj/install-files/R-4.0.1/tests/arith-true.R' ... OK
comparing 'arith-true.Rout' to
'/scratch/novosirj/install-files/R-4.0.1/tests/arith-true.Rout.save' ...
OK
running code in '/scratch/novosirj/install-files/R-4.0.1/tests/arith.R'
... OK
comparing 'arith.Rout' to
'/scratch/novosirj/install-files/R-4.0.1/tests/arith.Rout.save' ... OK
running code in
'/scratch/novosirj/install-files/R-4.0.1/tests/lm-tests.R' ... OK
comparing 'lm-tests.Rout' to
'/scratch/novosirj/install-files/R-4.0.1/tests/lm-tests.Rout.save' ...
OK
/bin/sh: line 1: 62064 Segmentation fault (core dumped) LANGUAGE=en
LC_ALL=C SRCDIR=/scratch/novosirj/install-files/R-4.0.1/tests
R_DEFAULT_PACKAGES= ../bin/R --vanilla <
/scratch/novosirj/install-files/R-4.0.1/tests/ok-errors.R >
ok-errors.Rout.fail 2>&1
running code in
'/scratch/novosirj/install-files/R-4.0.1/tests/ok-errors.R' ...make[2]:
*** [ok-errors.Rout] Error 1
make[2]: Leaving directory
`/mnt/scratch/novosirj/R-4.0.1-intel-19.1-build/tests'
make[1]: *** [test-Specific] Error 2
make[1]: Leaving directory
`/mnt/scratch/novosirj/R-4.0.1-intel-19.1-build/tests'
make: *** [test-all-basics] Error 1
Is this something I should be concerned about, or something I can fix? Not
seeing any real information about what?s going wrong here. Here?s what?s
contained in ok-errors.Rout.fail:
---
R version 4.0.1 (2020-06-06) -- "See Things Now"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> #### STRICT test suite in the spirit of no-segfaults,
> #### but with explicit statements.
>
> options(error=expression(NULL))
> stop("test of `options(error=expression(NULL))'")
Error: test of `options(error=expression(NULL))'>
> if(FALSE) {
+ ## these ought to work on machines with enough memory
+ ## These segfaulted in 1.3.x , give "could not allocate" errors now
+ integer(2^30+1)
+ double(2^30+1)
+ complex(2^30+1)
+ character(2^30+1)
+ vector("list", 2^30+2)
+ }>
> ## bad infinite recursion / on.exit / ... interactions
> ## catch the error to permit different error messages emitted
> ## (handling of infinite recursion is different in the AST interpreter
> ## and the byte-code interpreter)
>
> bar <- function() 1+1
> foo <- function() { on.exit(bar()); foo() }
> tryCatch(foo(), error=function(x) TRUE) # now simple "infinite
recursion"
*** caught segfault ***
address 0x7fff4dc1b9f8, cause 'memory not mapped'
Traceback:
1: foo()
2: foo()
3: foo()
4: foo()
...
2712: foo()
2713: foo()
2714: foo()
2715: foo()
2716: foo()
2717: foo()
2718: foo()
2719: doTryCatch(return(expr), name, parentenv, handler)
2720: tryCatchOne(expr, names, parentenv, handlers[[1L]])
2721: tryCatchList(expr, classes, parentenv, handlers)
2722: tryCatch(foo(), error = function(x) TRUE)
An irrecoverable exception occurred. R is aborting now ...
---
Thanks in advance.
--
____
|| \\UTGERS, |---------------------------*O*---------------------------
||_// the State | Ryan Novosielski - novosirj at rutgers.edu
|| \\ University | Sr. Technologist - 973/972.0922 (2x0922) ~*~ RBHS Campus
|| \\ of NJ | Office of Advanced Research Computing - MSB C630, Newark
`'
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Ryan Novosielski
2020-Jun-17 22:04 UTC
[R] R 4.0.1/R-devel 2020-06-16-r78702 built with Intel Composer 19.1.1, error in R CMD make check on CentOS 7.7
Same story with R-devel 2020-06-16-r78702, everything else the same. Should I be
reporting this someplace else?
--
____
|| \\UTGERS, |---------------------------*O*---------------------------
||_// the State | Ryan Novosielski - novosirj at rutgers.edu
|| \\ University | Sr. Technologist - 973/972.0922 (2x0922) ~*~ RBHS Campus
|| \\ of NJ | Office of Advanced Research Computing - MSB C630, Newark
`'
> On Jun 13, 2020, at 10:16 PM, Ryan Novosielski <novosirj at
rutgers.edu> wrote:
>
> Signed PGP part
> Hi there,
>
> Built R 4.0.1 with the Intel Composer 19.1.1. Build seems to go fine. I
built it like this:
>
> module purge
> module load intel/19.1.1
> module list
>
> export CC=icc
> export CXX=icpc
> export F77=ifort
> export FC=ifort
> export AR=xiar
> export LD=xild
>
> export CFLAGS="-O3 -ipo -qopenmp -axAVX,CORE-AVX2,CORE-AVX512"
> export F77FLAGS="-O3 -ipo -qopenmp -axAVX,CORE-AVX2,CORE-AVX512"
> export FFLAGS="-O3 -ipo -qopenmp -axAVX,CORE-AVX2,CORE-AVX512"
> export CXXFLAGS="-O3 -ipo -qopenmp -axAVX,CORE-AVX2,CORE-AVX512"
> export MKL="-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5
-lpthread"
>
> VERSION=4.0.1
>
> /scratch/novosirj/install-files/R-${VERSION}/configure
--with-blas="$MKL" --with-lapack
--prefix=/opt/sw/packages/intel-19_1/R-Project/${VERSION} && \
> make -j32 && make check && make -j32 install
>
> However, the ?make check" phase fails at this part:
>
> Testing examples for package ?parallel?
> make[2]: Leaving directory
`/mnt/scratch/novosirj/R-4.0.1-intel-19.1-build/tests/Examples'
> make[1]: Leaving directory
`/mnt/scratch/novosirj/R-4.0.1-intel-19.1-build/tests'
> make[1]: Entering directory
`/mnt/scratch/novosirj/R-4.0.1-intel-19.1-build/tests'
> running strict specific tests
> make[2]: Entering directory
`/mnt/scratch/novosirj/R-4.0.1-intel-19.1-build/tests'
> running code in
'/scratch/novosirj/install-files/R-4.0.1/tests/eval-etc.R' ... OK
> comparing 'eval-etc.Rout' to
'/scratch/novosirj/install-files/R-4.0.1/tests/eval-etc.Rout.save' ...
OK
> running code in
'/scratch/novosirj/install-files/R-4.0.1/tests/simple-true.R' ... OK
> comparing 'simple-true.Rout' to
'/scratch/novosirj/install-files/R-4.0.1/tests/simple-true.Rout.save'
... OK
> running code in
'/scratch/novosirj/install-files/R-4.0.1/tests/arith-true.R' ... OK
> comparing 'arith-true.Rout' to
'/scratch/novosirj/install-files/R-4.0.1/tests/arith-true.Rout.save' ...
OK
> running code in
'/scratch/novosirj/install-files/R-4.0.1/tests/arith.R' ... OK
> comparing 'arith.Rout' to
'/scratch/novosirj/install-files/R-4.0.1/tests/arith.Rout.save' ... OK
> running code in
'/scratch/novosirj/install-files/R-4.0.1/tests/lm-tests.R' ... OK
> comparing 'lm-tests.Rout' to
'/scratch/novosirj/install-files/R-4.0.1/tests/lm-tests.Rout.save' ...
OK
> /bin/sh: line 1: 62064 Segmentation fault (core dumped) LANGUAGE=en
LC_ALL=C SRCDIR=/scratch/novosirj/install-files/R-4.0.1/tests
R_DEFAULT_PACKAGES= ../bin/R --vanilla <
/scratch/novosirj/install-files/R-4.0.1/tests/ok-errors.R >
ok-errors.Rout.fail 2>&1
> running code in
'/scratch/novosirj/install-files/R-4.0.1/tests/ok-errors.R' ...make[2]:
*** [ok-errors.Rout] Error 1
> make[2]: Leaving directory
`/mnt/scratch/novosirj/R-4.0.1-intel-19.1-build/tests'
> make[1]: *** [test-Specific] Error 2
> make[1]: Leaving directory
`/mnt/scratch/novosirj/R-4.0.1-intel-19.1-build/tests'
> make: *** [test-all-basics] Error 1
>
> Is this something I should be concerned about, or something I can fix? Not
seeing any real information about what?s going wrong here. Here?s what?s
contained in ok-errors.Rout.fail:
>
> ---
> R version 4.0.1 (2020-06-06) -- "See Things Now"
> Copyright (C) 2020 The R Foundation for Statistical Computing
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
>> #### STRICT test suite in the spirit of no-segfaults,
>> #### but with explicit statements.
>>
>> options(error=expression(NULL))
>> stop("test of `options(error=expression(NULL))'")
> Error: test of `options(error=expression(NULL))'
>>
>> if(FALSE) {
> + ## these ought to work on machines with enough memory
> + ## These segfaulted in 1.3.x , give "could not allocate"
errors now
> + integer(2^30+1)
> + double(2^30+1)
> + complex(2^30+1)
> + character(2^30+1)
> + vector("list", 2^30+2)
> + }
>>
>> ## bad infinite recursion / on.exit / ... interactions
>> ## catch the error to permit different error messages emitted
>> ## (handling of infinite recursion is different in the AST
interpreter
>> ## and the byte-code interpreter)
>>
>> bar <- function() 1+1
>> foo <- function() { on.exit(bar()); foo() }
>> tryCatch(foo(), error=function(x) TRUE) # now simple "infinite
recursion"
>
> *** caught segfault ***
> address 0x7fff4dc1b9f8, cause 'memory not mapped'
>
> Traceback:
> 1: foo()
> 2: foo()
> 3: foo()
> 4: foo()
>
> ...
>
> 2712: foo()
> 2713: foo()
> 2714: foo()
> 2715: foo()
> 2716: foo()
> 2717: foo()
> 2718: foo()
> 2719: doTryCatch(return(expr), name, parentenv, handler)
> 2720: tryCatchOne(expr, names, parentenv, handlers[[1L]])
> 2721: tryCatchList(expr, classes, parentenv, handlers)
> 2722: tryCatch(foo(), error = function(x) TRUE)
> An irrecoverable exception occurred. R is aborting now ...
> ---
>
> Thanks in advance.
>
> --
> ____
> || \\UTGERS, |---------------------------*O*---------------------------
> ||_// the State | Ryan Novosielski - novosirj at rutgers.edu
> || \\ University | Sr. Technologist - 973/972.0922 (2x0922) ~*~ RBHS Campus
> || \\ of NJ | Office of Advanced Research Computing - MSB C630, Newark
> `'
>
>
>
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Jeff Newmiller
2020-Jun-18 00:13 UTC
[R] R 4.0.1/R-devel 2020-06-16-r78702 built with Intel Composer 19.1.1, error in R CMD make check on CentOS 7.7
Read the Posting Guide ... this is definitely off-topic here. I think this is an r-devel question, though I really don't know whether you will find interest in discussing compilation of R with a non-standard tool chain. There are a lot of "moving parts" in R and it can be challenging just to keep up with upgrades in the standard tool chain without getting caught up in yet another one. On June 17, 2020 3:04:30 PM PDT, Ryan Novosielski <novosirj at rutgers.edu> wrote:>Same story with R-devel 2020-06-16-r78702, everything else the same. >Should I be reporting this someplace else? > >-- >____ >|| \\UTGERS, >|---------------------------*O*--------------------------- >||_// the State | Ryan Novosielski - novosirj at rutgers.edu >|| \\ University | Sr. Technologist - 973/972.0922 (2x0922) ~*~ RBHS >Campus >|| \\ of NJ | Office of Advanced Research Computing - MSB C630, >Newark > `' > >> On Jun 13, 2020, at 10:16 PM, Ryan Novosielski <novosirj at rutgers.edu> >wrote: >> >> Signed PGP part >> Hi there, >> >> Built R 4.0.1 with the Intel Composer 19.1.1. Build seems to go fine. >I built it like this: >> >> module purge >> module load intel/19.1.1 >> module list >> >> export CC=icc >> export CXX=icpc >> export F77=ifort >> export FC=ifort >> export AR=xiar >> export LD=xild >> >> export CFLAGS="-O3 -ipo -qopenmp -axAVX,CORE-AVX2,CORE-AVX512" >> export F77FLAGS="-O3 -ipo -qopenmp -axAVX,CORE-AVX2,CORE-AVX512" >> export FFLAGS="-O3 -ipo -qopenmp -axAVX,CORE-AVX2,CORE-AVX512" >> export CXXFLAGS="-O3 -ipo -qopenmp -axAVX,CORE-AVX2,CORE-AVX512" >> export MKL="-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 >-lpthread" >> >> VERSION=4.0.1 >> >> /scratch/novosirj/install-files/R-${VERSION}/configure >--with-blas="$MKL" --with-lapack >--prefix=/opt/sw/packages/intel-19_1/R-Project/${VERSION} && \ >> make -j32 && make check && make -j32 install >> >> However, the ?make check" phase fails at this part: >> >> Testing examples for package ?parallel? >> make[2]: Leaving directory >`/mnt/scratch/novosirj/R-4.0.1-intel-19.1-build/tests/Examples' >> make[1]: Leaving directory >`/mnt/scratch/novosirj/R-4.0.1-intel-19.1-build/tests' >> make[1]: Entering directory >`/mnt/scratch/novosirj/R-4.0.1-intel-19.1-build/tests' >> running strict specific tests >> make[2]: Entering directory >`/mnt/scratch/novosirj/R-4.0.1-intel-19.1-build/tests' >> running code in >'/scratch/novosirj/install-files/R-4.0.1/tests/eval-etc.R' ... OK >> comparing 'eval-etc.Rout' to >'/scratch/novosirj/install-files/R-4.0.1/tests/eval-etc.Rout.save' ... >OK >> running code in >'/scratch/novosirj/install-files/R-4.0.1/tests/simple-true.R' ... OK >> comparing 'simple-true.Rout' to >'/scratch/novosirj/install-files/R-4.0.1/tests/simple-true.Rout.save' >... OK >> running code in >'/scratch/novosirj/install-files/R-4.0.1/tests/arith-true.R' ... OK >> comparing 'arith-true.Rout' to >'/scratch/novosirj/install-files/R-4.0.1/tests/arith-true.Rout.save' >... OK >> running code in >'/scratch/novosirj/install-files/R-4.0.1/tests/arith.R' ... OK >> comparing 'arith.Rout' to >'/scratch/novosirj/install-files/R-4.0.1/tests/arith.Rout.save' ... OK >> running code in >'/scratch/novosirj/install-files/R-4.0.1/tests/lm-tests.R' ... OK >> comparing 'lm-tests.Rout' to >'/scratch/novosirj/install-files/R-4.0.1/tests/lm-tests.Rout.save' ... >OK >> /bin/sh: line 1: 62064 Segmentation fault (core dumped) >LANGUAGE=en LC_ALL=C >SRCDIR=/scratch/novosirj/install-files/R-4.0.1/tests >R_DEFAULT_PACKAGES= ../bin/R --vanilla < >/scratch/novosirj/install-files/R-4.0.1/tests/ok-errors.R > >ok-errors.Rout.fail 2>&1 >> running code in >'/scratch/novosirj/install-files/R-4.0.1/tests/ok-errors.R' ...make[2]: >*** [ok-errors.Rout] Error 1 >> make[2]: Leaving directory >`/mnt/scratch/novosirj/R-4.0.1-intel-19.1-build/tests' >> make[1]: *** [test-Specific] Error 2 >> make[1]: Leaving directory >`/mnt/scratch/novosirj/R-4.0.1-intel-19.1-build/tests' >> make: *** [test-all-basics] Error 1 >> >> Is this something I should be concerned about, or something I can >fix? Not seeing any real information about what?s going wrong here. >Here?s what?s contained in ok-errors.Rout.fail: >> >> --- >> R version 4.0.1 (2020-06-06) -- "See Things Now" >> Copyright (C) 2020 The R Foundation for Statistical Computing >> Platform: x86_64-pc-linux-gnu (64-bit) >> >> R is free software and comes with ABSOLUTELY NO WARRANTY. >> You are welcome to redistribute it under certain conditions. >> Type 'license()' or 'licence()' for distribution details. >> >> R is a collaborative project with many contributors. >> Type 'contributors()' for more information and >> 'citation()' on how to cite R or R packages in publications. >> >> Type 'demo()' for some demos, 'help()' for on-line help, or >> 'help.start()' for an HTML browser interface to help. >> Type 'q()' to quit R. >> >>> #### STRICT test suite in the spirit of no-segfaults, >>> #### but with explicit statements. >>> >>> options(error=expression(NULL)) >>> stop("test of `options(error=expression(NULL))'") >> Error: test of `options(error=expression(NULL))' >>> >>> if(FALSE) { >> + ## these ought to work on machines with enough memory >> + ## These segfaulted in 1.3.x , give "could not allocate" errors >now >> + integer(2^30+1) >> + double(2^30+1) >> + complex(2^30+1) >> + character(2^30+1) >> + vector("list", 2^30+2) >> + } >>> >>> ## bad infinite recursion / on.exit / ... interactions >>> ## catch the error to permit different error messages emitted >>> ## (handling of infinite recursion is different in the AST >interpreter >>> ## and the byte-code interpreter) >>> >>> bar <- function() 1+1 >>> foo <- function() { on.exit(bar()); foo() } >>> tryCatch(foo(), error=function(x) TRUE) # now simple "infinite >recursion" >> >> *** caught segfault *** >> address 0x7fff4dc1b9f8, cause 'memory not mapped' >> >> Traceback: >> 1: foo() >> 2: foo() >> 3: foo() >> 4: foo() >> >> ... >> >> 2712: foo() >> 2713: foo() >> 2714: foo() >> 2715: foo() >> 2716: foo() >> 2717: foo() >> 2718: foo() >> 2719: doTryCatch(return(expr), name, parentenv, handler) >> 2720: tryCatchOne(expr, names, parentenv, handlers[[1L]]) >> 2721: tryCatchList(expr, classes, parentenv, handlers) >> 2722: tryCatch(foo(), error = function(x) TRUE) >> An irrecoverable exception occurred. R is aborting now ... >> --- >> >> Thanks in advance. >> >> -- >> ____ >> || \\UTGERS, >|---------------------------*O*--------------------------- >> ||_// the State | Ryan Novosielski - novosirj at rutgers.edu >> || \\ University | Sr. Technologist - 973/972.0922 (2x0922) ~*~ RBHS >Campus >> || \\ of NJ | Office of Advanced Research Computing - MSB C630, >Newark >> `' >> >> >>-- Sent from my phone. Please excuse my brevity.
Martin Maechler
2020-Jun-18 07:14 UTC
[R] R 4.0.1/R-devel 2020-06-16-r78702 built with Intel Composer 19.1.1, error in R CMD make check on CentOS 7.7
>>>>> Ryan Novosielski >>>>> on Wed, 17 Jun 2020 22:04:30 +0000 writes:> Same story with R-devel 2020-06-16-r78702, everything else the same. Should I be reporting this someplace else? Well, maybe Intel? {I've never heard of 'Intel Composer', and to me it does not look like Free / Open Source Software so why should I care} In any case, such issues belong more to the R-devel mailing list than R-help. Best regards, Martin Maechler ETH Zurich and R Core team > ____ > || \\UTGERS, |---------------------------*O*--------------------------- > ||_// the State | Ryan Novosielski - novosirj at rutgers.edu > || \\ University | Sr. Technologist - 973/972.0922 (2x0922) ~*~ RBHS Campus > || \\ of NJ | Office of Advanced Research Computing - MSB C630, Newark > `' >> On Jun 13, 2020, at 10:16 PM, Ryan Novosielski <novosirj at rutgers.edu> wrote: >> >> Signed PGP part >> Hi there, >> >> Built R 4.0.1 with the Intel Composer 19.1.1. Build seems to go fine. I built it like this: >> >> module purge >> module load intel/19.1.1 >> module list >> >> export CC=icc >> export CXX=icpc >> export F77=ifort >> export FC=ifort >> export AR=xiar >> export LD=xild >> >> export CFLAGS="-O3 -ipo -qopenmp -axAVX,CORE-AVX2,CORE-AVX512" >> export F77FLAGS="-O3 -ipo -qopenmp -axAVX,CORE-AVX2,CORE-AVX512" >> export FFLAGS="-O3 -ipo -qopenmp -axAVX,CORE-AVX2,CORE-AVX512" >> export CXXFLAGS="-O3 -ipo -qopenmp -axAVX,CORE-AVX2,CORE-AVX512" >> export MKL="-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread" >> >> VERSION=4.0.1 >> >> /scratch/novosirj/install-files/R-${VERSION}/configure --with-blas="$MKL" --with-lapack --prefix=/opt/sw/packages/intel-19_1/R-Project/${VERSION} && \ >> make -j32 && make check && make -j32 install >> >> However, the ?make check" phase fails at this part: >> >> Testing examples for package ?parallel? >> make[2]: Leaving directory `/mnt/scratch/novosirj/R-4.0.1-intel-19.1-build/tests/Examples' >> make[1]: Leaving directory `/mnt/scratch/novosirj/R-4.0.1-intel-19.1-build/tests' >> make[1]: Entering directory `/mnt/scratch/novosirj/R-4.0.1-intel-19.1-build/tests' >> running strict specific tests >> make[2]: Entering directory `/mnt/scratch/novosirj/R-4.0.1-intel-19.1-build/tests' >> running code in '/scratch/novosirj/install-files/R-4.0.1/tests/eval-etc.R' ... OK >> comparing 'eval-etc.Rout' to '/scratch/novosirj/install-files/R-4.0.1/tests/eval-etc.Rout.save' ... OK >> running code in '/scratch/novosirj/install-files/R-4.0.1/tests/simple-true.R' ... OK >> comparing 'simple-true.Rout' to '/scratch/novosirj/install-files/R-4.0.1/tests/simple-true.Rout.save' ... OK >> running code in '/scratch/novosirj/install-files/R-4.0.1/tests/arith-true.R' ... OK >> comparing 'arith-true.Rout' to '/scratch/novosirj/install-files/R-4.0.1/tests/arith-true.Rout.save' ... OK >> running code in '/scratch/novosirj/install-files/R-4.0.1/tests/arith.R' ... OK >> comparing 'arith.Rout' to '/scratch/novosirj/install-files/R-4.0.1/tests/arith.Rout.save' ... OK >> running code in '/scratch/novosirj/install-files/R-4.0.1/tests/lm-tests.R' ... OK >> comparing 'lm-tests.Rout' to '/scratch/novosirj/install-files/R-4.0.1/tests/lm-tests.Rout.save' ... OK >> /bin/sh: line 1: 62064 Segmentation fault (core dumped) LANGUAGE=en LC_ALL=C SRCDIR=/scratch/novosirj/install-files/R-4.0.1/tests R_DEFAULT_PACKAGES= ../bin/R --vanilla < /scratch/novosirj/install-files/R-4.0.1/tests/ok-errors.R > ok-errors.Rout.fail 2>&1 >> running code in '/scratch/novosirj/install-files/R-4.0.1/tests/ok-errors.R' ...make[2]: *** [ok-errors.Rout] Error 1 >> make[2]: Leaving directory `/mnt/scratch/novosirj/R-4.0.1-intel-19.1-build/tests' >> make[1]: *** [test-Specific] Error 2 >> make[1]: Leaving directory `/mnt/scratch/novosirj/R-4.0.1-intel-19.1-build/tests' >> make: *** [test-all-basics] Error 1 >> >> Is this something I should be concerned about, or something I can fix? Not seeing any real information about what?s going wrong here. Here?s what?s contained in ok-errors.Rout.fail: >> >> --- >> R version 4.0.1 (2020-06-06) -- "See Things Now" >> Copyright (C) 2020 The R Foundation for Statistical Computing >> Platform: x86_64-pc-linux-gnu (64-bit) >> >> R is free software and comes with ABSOLUTELY NO WARRANTY. >> You are welcome to redistribute it under certain conditions. >> Type 'license()' or 'licence()' for distribution details. >> >> R is a collaborative project with many contributors. >> Type 'contributors()' for more information and >> 'citation()' on how to cite R or R packages in publications. >> >> Type 'demo()' for some demos, 'help()' for on-line help, or >> 'help.start()' for an HTML browser interface to help. >> Type 'q()' to quit R. >> >>> #### STRICT test suite in the spirit of no-segfaults, >>> #### but with explicit statements. >>> >>> options(error=expression(NULL)) >>> stop("test of `options(error=expression(NULL))'") >> Error: test of `options(error=expression(NULL))' >>> >>> if(FALSE) { >> + ## these ought to work on machines with enough memory >> + ## These segfaulted in 1.3.x , give "could not allocate" errors now >> + integer(2^30+1) >> + double(2^30+1) >> + complex(2^30+1) >> + character(2^30+1) >> + vector("list", 2^30+2) >> + } >>> >>> ## bad infinite recursion / on.exit / ... interactions >>> ## catch the error to permit different error messages emitted >>> ## (handling of infinite recursion is different in the AST interpreter >>> ## and the byte-code interpreter) >>> >>> bar <- function() 1+1 >>> foo <- function() { on.exit(bar()); foo() } >>> tryCatch(foo(), error=function(x) TRUE) # now simple "infinite recursion" >> >> *** caught segfault *** >> address 0x7fff4dc1b9f8, cause 'memory not mapped' >> >> Traceback: >> 1: foo() >> 2: foo() >> 3: foo() >> 4: foo() >> >> ... >> >> 2712: foo() >> 2713: foo() >> 2714: foo() >> 2715: foo() >> 2716: foo() >> 2717: foo() >> 2718: foo() >> 2719: doTryCatch(return(expr), name, parentenv, handler) >> 2720: tryCatchOne(expr, names, parentenv, handlers[[1L]]) >> 2721: tryCatchList(expr, classes, parentenv, handlers) >> 2722: tryCatch(foo(), error = function(x) TRUE) >> An irrecoverable exception occurred. R is aborting now ... >> --- >> >> Thanks in advance. >> >> -- >> ____ >> || \\UTGERS, |---------------------------*O*--------------------------- >> ||_// the State | Ryan Novosielski - novosirj at rutgers.edu >> || \\ University | Sr. Technologist - 973/972.0922 (2x0922) ~*~ RBHS Campus >> || \\ of NJ | Office of Advanced Research Computing - MSB C630, Newark >> `' >> >> >> > x[DELETED ATTACHMENT signature.asc, application/pgp-signature] > ______________________________________________ > 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.