R 4.0.1 built with Intel Composer 19.1.1, error in R CMD make check on CentOS 7.7

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R 4.0.1 built with Intel Composer 19.1.1, error in R CMD make check on CentOS 7.7

Ryan Novosielski
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 - [hidden email]
|| \\ University | Sr. Technologist - 973/972.0922 (2x0922) ~*~ RBHS Campus
||  \\    of NJ | Office of Advanced Research Computing - MSB C630, Newark
     `'


______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
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Re: 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
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 - [hidden email]
|| \\ 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 <[hidden email]> 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 - [hidden email]
> || \\ University | Sr. Technologist - 973/972.0922 (2x0922) ~*~ RBHS Campus
> ||  \\    of NJ | Office of Advanced Research Computing - MSB C630, Newark
>     `'
>
>
>

______________________________________________
[hidden email] 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.

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Re: 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

Jeff Newmiller
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 <[hidden email]> 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 - [hidden email]
>|| \\ 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 <[hidden email]>
>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 - [hidden email]
>> || \\ 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.

______________________________________________
[hidden email] 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.
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Re: 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

Martin Maechler
In reply to this post by Ryan Novosielski
>>>>> 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 - [hidden email]
    > || \\ 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 <[hidden email]> 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 - [hidden email]
    >> || \\ University | Sr. Technologist - 973/972.0922 (2x0922) ~*~ RBHS Campus
    >> ||  \\    of NJ | Office of Advanced Research Computing - MSB C630, Newark
    >> `'
    >>
    >>
    >>

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    > and provide commented, minimal, self-contained, reproducible code.

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