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install.packages('RcppParallel')
trying URL 'https://cloud.r-project.org/src/contrib/RcppParallel_5.1.7.tar.gz'
Content type 'application/x-gzip' length 1629119 bytes (1.6 MB)
==================================================
downloaded 1.6 MB
* installing *source* package 'RcppParallel' ...
** package 'RcppParallel' successfully unpacked and MD5 sums checked
** using staged installation
** preparing to configure package 'RcppParallel' ...
*** configured file: 'R/tbb-autodetected.R.in' => 'R/tbb-autodetected.R'
*** configured file: 'src/Makevars.in' => 'src/Makevars'
*** configured file: 'src/install.libs.R.in' => 'src/install.libs.R'
** finished configure for package 'RcppParallel'
** libs
(tbb) Building TBB using bundled sources ...
make[1]: Entering directory '/scratch/nm31/ta0341/tmp/RtmpVAGh4q/R.INSTALL2e156974684a7d/RcppParallel/src/tbb/src'
../build/linux.inc:31: "Unknown Intel compiler"
OS: linux
arch=intel64
compiler=icc
runtime=cc8.5.0_libc2.28_kernel4.18.0
tbb_build_prefix=linux_intel64_icc_cc8.5.0_libc2.28_kernel4.18.0
work_dir=/scratch/nm31/ta0341/tmp/RtmpVAGh4q/R.INSTALL2e156974684a7d/RcppParallel/src/build/linux_intel64_icc_cc8.5.0_libc2.28_kernel4.18.0_release
make[1]: Leaving directory '/scratch/nm31/ta0341/tmp/RtmpVAGh4q/R.INSTALL2e156974684a7d/RcppParallel/src/tbb/src'
make[1]: Entering directory '/scratch/nm31/ta0341/tmp/RtmpVAGh4q/R.INSTALL2e156974684a7d/RcppParallel/src/tbb/src'
../build/linux.inc:31: "Unknown Intel compiler"
Created ../build/lib_release directory
make -C "../build/lib_release" -r -f ../../build/Makefile.tbb cfg=release
make[2]: Entering directory '/scratch/nm31/ta0341/tmp/RtmpVAGh4q/R.INSTALL2e156974684a7d/RcppParallel/src/tbb/build/lib_release'
/bin/sh: icc: command not found
/bin/sh: icc: command not found
/bin/sh: icc: command not found
../../build/Makefile.tbb:28: CONFIG: cfg=release arch=intel64 compiler=icc target=linux runtime=cc8.5.0_libc2.28_kernel4.18.0
/bin/sh: icc: command not found
icpc -I../inst/include -o concurrent_hash_map.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -strict-ansi -D_FORTIFY_SOURCE=2 -fpic -D__TBB_BUILD=1 -w1 -g -O2 -DTBB_NO_LEGACY=1 -I../../src -I../../src/rml/include -I../../include ../../src/tbb/concurrent_hash_map.cpp
make[2]: icpc: Command not found
make[2]: *** [../../build/common_rules.inc:76: concurrent_hash_map.o] Error 127
make[2]: Leaving directory '/scratch/nm31/ta0341/tmp/RtmpVAGh4q/R.INSTALL2e156974684a7d/RcppParallel/src/tbb/build/lib_release'
make[1]: *** [Makefile:100: tbb_release] Error 2
make[1]: Leaving directory '/scratch/nm31/ta0341/tmp/RtmpVAGh4q/R.INSTALL2e156974684a7d/RcppParallel/src/tbb/src'
icpc -std=gnu++14 -I"/apps/R/4.2.2/lib64/R/include" -DNDEBUG -I../inst/include -I/usr/local/include -std=gnu++11 -DRCPP_PARALLEL_USE_TBB=1 -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -fpic -g -O2 -c init.cpp -o init.o
/bin/sh: icpc: command not found
make: *** [/apps/R/4.2.2/lib64/R/etc/Makeconf:178: init.o] Error 127
ERROR: compilation failed for package 'RcppParallel'
* removing '/home/554/ta0341/R/x86_64-pc-linux-gnu-library/4.2/RcppParallel'
The downloaded source packages are in
'/scratch/nm31/ta0341/tmp/Rtmp5zVBSH/downloaded_packages'
Warning message:
In install.packages("RcppParallel") :
installation of package 'RcppParallel' had non-zero exit status
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theo-allnutt-bioinformatics commentedon Mar 15, 2023
After installing Rcpp, which worked ok, tried intel-compiler/2021.6.0:
eddelbuettel commentedon Mar 15, 2023
Could you share some pertinent details about your OS, version, compiler versions etc? In a nutshell, if it is too non-standard it may be hard for anyone to help you.
kevinushey commentedon Mar 15, 2023
My only guess is that your version of
icpc
is too old, or you need to install a newer one. I don't use it, so the amount of help I can provide is pretty low.theo-allnutt-bioinformatics commentedon Mar 15, 2023
Hi,
OS info:
NAME="Rocky Linux"
VERSION="8.7 (Green Obsidian)"
ID="rocky"
ID_LIKE="rhel centos fedora"
VERSION_ID="8.7"
PLATFORM_ID="platform:el8"
PRETTY_NAME="Rocky Linux 8.7 (Green Obsidian)"
ANSI_COLOR="0;32"
LOGO="fedora-logo-icon"
CPE_NAME="cpe:/o:rocky:rocky:8:GA"
HOME_URL="https://rockylinux.org/"
BUG_REPORT_URL="https://bugs.rockylinux.org/"
ROCKY_SUPPORT_PRODUCT="Rocky-Linux-8"
ROCKY_SUPPORT_PRODUCT_VERSION="8.7"
REDHAT_SUPPORT_PRODUCT="Rocky Linux"
REDHAT_SUPPORT_PRODUCT_VERSION="8.7"
I am working on an HPC login node (don't need many resources for script I need to run which uses 'rbiom' of which rcppParallel is a dependency. In turn, rbiom is used by calculate_diversity.R here: https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-4)
I am not sure which compiler R is using, but I normally have to load this module for R installs to work:
module load intel-compiler/2021.6.0
Thanks.
eddelbuettel commentedon Mar 16, 2023
R can tell you:
That is my system here where
~/.R/Makevars
takes over. Otherwise in a clean(er) Docker setup:(from today's rocker/r-base with R 4.2.3)
theo-allnutt-bioinformatics commentedon Mar 16, 2023
As above - using icc
R CMD config CC
icc
eddelbuettel commentedon Mar 16, 2023
What does
icc --version
(or alike, not anicc
user myself) say?theo-allnutt-bioinformatics commentedon Mar 16, 2023
As above, the module used is:
icc (ICC) 2021.6.0 20220226
Copyright (C) 1985-2022 Intel Corporation. All rights reserved.
But can also use 2021.8.0
There is no ~/.R on my system so do not know how to change to gcc. If I unload icc I get the first set of errors above.
eddelbuettel commentedon Mar 16, 2023
See https://rstudio.github.io/r-manuals/r-admin/Add-on-packages.html#customizing-package-compilation for that
theo-allnutt-bioinformatics commentedon Mar 16, 2023
Thanks. Can't do that on my system as far as I know so I'll just leave it... Happens a lot with R.
eddelbuettel commentedon Mar 16, 2023
We'll probably close this then as the issue appears to be more related to your specific setup than a general actionable item for all users of RcppParallel. I know this can be frustrating for you but there simply is not much for us here.
theo-allnutt-bioinformatics commentedon Mar 16, 2023
Yes, no problem. Thanks for your help.
eddelbuettel commentedon Mar 16, 2023
On RHEL/CentOS/Rockly/... one often needs devtoolset to access a recent enough compiler. That is known to work for building current CRAN packages on these OS variants with their somewhat dated default tool stacks.
Switching to yet another compiler is likely tricky. Sorry.
eddelbuettel commentedon Aug 18, 2023
Closing as duplicate of #184