Version 2.0.0 fails to install on R 4.0.2 #104

frasernutricia · 2022-02-01T06:51:51Z

Hi,
as of 2.0.0 nloptr does not install on our R system. I've put the error below and sessionInfo(). I don't understand the error. Any advice much appreciated! thanks. Fraser

install.packages("nloptr")
Installing package into ‘/home/sagemaker-user/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/nloptr_2.0.0.tar.gz'
Content type 'application/x-gzip' length 2219414 bytes (2.1 MB)
==================================================
downloaded 2.1 MB

installing source package ‘nloptr’ ...
** package ‘nloptr’ successfully unpacked and MD5 sums checked
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -std=gnu++11 accepts -g... yes
checking how to run the C++ preprocessor... g++ -std=gnu++11 -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ -std=gnu++11 accepts -g... (cached) yes
checking for pkg-config... /usr/bin/pkg-config
checking if pkg-config knows NLopt... no
using NLopt via local cmake build on x86_64
set CMAKE_BIN=/usr/bin/cmake
set CC=gcc
set CFLAGS=-I/usr/local/include -fpic -g -O2
set CXX=g++
set CXXFLAGS=-std=gnu++11 -I/usr/local/include -fpic -g -O2
set LDFLAGS=-L/usr/local/lib
CMake Error: The source directory "/tmp/RtmpEKY5cd/R.INSTALL44a59ba24ad/nloptr/src/nlopt-build" does not exist.
Specify --help for usage, or press the help button on the CMake GUI.
Unknown argument -j
Unknown argument 2
Usage: cmake --build [options] [-- [native-options]]
Options: = Project binary directory to be built. --target = Build instead of default targets. May only be specified once. --config = For multi-configuration tools, choose . --clean-first = Build target 'clean' first, then build. (To clean only, use --target 'clean'.) --use-stderr = Ignored. Behavior is default in CMake >= 3.0. -- = Pass remaining options to the native tool.

CMake Error: The source directory "/tmp/RtmpEKY5cd/R.INSTALL44a59ba24ad/nloptr/src/nlopt" does not exist.
Specify --help for usage, or press the help button on the CMake GUI.
cp: cannot stat 'nlopt/include/*': No such file or directory
configure: creating ./config.status
config.status: creating src/Makevars
** libs

sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base

other attached packages:
[1] pcalg_2.7-4 graph_1.68.0 BiocGenerics_0.36.1

loaded via a namespace (and not attached):
[1] bdsmatrix_1.3-4 Rcpp_1.0.7 corpcor_1.6.10 RBGL_1.66.0 ggm_2.5 stats4_4.0.2
[7] magrittr_2.0.2 robustbase_0.93-9 fastICA_1.2-3 tools_4.0.2 igraph_1.2.11 DEoptimR_1.0-10
[13] sfsmisc_1.1-12 abind_1.4-5 compiler_4.0.2 clue_0.3-60 pkgconfig_2.0.3 cluster_2.1.0

astamm · 2022-02-01T09:21:08Z

Hi. Thanks for reporting this. It is the same error reported in #100. You are using a version of cmake which is prior to 3.15.0. If you update cmake, it should work flawlessly. In the dev version, I have updated the SystemRequirements field in the DESCRIPTION file to make it clearer what minimal version of cmake is required.

frasernutricia · 2022-02-01T09:47:28Z

thanks for the speedy reply! I understand the fix, and thanks for that, but just as a remark this is a rather problematic upgrade for us as it's a system level dependency and we are using the latest version of R Studio Workbench Enterprise on AWS SageMaker - literally just released a few weeks ago - and R Studio has chosen Ubuntu 18.04 LTS as the base distro, which has cmake 3.10. It's faster and easier to install nlopt as a system library than try to upgrade cmake. But thanks for the fix, we will also look into how to do this.

astamm · 2022-02-01T09:51:39Z

Well, the reason that we need cmake >= 3.15.0 is because earlier versions did not allow the use of multiple threads through the -j argument. Since nlopt is pretty quick to compile, we might consider do this on one thread only, hence avoiding the use of -j which would make nloptr compatible with older cmake versions as well. I will think about that when releasing the next version.

eddelbuettel · 2022-02-01T12:56:34Z

You could also test for that and use -j N only if a new-enough cmake is found.

HenrikBengtsson · 2022-02-03T22:17:44Z

You could also test for that and use -j N only if a new-enough cmake is found.

I tried to remove -j N and that was unfortunately not sufficient. There were additional problems showing up. See #100 (comment) for details.

HenrikBengtsson · 2022-02-03T22:32:28Z

@frasernutricia, CMake provides pre-built binaries for Linux, so installation is simple:

cd /path/to/software
curl -L -O https://github.com/Kitware/CMake/releases/download/v3.19.3/cmake-3.19.3-Linux-x86_64.tar.gz
tar xf cmake-3.19.3-Linux-x86_64.tar.gz

Then add its bin/ folder to the PATH;

PATH=/path/to/software/cmake-3.19.3-Linux-x86_64/bin:$PATH
export PATH

and you're good to go. If you can set that up on the server, then that might be better than having to maintain a system/site-wide nloptr install.

eddelbuettel · 2022-02-03T22:41:24Z

(Or maybe use a more current distro. Tossing random newer binaries into an older LTS may have other side effects. Lots of competing tradeoffs here.)

eddelbuettel · 2022-02-03T23:06:44Z

One thought I keep having: given that a) the set of files in nlopt is fixed and b) cmake does not seem to do that much 'discovery' could we possibly do away with cmake and just list an explicit list of dependencies of libnlopt.a in src/Makevars?

The Matrix package had long done that (across different subdirectories / sublibraries), I more recently converted RDieHarder to build its lib that way.

Or am I overlooking some "critical" parts for which we really need cmake? This could and should really build "widely" as we do not depend on anything crazy. Apart from, well, one component of the build chain. And maybe that is a price worth paying. Not my call here.

astamm · 2022-02-04T13:48:30Z

We might do that in a future release yes. Looking at the nlopt sources, it seems that folders algs, api and util only should be needed, all of which containing pairs of header/c files that I suppose should be listed in Makevars to form libnlopt.a from AR and RANLIB.

eddelbuettel · 2022-02-04T14:09:39Z

Yes. Package Matrix even has a tool that creates the snippet then included into src/Makevars. When I set up a simpler one I started from a simple recursive find for files... algs has subdirectories we may need to list too.

astamm · 2022-02-04T15:16:57Z

You could also test for that and use -j N only if a new-enough cmake is found.

I tried to remove -j N and that was unfortunately not sufficient. There were additional problems showing up. See #100 (comment) for details.

Yes that is why I updated SystemRequirements to cmake (>= 3.15.0) at the moment. Thanks @HenrikBengtsson.

eddelbuettel · 2022-02-05T04:16:25Z

just list an explicit list of dependencies of libnlopt.a in src/Makevars?

I just gave that a spin and it is far from a cake walk.

astamm · 2022-02-05T07:49:04Z

You mean listing in Makevars appears insufficient?

eddelbuettel · 2022-02-05T14:24:19Z

Yes. Small points are e.g. that each dir in src/algs/ has a header in its subdir (without the directory in the #include so that is an -I statement for each I got tired off. If you want to play. a quick-ish find-assisted list is

## find src/{algs,api,util} -type f | grep -v "pdf\|README\|COPYRIGHT\|AUTHORS\|COPYING\|\.h\|\.txt\|\.3"
SOURCES = \
	nlopt-src/src/algs/crs/crs.c \
	nlopt-src/src/algs/newuoa/newuoa.c \
	nlopt-src/src/algs/neldermead/nldrmd.c \
	nlopt-src/src/algs/neldermead/sbplx.c \
	nlopt-src/src/algs/cquad/cquad.c \
	nlopt-src/src/algs/cdirect/hybrid.c \
	nlopt-src/src/algs/cdirect/cdirect.c \
	nlopt-src/src/algs/ags/tst.cc \
	nlopt-src/src/algs/ags/ags.cc \
	nlopt-src/src/algs/ags/local_optimizer.cc \
	nlopt-src/src/algs/ags/solver.cc \
	nlopt-src/src/algs/ags/evolvent.cc \
	nlopt-src/src/algs/mma/mma.c \
	nlopt-src/src/algs/mma/ccsa_quadratic.c \
	nlopt-src/src/algs/subplex/subplex.c \
	nlopt-src/src/algs/direct/DIRect.c \
	nlopt-src/src/algs/direct/DIRserial.c \
	nlopt-src/src/algs/direct/tstc.c \
	nlopt-src/src/algs/direct/direct_wrap.c \
	nlopt-src/src/algs/direct/DIRsubrout.c \
	nlopt-src/src/algs/praxis/praxis.c \
	nlopt-src/src/algs/auglag/auglag.c \
	nlopt-src/src/algs/mlsl/mlsl.c \
	nlopt-src/src/algs/luksan/plip.for \
	nlopt-src/src/algs/luksan/pnet.c \
	nlopt-src/src/algs/luksan/pnet.for \
	nlopt-src/src/algs/luksan/plis.c \
	nlopt-src/src/algs/luksan/plis.for \
	nlopt-src/src/algs/luksan/mssubs.for \
	nlopt-src/src/algs/luksan/pssubs.for \
	nlopt-src/src/algs/luksan/mssubs.c \
	nlopt-src/src/algs/luksan/pssubs.c \
	nlopt-src/src/algs/luksan/plip.c \
	nlopt-src/src/algs/cobyla/cobyla.c \
	nlopt-src/src/algs/isres/isres.c \
	nlopt-src/src/algs/slsqp/slsqp.c \
	nlopt-src/src/algs/esch/esch.c \
	nlopt-src/src/algs/bobyqa/bobyqa.c \
	nlopt-src/src/algs/stogo/prog.cc \
	nlopt-src/src/algs/stogo/global.cc \
	nlopt-src/src/algs/stogo/tst.cc \
	nlopt-src/src/algs/stogo/tstc.c \
	nlopt-src/src/algs/stogo/testros.cc \
	nlopt-src/src/algs/stogo/stogo.cc \
	nlopt-src/src/algs/stogo/local.cc \
	nlopt-src/src/algs/stogo/linalg.cc \
	nlopt-src/src/algs/stogo/tools.cc \
	nlopt-src/src/api/options.c \
	nlopt-src/src/api/f77api.c \
	nlopt-src/src/api/deprecated.c \
	nlopt-src/src/api/general.c \
	nlopt-src/src/api/optimize.c \
	nlopt-src/src/util/rescale.c \
	nlopt-src/src/util/mt19937ar.c \
	nlopt-src/src/util/nlopt-getopt.c \
	nlopt-src/src/util/qsort_r.c \
	nlopt-src/src/util/stop.c \
	nlopt-src/src/util/mt19937ar_test.c \
	nlopt-src/src/util/sobolseq_test.c \
	nlopt-src/src/util/sobolseq.c \
	nlopt-src/src/util/redblack_test.c \
	nlopt-src/src/util/timer.c \
	nlopt-src/src/util/redblack.c

#	nlopt-src/src/algs/direct/DIRparallel.c \


OBJECTS = $(SOURCES:.c=.o) $(SOURCES:.cc=.o) $(SOURCES:.for:.o)

$(SHLIB): $(OBJECTS)

and I currently have

PKG_CPPFLAGS = -I../inst/include -Inlopt-src/src -I. -Isrc -Inlopt-src/src/util/ -Inlopt-src/src/algs/praxis -Inlopt-src/src/algs/direct -Inlopt-src/src/algs/stogo
PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

It also generates a bazillion and a half warnings. Also needed nlopt-config.h which I let cmake generate and copied in (not a problem per see as I have been doing the same with Armadillo for RcppArmadillo for over a decade and millions of uses -- not as powerful as running a local detection on build but much lighter in use).

astamm · 2022-02-06T17:35:34Z

We could use the sources listed in the CMakeLists.txt file from the NLopt repo:
https://github.com/stevengj/nlopt/blob/ad8ba827fc2bafb103e01736f261a1faa7ea875e/CMakeLists.txt#L203-L221

I am not quite sure why he is including the header files into the SOURCES though. We might try not to do that first maybe.

We could also start with the includes he lists here:
https://github.com/stevengj/nlopt/blob/ad8ba827fc2bafb103e01736f261a1faa7ea875e/CMakeLists.txt#L245-L266

And see if that is sufficient.

eddelbuettel · 2022-02-06T17:38:50Z

Sorry I may have been unclear. Establishing the list of needed files is somewhat trivial and the first thing I did. But it's the old "necessary but not sufficient": as this is not enough to build libnlopt.a we likely need to glue a bit more make logic around it. Which amounts to reworking / reinventing a build system. Now that you placed your bet on cmake. Hm.

A related problem is that if we "own" the full nlopt compilation we also own (and have to defend to CRAN / clean up for CRAN) all messages and errrors. Sometimes it may just be easier to tell people to 'please show up at game time with the equipment' i.e. to please compile libnlopt.a locally (or have a proper cmake around). It's hard -- can't really win all cases for all users on all systems. So those who want the latest and greatest from CRAN on a system they insist to keep otherwise frozen at toolchains from half a decade ago with have to locally accomodate. Seems fair to me as we work well and reliably on current systems.

astamm · 2022-02-06T17:43:03Z

Oh I understand. It was worth trying that way in case cmake did not do much discovery but it seems in the end it does some.

eddelbuettel · 2022-02-06T17:45:27Z

Yep there is some extra 'sauce' in the CMakeLists.txt files we'd need to pick up. Might be enoght to let make recurse into the directories (to say let is build in each algo with -I. to find the header there) and have the outer src/Makevars/ pick up all the object files -- but I have somewhat limited motivation to rework all that. We achieved the main goal: we're good at CRAN.

frasernutricia · 2022-02-06T18:34:20Z

Hi @astamm - this is my ignorance here, but do you really need to move to cmake? We don't have a choice in the distro being used - Ubuntu 18.04.5 LTS - released Aug 2020 - as this was chosen by R Studio as part of their new SageMaker AWS offering. This distro does not seem so very old. We've installed a whole host of other cran packages with no issues, including rstan which has a parallel build process. nloptr seems an unfortunate outlier. But I fully realize I'm not actually offering help here! and we can workaround.

eddelbuettel · 2022-02-06T19:08:06Z

@frasernutricia Ubuntu 18.04 LTS is already an outdated (even if still supported) LTS as 20.04 is current (and we are weeks away from 22.04). By being on an older version (not entirely by your choice, I understand) you must expect some "delta" to creep in. If I were you I'd clone the instance and see if an update to 20.04 (which I happen to run at AWS) is feasible.

frasernutricia · 2022-02-06T19:35:22Z

Thanks @eddelbuettel, we're using a new version of R Workbench which is built inside SageMaker (and the underlying EC2 instance is destroyed after each session, so any updates/system libraries need re-installed each time, but personal R libraries are persistent between sessions). A bring your own container model (docker etc) is on the R Workbench SageMaker roadmap for sometime in 2022 Q2 so fingers-crossed that will allow us something similar to a CRAN build.

eddelbuettel · 2022-02-06T19:53:58Z

I happily used RStudio Cloud for a few years to teach (but campus appears to be moving away from it), generally liked it -- and that deployed a newer / more reasonable Ubuntu. Oh well.

You can also 'persist' a local library and/or rely on binaries. As mentioned, 18.04 starts you at a disadvantage but the c2d4u.team repo has you covered on this one. A quick apt-cache policy r-cran-nloptr in an 18.04 container:

root@88688a322f3b:/work# apt-cache search r-cran-nloptr
r-cran-nloptr - GNU R package "R Interface to NLopt"
root@88688a322f3b:/work# apt-cache policy r-cran-nloptr
r-cran-nloptr:
  Installed: (none)
  Candidate: 2.0.0-1cran1.1804.0
  Version table:
     2.0.0-1cran1.1804.0 500
        500 http://ppa.launchpad.net/c2d4u.team/c2d4u4.0+/ubuntu bionic/main amd64 Packages
     1.0.4-1build1 500
        500 http://archive.ubuntu.com/ubuntu bionic/universe amd64 Packages
root@88688a322f3b:/work#

And better still thanks to the magic of bspm you even get installed via installed.packages("nloptr") as I just did in this rocker/r-bspm:18.04 container:

root@88688a322f3b:/work# install.r nloptr                            # install.r is a little wrapper around install.packages() from littler                                                                                                                                              
(loaded the methods namespace)                                                                                                                                                                                     
Loading required package: utils                                                                                                                                                                                    
Tracing function "install.packages" in package "utils"                                                                                                                                                             
Install system packages as root...                                                                                                                                                                                 
Reading package lists... Done                                                                            
Building dependency tree                                                                                 
Reading state information... Done                                                                        
Hit http://archive.ubuntu.com/ubuntu bionic InRelease                                                                                                                                                              
Hit http://security.ubuntu.com/ubuntu bionic-security InRelease                                                                                                                                                    
Hit http://ppa.launchpad.net/c2d4u.team/c2d4u4.0+/ubuntu bionic InRelease                                                                                                                                          
Hit http://archive.ubuntu.com/ubuntu bionic-updates InRelease                                                                                                                                                      
Hit http://archive.ubuntu.com/ubuntu bionic-backports InRelease                                                                                                                                                    
Hit http://ppa.launchpad.net/edd/r-4.0/ubuntu bionic InRelease                                                                                                                                                     
Hit http://ppa.launchpad.net/marutter/rrutter4.0/ubuntu bionic InRelease                                                                                                                                           
Fetched 0 B in 0s (0 B/s)                                                                                                                                                                                          
Reading package lists... Done                                                                            
Building dependency tree                                                                                 
Reading state information... Done                                                                        
Get:1 http://ppa.launchpad.net/c2d4u.team/c2d4u4.0+/ubuntu bionic/main amd64 r-cran-brio amd64 1.1.3-1cran1.1804.0 [32.0 kB]                                                                                      
Get:2 http://archive.ubuntu.com/ubuntu bionic/universe amd64 libnlopt0 amd64 2.4.2+dfsg-4 [162 kB]                                                                                                                 
Get:3 http://ppa.launchpad.net/c2d4u.team/c2d4u4.0+/ubuntu bionic/main amd64 r-cran-ps amd64 1.6.0-1cran1.1804.0 [270 kB]                                                                                         
Get:4 http://ppa.launchpad.net/c2d4u.team/c2d4u4.0+/ubuntu bionic/main amd64 r-cran-r6 all 2.5.1-1cran1.1804.0 [86.1 kB]                                                                                          
Get:5 http://ppa.launchpad.net/c2d4u.team/c2d4u4.0+/ubuntu bionic/main amd64 r-cran-processx amd64 3.5.2-1cran1.1804.0 [303 kB]                                                                                   
Get:6 http://ppa.launchpad.net/c2d4u.team/c2d4u4.0+/ubuntu bionic/main amd64 r-cran-callr all 3.7.0-1cran1.1804.0 [421 kB]                                                                                        
Get:7 http://ppa.launchpad.net/c2d4u.team/c2d4u4.0+/ubuntu bionic/main amd64 r-cran-glue amd64 1.6.1-1cran1.1804.0 [143 kB]                                                                                       
Get:8 http://ppa.launchpad.net/c2d4u.team/c2d4u4.0+/ubuntu bionic/main amd64 r-cran-cli amd64 3.1.1-1cran1.1804.0 [1038 kB]                                                                                       
Get:9 http://ppa.launchpad.net/c2d4u.team/c2d4u4.0+/ubuntu bionic/main amd64 r-cran-crayon all 1.4.2-1cran1.1804.0 [151 kB]                                                                                       
Get:10 http://ppa.launchpad.net/c2d4u.team/c2d4u4.0+/ubuntu bionic/main amd64 r-cran-rprojroot all 2.0.2-1cran1.1804.0 [92.1 kB]    
[.... lots of lines omitted here ...]
Setting up r-cran-vctrs (0.3.8-1cran1.1804.0) ...
Setting up r-cran-lifecycle (1.0.1-1cran1.1804.0) ...
Setting up r-cran-cli (3.1.1-1cran1.1804.0) ...
Setting up r-cran-callr (3.7.0-1cran1.1804.0) ...
Setting up r-cran-pkgload (1.2.4-1cran1.1804.0) ...
Setting up r-cran-pillar (1.6.5-1cran1.1804.0) ...
Setting up r-cran-tibble (3.1.6-1cran1.1804.0) ...
Setting up r-cran-rematch2 (2.1.2-1cran1.1804.0) ...
Setting up r-cran-waldo (0.3.1-1cran1.1804.0) ...
Setting up r-cran-testthat (3.1.2-1cran1.1804.0) ...
Setting up r-cran-nloptr (2.0.0-1cran1.1804.0) ...
Processing triggers for libc-bin (2.27-3ubuntu1.2) ...
root@88688a322f3b:/work# 
root@88688a322f3b:/work# R -q
Loading required package: utils
Tracing function "install.packages" in package "utils"
> library(nloptr)
Warning message:
package ‘nloptr’ was built under R version 4.1.2 
>

Not bad for free, eh? More on bspm, and more on how @Enchufa2 and I see "binaries for linux" in this arXiv paper.

Enchufa2 · 2022-02-07T09:58:37Z

Thanks to the mention, I noticed that I had this package failing to build in Fedora. Added the cmake dependency and all good.

FMKerckhof · 2022-02-09T19:01:25Z

If I may add another use-case where updating cmake or the OS is not very evident: I am facing the same issue in trying to use nloptr as a dependency in a containerized lambda (public.ecr.aws/lambda/provided) which is based on CentOS 7 - CentOS 7 is supported until June 2024. I know this is probably comparable to the 18.04 vs 20.04 LTS debate above, but still it is a pain. I will see how I can change my dockerfile based upon the suggestions above while trying to retain a container of limited size and adequate robustness.

eddelbuettel · 2022-02-09T19:11:31Z

Just in case it wasn't clear, cmake is a conditional dependency that is relied upon to build NLopt in case it has not been built. If NLopt is present (as verified via pkg-config) you will not need cmake.

So if you can get a recent enough NLopt onto such a CentOS 7 system you are fine. Of course, NLopt also uses cmake itself so it this a little circular. But if, say, you create a rpm which contains NLopt (the library and headers) you may be able to get by without cmake on that box.

FMKerckhof · 2022-02-09T19:32:09Z

Thank you @eddelbuettel , that did clarify things. The current EPEL version of NLopt and NLopt-devel is 2.4.2, but this did not seam recent enough to install nloptr. I will consider your suggested solution with the rpm.

eddelbuettel · 2022-02-09T19:35:43Z

Right -- it might be easier for us to relax the hard dependency on 2.7.0 or later (to permit your use with 2.4.2) and maybe condition out a method or two requiring 2.6.* or 2.7.* than to replace cmake. Something to consider...

The fact of the matter remains that brandnew released in 2022 software may have diffculties on dated / very conservative host system. You may also want to consider an older nloptr release.

FMKerckhof · 2022-02-09T21:56:21Z

For CentOS 7, I stumbled upon a workaround using cmake3 in CentOS, which is recent enough 3.17. In case of potential link rot I will just re-iterate the fix here, if someone else would run into the same issue with nloptr on public.ecr.aws/lambda/provided. Adding the below lines to the Dockerfile will allow you to build nloptr:

RUN yum -y install https://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm \
  && yum -y install cmake3 NLopt NLopt-devel \
  && ln -s /usr/bin/cmake3 /usr/bin/cmake

eddelbuettel · 2022-02-09T22:37:15Z

Nice. I'd recommend making the soft-link in /usr/local/bin though. And now that you have a good-enough cmake you do not need system-level NLopt which will likely be seen as 'too old' and just rely on nloptr and the cmake you found to build you nloptr with its included copy of NLopt.

ggrrll · 2022-03-02T16:49:06Z

@FMKerckhof thank you a lot for you suggestion ! -- did not work completely , but at least I managed to get to 96% 😅 ...where I get this error

[96%] Linking CXX static library libnlopt.a
Error running link command: No such file or directory
make[2]: *** [libnlopt.a] Error 2
make[1]: *** [CMakeFiles/nlopt.dir/all] Error 2
gmake: *** [all] Error 2
-- Install configuration: "Release"
-- Installing: /tmp/RtmpY66giU/R.INSTALL5c10ab97f09/nloptr/src/nlopt/lib/pkgconfig/nlopt.pc
-- Installing: /tmp/RtmpY66giU/R.INSTALL5c10ab97f09/nloptr/src/nlopt/include/nlopt.h
-- Installing: /tmp/RtmpY66giU/R.INSTALL5c10ab97f09/nloptr/src/nlopt/include/nlopt.hpp
-- Installing: /tmp/RtmpY66giU/R.INSTALL5c10ab97f09/nloptr/src/nlopt/include/nlopt.f
CMake Error at nlopt-build/cmake_install.cmake:69 (file):
  file INSTALL cannot find
  "/tmp/RtmpY66giU/R.INSTALL5c10ab97f09/nloptr/src/nlopt-build/libnlopt.a":
  No such file or directory.

any idea?
thanks

this seems to be related with #105

eddelbuettel · 2022-03-02T17:10:59Z

Error running link command: No such file or directory

I'd start there

FMKerckhof · 2022-03-03T09:09:54Z

Nice. I'd recommend making the soft-link in /usr/local/bin though. And now that you have a good-enough cmake you do not need system-level NLopt which will likely be seen as 'too old' and just rely on nloptr and the cmake you found to build you nloptr with its included copy of NLopt.

@ggrrll see above reply by @eddelbuettel - normally, if you have a recent enough cmake you don't need to have a system-level NLopt, as nloptr has an included copy of NLopt. As you can see from my code above I downloaded the latest epel release for CentOS 7 from https://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm - but indeed this would result in NLopt 2.4.2.

ggrrll · 2022-03-03T09:26:29Z

ok, so basically the error I am getting there
#104 (comment)
has nothing to do with the NLopt v. (?)

(afterall, this does not seem too bad...)

checking for pkg-config checking NLopt version... insufficient: NLopt 2.7.0 or later is preferred.

ggrrll · 2022-03-09T10:58:35Z

🎊
I managed to install ✔️ (finally!) factoextra , which needs nloptr, the 2nd requirement being R v. >= 4
(at least , it worked when I upgraded it from v. 3.6 to 4.0)

also posted https://stackoverflow.com/a/71407734/5533078

astamm · 2022-03-09T11:03:42Z

Nice to read you managed to solve your issue. We have an ongoing PR #106 that should fix an issue with earlier versions of R. I will merge it soon.

bhogan-mitre · 2022-04-27T20:53:57Z

In case it's useful for others, the following snippet prior to install.packages got me unstuck when I needed to point to cmake3 instead of cmake (2).

Sys.setenv(CMAKE_BIN = "/usr/bin/cmake3")

HenrikBengtsson · 2022-04-27T21:25:11Z

In case it's useful for others, the following snippet prior to install.packages got me unstuck when I needed to point to cmake3 instead of cmake (2).
Sys.setenv(CMAKE_BIN = "/usr/bin/cmake3")

This is excellent, because RedHat/CentOS has cmake and cmake3. Maybe other distros use this too(?). For example, on CentOS 7, cmake is 2.8.12.2 and cmake3 is 3.17.5.

I didn't know about the CMAKE_BIN environment variable. I don't know CMake well enough, but this env var looks specific to this R package - is that correct?

I think improvement that can be done this package is to look for cmake3 first, e.g.

if test -z "$CMAKE_BIN"; then
  # Look for a cmake3 binary in the current path
  CMAKE_BIN=`which cmake3 2>/dev/null`
fi

if test -z "$CMAKE_BIN"; then
  # Look for a cmake binary in the current path
  CMAKE_BIN=`which cmake 2>/dev/null`
fi

That should be backward compatible, and automagically solve it for, at least, everyone on RHEL/CentOS running into this problem.

astamm · 2022-04-28T05:32:22Z

Thanks @HenrikBengtsson for the suggestion. I might implement it, it seems indeed a good idea.

astamm added the enhancement label Feb 4, 2022

HenrikBengtsson mentioned this issue Apr 27, 2022

R: Set CMAKE_BIN=$(command -v cmake3) HenrikBengtsson/CBI-software#63

Closed

astamm closed this as completed in 3753264 May 25, 2022

Version 2.0.0 fails to install on R 4.0.2 #104

Version 2.0.0 fails to install on R 4.0.2 #104

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