R devel - Mar 2022 - Compiling error with glmnet and nloptr

Also for now, I commented on self().template update<update_type::full> at
lines 59,90 of glmnetpp/include/glmnetpp_bits/elnet_point/gaussian_base.hpp and
glmnet also passed , so example(glmnet) gives the familiar results. Ideally,
some better solution is preferable. Jing Hua
________________________________
From: jing hua zhao <jinghuazhao at hotmail.com>
Sent: 10 March 2022 10:45
To: R-devel <r-devel at r-project.org>
Subject: Re: Compiling error with glmnet and nloptr

Just a note that I used R 4.1.2 and with R 4.1.3 I had the same issues
nevertheless I was able to go through with (not entirely sure preferable) nloptr
once abs() is changed into fabs() within ?src/test-C-API.cpp. Thanks. Jing Hua

________________________________
From: jing hua zhao <jinghuazhao at hotmail.com>
Sent: 10 March 2022 09:22
To: R-devel <r-devel at r-project.org>
Subject: Compiling error with glmnet and nloptr

Dear All,

I haven't been able to compile the latest glmnet and nloptr from CRAN wth
the following error messages,

glmnet:

elnet_exp.cpp:141:59:   required from here
glmnetpp/include/glmnetpp_bits/elnet_point/gaussian_base.hpp:90:39: error:
'self' was not declared in this scope
                     [=](auto k) { self().template
update<update_type::partial>(k, ab, dem); },
...
make: *** [elnet_exp.o] Error 1
ERROR: compilation failed for package ?glmnet?
* removing ?/rds/user/jhz22/hpc-work/R/glmnet?
* restoring previous ?/rds/user/jhz22/hpc-work/R/glmnet?

nloptr:

test-C-API.cpp:108:35: error: call of overloaded
'abs(__gnu_cxx::__alloc_traits<std::allocator<double>
>::value_type)' is ambiguous
     expect_true(abs(res[1] - 8./27) < 1.0e-4);
 ...
/usr/local/software/archive/linux-scientific7-x86_64/gcc-9/gcc-6.5.0-dtb6lagchexqdijlx6xgkin3zlfddpzi/include/c++/6.5.0/cstdlib:172:3:
note: candidate: long int std::abs(long int)
   abs(long __i) { return __builtin_labs(__i); }
   ^~~
make: *** [test-C-API.o] Error 1
ERROR: compilation failed for package ?nloptr?

Any suggestions to fix these? I use gcc/6 and have

$ uname -a
Linux login-e-16 3.10.0-1160.59.1.el7.x86_64 #1 SMP Tue Feb 22 10:57:56 CST 2022
x86_64 x86_64 x86_64 GNU/Linux

Many thanks in advance,


Jing Hua


	[[alternative HTML version deleted]]

Dear jing hua zhao,

You appear to have issues with a particular (pair or single) package; it is
usually better to contact the author / maintainers of the package.  I help a
little with nloptr which had its share of similar issues after its recent as
it (conditionall, if no libnlopr is found) will require cmake, and in a
fairly recentish flavor.  That can pose issues on systems such as yours which
identifies itself per the error message as Scientific Linux 

   linux-scientific7-x86_64/gcc-9/gcc-6.5.0

which is actually dead:  https://en.wikipedia.org/wiki/Scientific_Linux

Stepping back, there is a bit of a disconnect between working on old OS
releases -- sometimes not by choice as your institution, employer, $whoever
... may make you do that -- yet requiring / desiring / attempting to use
bleeding-edge newest versions of R or packages.  That can have friction as
new versions can at times require new tools. The developers try to not
require it, but sometimes it happens, and usually for a reason (as
e.g. nloptr need libnlopt which itself relies on cmake).

So if you can, please considering upgrading to a more current and supported
operating system. For issues specific with a package (as opposed to R and in
particular development on R) the repository may be a better place than this
list.

Cheers,  Dirk

-- 
https://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org