[Rd] 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(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 >::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
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Re: [Rd] Compiling error with glmnet and nloptr
Also for now, I commented on self().template update 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
Sent: 10 March 2022 10:45
To: R-devel
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
Sent: 10 March 2022 09:22
To: R-devel
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(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 >::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
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[Rd] security holes in system2
Dear R Developers,
The documentation for "system2" only defines "args" as
args: a character vector of arguments to 'command'.
This encourages the reader to think that R's system2 interface is passing its
arguments unchanged to exec().
But I was surprised to find that under the hood, you're just pasting my
arguments together and sending them to a subshell to be re-parsed:
command <- paste(c(env, shQuote(command), args), collapse = " ")
What horror! Please fix or document the fact that system2 executes its
ARGUMENTS and not just the command.
Aside from being relevant to data scientists, it's a big security hole. It
means that, in some cases, something that looks like plain text in my R code
will end up being executed as a command on my system, which seems dangerous to
me.
> my_data=c("<(>&2 echo oops)")
> system2("echo",args=my_data)
/dev/fd/63
oops
Thank you,
Frederick
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