not reading default.file parameter?

[bheavner]

Something appears to have changed, and previously working code is not working for me now.

I have previously successfully established a database connection thus:

con <- DBI::dbConnect(RMariaDB::MariaDB(),
                 default.file = "~/.mysql-uwit.cnf",
                 groups = "client",
                 ssl.ca = ssl.ca,
                 ssl.cert = ssl.cert,
                 ssl.key = ssl.key)

Where ~/.mysql-uwit.cnf looks like this:

[client]
host = <my host>
user = <my user>
password = <my password>
database = <the desired database>

But now that returns an error that appears to show an attempt to connect to a local MySQL, instead of the one running at my host:

Error in connection_create(host, username, password, dbname, as.integer(port),  : 
  Failed to connect: Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2)

I have confirmed that I can connect from the command line with mysql --defaults-file=~/.mysql-uwit.cnf, and I can connect without a .cnf file, like this:

con <- DBI::dbConnect(RMariaDB::MariaDB(),
                      host = <my host>
                      user = <my user>,
                      password = <my password>
                      database = <the desired database>,
                      ssl.ca = ssl.ca,
                      ssl.cert = ssl.cert,
                      ssl.key = ssl.key)

A further clue - if I try to specify the host in dbConnect(), but get other values from .cnf file, it appears to not load the username or password from the .cnf file:

> con <- DBI::dbConnect(RMariaDB::MariaDB(),
+                       default.file = "/Users/bheavner/.mysql-uwit.cnf",
+                       user = NULL,
+                       password = NULL,
+                       database = NULL,
+                       host = <my host>)
Error in connection_create(host, username, password, dbname, as.integer(port),  : 
  Failed to connect: Access denied for user 'bheavner'@'<my machine name>' (using password: NO)
> con <- DBI::dbConnect(RMariaDB::MariaDB(),
+                       default.file = "/Users/bheavner/.mysql-uwit.cnf",
+                       host = "biostats1.s.uw.edu")
Error in connection_create(host, username, password, dbname, as.integer(port),  : 
  Failed to connect: Access denied for user 'bheavner'@'<my machine name>' (using password: NO)

I'm working in RStudio on a mac, and here's my sessionInfo:

> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] rlang_0.2.0   readr_1.1.1   stringr_1.3.0 dplyr_0.7.4   purrr_0.2.4   dbplyr_1.2.1 

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.16     assertthat_0.2.0 R6_2.2.2         DBI_0.8          magrittr_1.5     pillar_1.2.1     stringi_1.1.7   
 [8] bindrcpp_0.2.2   tools_3.4.3      bit64_0.9-7      glue_1.2.0       bit_1.1-12       hms_0.4.2        RMariaDB_1.0.5  
[15] yaml_2.1.18      compiler_3.4.3   pkgconfig_2.0.1  bindr_0.1.1      tibble_1.4.2    

[krlmlr]

Thanks. I'm at a loss here, this will need a bit more digging.

[bheavner]

Same here. :) Can you think of anything that might be useful for troubleshooting or digging in under the hood more?

[plasalvia]

I have a very similar issue and I arrived to similar conclusions (the .cnf file is not being loaded but defaults are)

[krlmlr]

We could use strace (or an OS X equivalent) to trace all files that are accessed, something like strace R -q -e 'DBI::dbConnect(...)' . The default.file argument requires the groups argument, but the first example looks correct.

[bheavner]

I don't have root to this box, so haven't had luck with strace... but I may have come across another clue: I'm using macports, and just got this error from the command line:

gcc-mac-008:foo bheavner$ mysql —-defaults-file=~/.mysql.cnf 
ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/Users/bheavner/macports/var/run/mysql57/mysqld.sock' (2)

It could be that this is a macports issue, not a RMariaDB issue... still a mystery, but I'll poke around on that front a bit and update here.

[bheavner]

Follow-up: not sure if related or not. My error from the command line arose because the first dash in my command above was an em-dash (stupid autocorrect and copy-paste!). The command works from the command line if I manually type it instead of copy/paste.

[krlmlr]

Can you please try default.file = path.expand("~/.mysql-uwit.cnf") ?

[bheavner]

Same story. :(

> con <- DBI::dbConnect(RMariaDB::MariaDB(),
+                       default.file = path.expand("~/.mysql-uwit.cnf"),
+                       groups = "client",
+                       ssl.ca = ssl.ca,
+                       ssl.cert = ssl.cert,
+                       ssl.key = ssl.key)
Error in connection_create(host, username, password, dbname, as.integer(port),  : 
  Failed to connect: Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2)

with

> path.expand("~/.mysql-uwit.cnf")
[1] "/Users/bheavner/.mysql-uwit.cnf"

[krlmlr]

In your console example you used .mysql.cnf, the R code uses .mysql-uwit.cnf . Just to be sure -- can you please check that the connection works from the console with .mysql-uwit.cnf ?

[bheavner]

Yep, it's always good to check:

gcc-mac-008:~ bheavner$ mysql --defaults-file=~/.mysql-uwit.cnf
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 12
Server version: 5.5.5-10.2.11-MariaDB-log MariaDB Server

[bheavner]

potentially related: r-dbi/RMySQL#222

[amstilp]

I am having the same problem as @bheavner (who is also my colleague, and thus we have a similar computing set up). I tried compiling RMariaDB from source, since it fixed the problem with the new version of RMySQL, and calling dbConnect with the default.file and groups arguments, but unfortunately it didn't fix the problem. I am also on a Mac and installed the mysql client installed using macports.

Interestingly, dbConnect works with the default.file argument on a linux box where the mysql client is (probably) installed in a standard location.

[krlmlr]

I'm not sure if mysql_options() copies the argument into a private buffer. If not, this could explain the behavior we're seeing.

RMariaDB/src/DbConnection.cpp

Lines 40 to 42 in 9f88fb6

	if (!default_file.isNull())
	mysql_options(this->pConn_, MYSQL_READ_DEFAULT_FILE,
	as<std::string>(default_file).c_str());

Could you please try installing RMariaDB from my branch, and connect again?

remotes::install_github("r-dbi/RMariaDB@18a071c")

[amstilp]

That worked! I can connect with a .cnf file with that branch.

[bheavner]

Weird! It did not work for me. @amstilp and I have found a difference in the installation step, and I'm digging more. I get this output:

* installing *source* package ‘RMariaDB’ ...
Auto-brewing mariadb-connector-c in /var/folders/h9/jflh25vj2b1cfzz61lph7fp80001mq/T//build-mariadb-connector-c...
Initialized empty Git repository in /private/var/folders/h9/jflh25vj2b1cfzz61lph7fp80001mq/T/build-mariadb-connector-c/.git/
... 

(then much more weird homebrew stuff happens). I do not think I have brew installed on my machine.

@amstilp does not get any brew output, and it works for her. Surprisingly, we get the same output from things like
which mysql, port select --list mysql, and mysql --version

I am digging more into why my box is doing brew-y things, and will update here. I strongly suspect something weird in my library paths because of this brew-related mystery.

[bheavner]

IT WORKS FOR ME! Woot!

Thanks very much for your patience and perseverance on this issue, @krlmlr!

Here's what I found as the root cause of my weirdness and the difference with @amstilp 's first success: although we are both using RStudio, she always starts from the terminal, and I start using a pinned icon in my taskbar.

Apparently, macOS doesn't read bash environmental variables when starting from the taskbar, so my RStudio did not have the correct $PATH. Critically, it was missing the path to ~/macports/bin and ~/macports/sbin.

I haven't figured out how to force RStudio to get the bash environmental variables and set the path correctly when starting from the taskbar, but that is not the problem of RMariaDB.

If there was a change in RMariaDB that led to this behavior, I now have a way to work with the current implementation. I think it's more likely that there was a change in the underlying library on the Mac OS, so the things that fall within the default path weren't working.

As one final point of information, I have the following $PATH in my RStudio when starting from the pinned icon:

> Sys.getenv("PATH")
[1] "/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/Library/TeX/texbin"

Thanks again, very much!

[amstilp]

Hmm, it seems like the CRAN version (1.0.6) is also working for me, but I'm not sure why it wasn't working last week. I may have installed it differently or forgotten to restart my R session in between testing. Sorry about the confusion, I think we have it figured out here!

[bheavner]

To confirm, the CRAN version works for me as well - if I install from source. It does not work (and gives the familiar error), if I just do a vanilla CRAN install.

[amstilp]

Same for me. I should have said I had to install from source. Thanks again! We can probably close this issue.

[bheavner]

Though ideally, the vanilla CRAN install should work, too, yes? The $PATH issue seems to only matter when I'm compiling source.

[krlmlr]

Yes, binary install from CRAN should work too.

The Auto-brewing ... is an indicator that mariadb_config nor mysql_config were found on the $PATH, and a static library is used . I'd imagine that CRAN builds with one of these available on the $PATH, which links to a dynamic library .

Could you please set up your system so that Using mariadb_config or Using mysql_config is printed during installation, and then test if you see the faulty behavior (and if my hotfix changes it)? Thanks for your help!

[bheavner]

I think you're asking for more output when I run the remotes::install_github("r-dbi/RMariaDB@18a071c") to see which macports library it's using? If so, here's a longer snip:

> remotes::install_github("r-dbi/RMariaDB@18a071c")
Downloading GitHub repo r-dbi/RMariaDB@18a071c
Downloading GitHub repo r-dbi/DBI@master
Installing package into ‘/Users/bheavner/Library/R/3.5/library’
(as ‘lib’ is unspecified)
* installing *source* package ‘DBI’ ...
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DBI)
Downloading GitHub repo r-dbi/DBItest@master
Skipping 1 packages ahead of CRAN: DBI
Installing package into ‘/Users/bheavner/Library/R/3.5/library’
(as ‘lib’ is unspecified)
* installing *source* package ‘DBItest’ ...
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DBItest)
Skipping 1 packages ahead of CRAN: DBI
Installing package into ‘/Users/bheavner/Library/R/3.5/library’
(as ‘lib’ is unspecified)
* installing *source* package ‘RMariaDB’ ...
Using mysql_config
Found mysql_config/mariadb_config cflags and libs!
Using PKG_CFLAGS=-I/Users/bheavner/macports/include/mysql57/mysql -Os -fno-omit-frame-pointer -arch x86_64
Using PKG_LIBS=-L/usr/local/opt/openssl/lib -L/Users/bheavner/macports/lib/mysql57/mysql -lmysqlclient -lz
** libs
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/bheavner/macports/include/mysql57/mysql -Os -fno-omit-frame-pointer -arch x86_64 -I"/Users/bheavner/Library/R/3.5/library/BH/include" -I"/Users/bheavner/Library/R/3.5/library/plogr/include" -I"/Users/bheavner/Library/R/3.5/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c DbConnection.cpp -o DbConnection.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/bheavner/macports/include/mysql57/mysql -Os -fno-omit-frame-pointer -arch x86_64 -I"/Users/bheavner/Library/R/3.5/library/BH/include" -I"/Users/bheavner/Library/R/3.5/library/plogr/include" -I"/Users/bheavner/Library/R/3.5/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c DbResult.cpp -o DbResult.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/bheavner/macports/include/mysql57/mysql -Os -fno-omit-frame-pointer -arch x86_64 -I"/Users/bheavner/Library/R/3.5/library/BH/include" -I"/Users/bheavner/Library/R/3.5/library/plogr/include" -I"/Users/bheavner/Library/R/3.5/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c MariaBinding.cpp -o MariaBinding.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/bheavner/macports/include/mysql57/mysql -Os -fno-omit-frame-pointer -arch x86_64 -I"/Users/bheavner/Library/R/3.5/library/BH/include" -I"/Users/bheavner/Library/R/3.5/library/plogr/include" -I"/Users/bheavner/Library/R/3.5/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c MariaResultImpl.cpp -o MariaResultImpl.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/bheavner/macports/include/mysql57/mysql -Os -fno-omit-frame-pointer -arch x86_64 -I"/Users/bheavner/Library/R/3.5/library/BH/include" -I"/Users/bheavner/Library/R/3.5/library/plogr/include" -I"/Users/bheavner/Library/R/3.5/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c MariaResultPrep.cpp -o MariaResultPrep.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/bheavner/macports/include/mysql57/mysql -Os -fno-omit-frame-pointer -arch x86_64 -I"/Users/bheavner/Library/R/3.5/library/BH/include" -I"/Users/bheavner/Library/R/3.5/library/plogr/include" -I"/Users/bheavner/Library/R/3.5/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c MariaResultSimple.cpp -o MariaResultSimple.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/bheavner/macports/include/mysql57/mysql -Os -fno-omit-frame-pointer -arch x86_64 -I"/Users/bheavner/Library/R/3.5/library/BH/include" -I"/Users/bheavner/Library/R/3.5/library/plogr/include" -I"/Users/bheavner/Library/R/3.5/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c MariaRow.cpp -o MariaRow.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/bheavner/macports/include/mysql57/mysql -Os -fno-omit-frame-pointer -arch x86_64 -I"/Users/bheavner/Library/R/3.5/library/BH/include" -I"/Users/bheavner/Library/R/3.5/library/plogr/include" -I"/Users/bheavner/Library/R/3.5/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c MariaTypes.cpp -o MariaTypes.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/bheavner/macports/include/mysql57/mysql -Os -fno-omit-frame-pointer -arch x86_64 -I"/Users/bheavner/Library/R/3.5/library/BH/include" -I"/Users/bheavner/Library/R/3.5/library/plogr/include" -I"/Users/bheavner/Library/R/3.5/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c MariaUtils.cpp -o MariaUtils.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/bheavner/macports/include/mysql57/mysql -Os -fno-omit-frame-pointer -arch x86_64 -I"/Users/bheavner/Library/R/3.5/library/BH/include" -I"/Users/bheavner/Library/R/3.5/library/plogr/include" -I"/Users/bheavner/Library/R/3.5/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/bheavner/macports/include/mysql57/mysql -Os -fno-omit-frame-pointer -arch x86_64 -I"/Users/bheavner/Library/R/3.5/library/BH/include" -I"/Users/bheavner/Library/R/3.5/library/plogr/include" -I"/Users/bheavner/Library/R/3.5/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c connection.cpp -o connection.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/bheavner/macports/include/mysql57/mysql -Os -fno-omit-frame-pointer -arch x86_64 -I"/Users/bheavner/Library/R/3.5/library/BH/include" -I"/Users/bheavner/Library/R/3.5/library/plogr/include" -I"/Users/bheavner/Library/R/3.5/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c driver.cpp -o driver.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/bheavner/macports/include/mysql57/mysql -Os -fno-omit-frame-pointer -arch x86_64 -I"/Users/bheavner/Library/R/3.5/library/BH/include" -I"/Users/bheavner/Library/R/3.5/library/plogr/include" -I"/Users/bheavner/Library/R/3.5/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c result.cpp -o result.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o RMariaDB.so DbConnection.o DbResult.o MariaBinding.o MariaResultImpl.o MariaResultPrep.o MariaResultSimple.o MariaRow.o MariaTypes.o MariaUtils.o RcppExports.o connection.o driver.o result.o -L/usr/local/opt/openssl/lib -L/Users/bheavner/macports/lib/mysql57/mysql -lmysqlclient -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/opt/openssl/lib'
installing to /Users/bheavner/Library/R/3.5/library/RMariaDB/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (RMariaDB)

With that, con <- DBI::dbConnect(RMariaDB::MariaDB(), default.file = "~/.mysql-uwit-6.cnf") works.

... Is that helpful?

[krlmlr]

Absolutely. What happens if you install remotes::install_github("r-dbi/RMariaDB") in the same way? Can you use the configuration file then?

[bheavner]

Yes, it does! But with more compilation warnings:

> remotes::install_github("r-dbi/RMariaDB")
Downloading GitHub repo r-dbi/RMariaDB@master
Downloading GitHub repo r-dbi/DBI@master
Installing package into ‘/Users/bheavner/Library/R/3.5/library’
(as ‘lib’ is unspecified)
* installing *source* package ‘DBI’ ...
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DBI)
Downloading GitHub repo r-dbi/DBItest@master
Skipping 1 packages ahead of CRAN: DBI
Installing package into ‘/Users/bheavner/Library/R/3.5/library’
(as ‘lib’ is unspecified)
* installing *source* package ‘DBItest’ ...
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DBItest)
Skipping 1 packages ahead of CRAN: DBI
Installing package into ‘/Users/bheavner/Library/R/3.5/library’
(as ‘lib’ is unspecified)
* installing *source* package ‘RMariaDB’ ...
Using mysql_config
Found mysql_config/mariadb_config cflags and libs!
Using PKG_CFLAGS=-I/Users/bheavner/macports/include/mysql57/mysql -Os -fno-omit-frame-pointer -arch x86_64
Using PKG_LIBS=-L/usr/local/opt/openssl/lib -L/Users/bheavner/macports/lib/mysql57/mysql -lmysqlclient -lz
** libs
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/bheavner/macports/include/mysql57/mysql -Os -fno-omit-frame-pointer -arch x86_64 -I"/Users/bheavner/Library/R/3.5/library/BH/include" -I"/Users/bheavner/Library/R/3.5/library/plogr/include" -I"/Users/bheavner/Library/R/3.5/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c DbConnection.cpp -o DbConnection.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/bheavner/macports/include/mysql57/mysql -Os -fno-omit-frame-pointer -arch x86_64 -I"/Users/bheavner/Library/R/3.5/library/BH/include" -I"/Users/bheavner/Library/R/3.5/library/plogr/include" -I"/Users/bheavner/Library/R/3.5/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c DbResult.cpp -o DbResult.o
In file included from DbResult.cpp:4:
In file included from ./MariaResultPrep.h:6:
In file included from ./MariaBinding.h:4:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/vector.hpp:26:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/container_fwd.hpp:61:
/Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Users/bheavner/Library/R/3.5/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/__config:390:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
                                                   ^
In file included from DbResult.cpp:4:
In file included from ./MariaResultPrep.h:6:
In file included from ./MariaBinding.h:4:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/vector.hpp:31:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/advanced_insert_int.hpp:28:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/copy_move_algo.hpp:24:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/iterator.hpp:24:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/intrusive/detail/iterator.hpp:25:
/Users/bheavner/Library/R/3.5/library/BH/include/boost/intrusive/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Users/bheavner/Library/R/3.5/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/__config:390:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
                                                   ^
In file included from DbResult.cpp:4:
In file included from ./MariaResultPrep.h:6:
In file included from ./MariaBinding.h:4:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/vector.hpp:31:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/advanced_insert_int.hpp:28:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/copy_move_algo.hpp:24:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/iterator.hpp:24:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/intrusive/detail/iterator.hpp:27:
/Users/bheavner/Library/R/3.5/library/BH/include/boost/move/detail/iterator_traits.hpp:29:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Users/bheavner/Library/R/3.5/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/__config:390:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
                                                   ^
3 warnings generated.
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/bheavner/macports/include/mysql57/mysql -Os -fno-omit-frame-pointer -arch x86_64 -I"/Users/bheavner/Library/R/3.5/library/BH/include" -I"/Users/bheavner/Library/R/3.5/library/plogr/include" -I"/Users/bheavner/Library/R/3.5/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c MariaBinding.cpp -o MariaBinding.o
In file included from MariaBinding.cpp:4:
In file included from ./MariaBinding.h:4:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/vector.hpp:26:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/container_fwd.hpp:61:
/Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Users/bheavner/Library/R/3.5/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/__config:390:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
                                                   ^
In file included from MariaBinding.cpp:4:
In file included from ./MariaBinding.h:4:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/vector.hpp:31:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/advanced_insert_int.hpp:28:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/copy_move_algo.hpp:24:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/iterator.hpp:24:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/intrusive/detail/iterator.hpp:25:
/Users/bheavner/Library/R/3.5/library/BH/include/boost/intrusive/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Users/bheavner/Library/R/3.5/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/__config:390:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
                                                   ^
In file included from MariaBinding.cpp:4:
In file included from ./MariaBinding.h:4:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/vector.hpp:31:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/advanced_insert_int.hpp:28:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/copy_move_algo.hpp:24:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/iterator.hpp:24:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/intrusive/detail/iterator.hpp:27:
/Users/bheavner/Library/R/3.5/library/BH/include/boost/move/detail/iterator_traits.hpp:29:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Users/bheavner/Library/R/3.5/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/__config:390:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
                                                   ^
3 warnings generated.
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/bheavner/macports/include/mysql57/mysql -Os -fno-omit-frame-pointer -arch x86_64 -I"/Users/bheavner/Library/R/3.5/library/BH/include" -I"/Users/bheavner/Library/R/3.5/library/plogr/include" -I"/Users/bheavner/Library/R/3.5/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c MariaResultImpl.cpp -o MariaResultImpl.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/bheavner/macports/include/mysql57/mysql -Os -fno-omit-frame-pointer -arch x86_64 -I"/Users/bheavner/Library/R/3.5/library/BH/include" -I"/Users/bheavner/Library/R/3.5/library/plogr/include" -I"/Users/bheavner/Library/R/3.5/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c MariaResultPrep.cpp -o MariaResultPrep.o
In file included from MariaResultPrep.cpp:3:
In file included from ./MariaResultPrep.h:6:
In file included from ./MariaBinding.h:4:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/vector.hpp:26:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/container_fwd.hpp:61:
/Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Users/bheavner/Library/R/3.5/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/__config:390:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
                                                   ^
In file included from MariaResultPrep.cpp:3:
In file included from ./MariaResultPrep.h:6:
In file included from ./MariaBinding.h:4:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/vector.hpp:31:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/advanced_insert_int.hpp:28:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/copy_move_algo.hpp:24:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/iterator.hpp:24:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/intrusive/detail/iterator.hpp:25:
/Users/bheavner/Library/R/3.5/library/BH/include/boost/intrusive/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Users/bheavner/Library/R/3.5/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/__config:390:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
                                                   ^
In file included from MariaResultPrep.cpp:3:
In file included from ./MariaResultPrep.h:6:
In file included from ./MariaBinding.h:4:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/vector.hpp:31:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/advanced_insert_int.hpp:28:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/copy_move_algo.hpp:24:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/iterator.hpp:24:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/intrusive/detail/iterator.hpp:27:
/Users/bheavner/Library/R/3.5/library/BH/include/boost/move/detail/iterator_traits.hpp:29:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Users/bheavner/Library/R/3.5/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/__config:390:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
                                                   ^
3 warnings generated.
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/bheavner/macports/include/mysql57/mysql -Os -fno-omit-frame-pointer -arch x86_64 -I"/Users/bheavner/Library/R/3.5/library/BH/include" -I"/Users/bheavner/Library/R/3.5/library/plogr/include" -I"/Users/bheavner/Library/R/3.5/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c MariaResultSimple.cpp -o MariaResultSimple.o
In file included from MariaResultSimple.cpp:3:
In file included from ./MariaResultSimple.h:6:
In file included from ./MariaBinding.h:4:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/vector.hpp:26:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/container_fwd.hpp:61:
/Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Users/bheavner/Library/R/3.5/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/__config:390:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
                                                   ^
In file included from MariaResultSimple.cpp:3:
In file included from ./MariaResultSimple.h:6:
In file included from ./MariaBinding.h:4:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/vector.hpp:31:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/advanced_insert_int.hpp:28:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/copy_move_algo.hpp:24:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/iterator.hpp:24:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/intrusive/detail/iterator.hpp:25:
/Users/bheavner/Library/R/3.5/library/BH/include/boost/intrusive/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Users/bheavner/Library/R/3.5/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/__config:390:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
                                                   ^
In file included from MariaResultSimple.cpp:3:
In file included from ./MariaResultSimple.h:6:
In file included from ./MariaBinding.h:4:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/vector.hpp:31:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/advanced_insert_int.hpp:28:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/copy_move_algo.hpp:24:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/iterator.hpp:24:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/intrusive/detail/iterator.hpp:27:
/Users/bheavner/Library/R/3.5/library/BH/include/boost/move/detail/iterator_traits.hpp:29:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Users/bheavner/Library/R/3.5/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/__config:390:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
                                                   ^
3 warnings generated.
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/bheavner/macports/include/mysql57/mysql -Os -fno-omit-frame-pointer -arch x86_64 -I"/Users/bheavner/Library/R/3.5/library/BH/include" -I"/Users/bheavner/Library/R/3.5/library/plogr/include" -I"/Users/bheavner/Library/R/3.5/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c MariaRow.cpp -o MariaRow.o
In file included from MariaRow.cpp:3:
In file included from ./MariaRow.h:5:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/vector.hpp:26:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/container_fwd.hpp:61:
/Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Users/bheavner/Library/R/3.5/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/__config:390:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
                                                   ^
In file included from MariaRow.cpp:3:
In file included from ./MariaRow.h:5:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/vector.hpp:31:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/advanced_insert_int.hpp:28:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/copy_move_algo.hpp:24:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/iterator.hpp:24:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/intrusive/detail/iterator.hpp:25:
/Users/bheavner/Library/R/3.5/library/BH/include/boost/intrusive/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Users/bheavner/Library/R/3.5/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/__config:390:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
                                                   ^
In file included from MariaRow.cpp:3:
In file included from ./MariaRow.h:5:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/vector.hpp:31:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/advanced_insert_int.hpp:28:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/copy_move_algo.hpp:24:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/iterator.hpp:24:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/intrusive/detail/iterator.hpp:27:
/Users/bheavner/Library/R/3.5/library/BH/include/boost/move/detail/iterator_traits.hpp:29:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Users/bheavner/Library/R/3.5/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/__config:390:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
                                                   ^
3 warnings generated.
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/bheavner/macports/include/mysql57/mysql -Os -fno-omit-frame-pointer -arch x86_64 -I"/Users/bheavner/Library/R/3.5/library/BH/include" -I"/Users/bheavner/Library/R/3.5/library/plogr/include" -I"/Users/bheavner/Library/R/3.5/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c MariaTypes.cpp -o MariaTypes.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/bheavner/macports/include/mysql57/mysql -Os -fno-omit-frame-pointer -arch x86_64 -I"/Users/bheavner/Library/R/3.5/library/BH/include" -I"/Users/bheavner/Library/R/3.5/library/plogr/include" -I"/Users/bheavner/Library/R/3.5/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c MariaUtils.cpp -o MariaUtils.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/bheavner/macports/include/mysql57/mysql -Os -fno-omit-frame-pointer -arch x86_64 -I"/Users/bheavner/Library/R/3.5/library/BH/include" -I"/Users/bheavner/Library/R/3.5/library/plogr/include" -I"/Users/bheavner/Library/R/3.5/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from ./RMariaDB_types.h:8:
In file included from ./MariaBinding.h:4:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/vector.hpp:26:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/container_fwd.hpp:61:
/Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Users/bheavner/Library/R/3.5/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/__config:390:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
                                                   ^
In file included from RcppExports.cpp:4:
In file included from ./RMariaDB_types.h:8:
In file included from ./MariaBinding.h:4:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/vector.hpp:31:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/advanced_insert_int.hpp:28:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/copy_move_algo.hpp:24:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/iterator.hpp:24:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/intrusive/detail/iterator.hpp:25:
/Users/bheavner/Library/R/3.5/library/BH/include/boost/intrusive/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Users/bheavner/Library/R/3.5/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/__config:390:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
                                                   ^
In file included from RcppExports.cpp:4:
In file included from ./RMariaDB_types.h:8:
In file included from ./MariaBinding.h:4:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/vector.hpp:31:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/advanced_insert_int.hpp:28:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/copy_move_algo.hpp:24:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/iterator.hpp:24:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/intrusive/detail/iterator.hpp:27:
/Users/bheavner/Library/R/3.5/library/BH/include/boost/move/detail/iterator_traits.hpp:29:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Users/bheavner/Library/R/3.5/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/__config:390:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
                                                   ^
3 warnings generated.
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/bheavner/macports/include/mysql57/mysql -Os -fno-omit-frame-pointer -arch x86_64 -I"/Users/bheavner/Library/R/3.5/library/BH/include" -I"/Users/bheavner/Library/R/3.5/library/plogr/include" -I"/Users/bheavner/Library/R/3.5/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c connection.cpp -o connection.o
In file included from connection.cpp:2:
In file included from ./RMariaDB_types.h:8:
In file included from ./MariaBinding.h:4:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/vector.hpp:26:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/container_fwd.hpp:61:
/Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Users/bheavner/Library/R/3.5/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/__config:390:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
                                                   ^
In file included from connection.cpp:2:
In file included from ./RMariaDB_types.h:8:
In file included from ./MariaBinding.h:4:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/vector.hpp:31:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/advanced_insert_int.hpp:28:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/copy_move_algo.hpp:24:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/iterator.hpp:24:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/intrusive/detail/iterator.hpp:25:
/Users/bheavner/Library/R/3.5/library/BH/include/boost/intrusive/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Users/bheavner/Library/R/3.5/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/__config:390:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
                                                   ^
In file included from connection.cpp:2:
In file included from ./RMariaDB_types.h:8:
In file included from ./MariaBinding.h:4:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/vector.hpp:31:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/advanced_insert_int.hpp:28:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/copy_move_algo.hpp:24:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/iterator.hpp:24:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/intrusive/detail/iterator.hpp:27:
/Users/bheavner/Library/R/3.5/library/BH/include/boost/move/detail/iterator_traits.hpp:29:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Users/bheavner/Library/R/3.5/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/__config:390:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
                                                   ^
3 warnings generated.
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/bheavner/macports/include/mysql57/mysql -Os -fno-omit-frame-pointer -arch x86_64 -I"/Users/bheavner/Library/R/3.5/library/BH/include" -I"/Users/bheavner/Library/R/3.5/library/plogr/include" -I"/Users/bheavner/Library/R/3.5/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c driver.cpp -o driver.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/bheavner/macports/include/mysql57/mysql -Os -fno-omit-frame-pointer -arch x86_64 -I"/Users/bheavner/Library/R/3.5/library/BH/include" -I"/Users/bheavner/Library/R/3.5/library/plogr/include" -I"/Users/bheavner/Library/R/3.5/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c result.cpp -o result.o
In file included from result.cpp:3:
In file included from ./RMariaDB_types.h:8:
In file included from ./MariaBinding.h:4:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/vector.hpp:26:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/container_fwd.hpp:61:
/Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Users/bheavner/Library/R/3.5/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/__config:390:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
                                                   ^
In file included from result.cpp:3:
In file included from ./RMariaDB_types.h:8:
In file included from ./MariaBinding.h:4:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/vector.hpp:31:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/advanced_insert_int.hpp:28:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/copy_move_algo.hpp:24:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/iterator.hpp:24:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/intrusive/detail/iterator.hpp:25:
/Users/bheavner/Library/R/3.5/library/BH/include/boost/intrusive/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Users/bheavner/Library/R/3.5/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/__config:390:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
                                                   ^
In file included from result.cpp:3:
In file included from ./RMariaDB_types.h:8:
In file included from ./MariaBinding.h:4:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/vector.hpp:31:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/advanced_insert_int.hpp:28:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/copy_move_algo.hpp:24:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/container/detail/iterator.hpp:24:
In file included from /Users/bheavner/Library/R/3.5/library/BH/include/boost/intrusive/detail/iterator.hpp:27:
/Users/bheavner/Library/R/3.5/library/BH/include/boost/move/detail/iterator_traits.hpp:29:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Users/bheavner/Library/R/3.5/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/__config:390:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
                                                   ^
3 warnings generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o RMariaDB.so DbConnection.o DbResult.o MariaBinding.o MariaResultImpl.o MariaResultPrep.o MariaResultSimple.o MariaRow.o MariaTypes.o MariaUtils.o RcppExports.o connection.o driver.o result.o -L/usr/local/opt/openssl/lib -L/Users/bheavner/macports/lib/mysql57/mysql -lmysqlclient -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/opt/openssl/lib'
installing to /Users/bheavner/Library/R/3.5/library/RMariaDB/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (RMariaDB)
> con <- DBI::dbConnect(RMariaDB::MariaDB(), default.file = "~/.mysql-uwit-6.cnf")
> # close db connection
>   DBI::dbDisconnect(con)

[krlmlr]

Thanks. Does this mean that the change in 18a071c doesn't affect if the .cnf file works? (I don't see why you're seeing many more compilation warnings when you install from master.) Can you still replicate the failures when installing from CRAN?

[bheavner]

I think that's correct - the change in 18a071c doesn't seem to affect if the .cnf file works, whether I have my $PATH correct or not.

Building from source on mac seems to matter - the CRAN binary does not work for me in an R session started from the terminal or from RStudio (which I've now hacked to get my environmental variables).

If I begin by deleting the DBI, DBITest, and RMariaDB packages, then start an R session in the terminal, installing the binary package from CRAN does not work:

> install.packages("RMariaDB")
Installing package into ‘/Users/bheavner/Library/R/3.5/library’
(as ‘lib’ is unspecified)
also installing the dependency ‘DBI’
> con <- DBI::dbConnect(RMariaDB::MariaDB(), default.file = "~/.mysql-uwit-6.cnf")
Error in connection_create(host, username, password, dbname, as.integer(port),  : 
  Failed to connect: Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2)

If I again delete the DBI, DBITest, and RMariaDB packages, then start an R session in the terminal. Installing from github master does work:

> remotes::install_github("r-dbi/RMariaDB")
...
* installing *source* package ‘DBI’ ...
...
* installing *source* package ‘DBItest’ ...
...
* installing *source* package ‘RMariaDB’ ...
...
* DONE (RMariaDB)
> con <- DBI::dbConnect(RMariaDB::MariaDB(), default.file = "~/.mysql-uwit-6.cnf")
> 

Similarly, if I install a source package (after deleting DBI, DBITest, and RMariaDB packages) from CRAN, it works:

> install.packages("RMariaDB", type = "source")
...
* installing *source* package ‘DBI’ ...
...
* installing *source* package ‘RMariaDB’ ...
...
* DONE (RMariaDB)
> con <- DBI::dbConnect(RMariaDB::MariaDB(), default.file = "~/.mysql-uwit-6.cnf")
>

I see the same behavior in my RStudio session, now that I have have confirmed my path includes macports binaries:

> Sys.getenv("PATH")
[1] "/Users/bheavner/anaconda3/bin:/Users/bheavner/google-cloud-sdk/bin:/Users/bheavner/Applications/phantomjs-2.1.1-macosx/bin/:/Users/bheavner/texlive/2016/bin/x86_64-darwin:/Users/bheavner/macports/bin:/Users/bheavner/macports/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/Library/TeX/texbin"

If I install the source package from CRAN with the default RStudio path, I see the various brewing messages, and it does not work:

> Sys.getenv("PATH")
[1] "/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/Library/TeX/texbin"

>install.packages("RMariaDB", type = "source")
> con <- DBI::dbConnect(RMariaDB::MariaDB(), default.file = "~/.mysql-uwit-6.cnf")
Error in connection_create(host, username, password, dbname, as.integer(port),  : 
  Failed to connect: Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2)

Similarly, it does not work if I have the default $PATH and install from 18a071c:

> Sys.getenv("PATH")
[1] "/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/Library/TeX/texbin"

> remotes::install_github("r-dbi/RMariaDB@18a071c")
> con <- DBI::dbConnect(RMariaDB::MariaDB(), default.file = "~/.mysql-uwit-6.cnf")
Error in connection_create(host, username, password, dbname, as.integer(port),  : 
  Failed to connect: Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2)

[krlmlr]

To me, this boils down to:

• Installing a binary from CRAN doesn't work
• Installing from source (CRAN or GitHub) works iff the PATH is set correctly

As @bheavner confirmed, even without having to change the code. Can we close this issue then?

It remains to see why installing from binary fails. Unfortunately, I have a very limited (read: no) understanding of how these thins work on the Mac, only https://xkcd.com/1987/ comes to mind. What does a successful installation using CRAN binaries look like?

[github-actions]

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