README.md

In jonkatz2/rmongodb: R-MongoDB driver

This is an unofficial version of rmongodb --

I have not yet changed the DESCRIPTION file!

It does not yet correctly compile rmongodb.so, so it will fail install.

Sometime in the summer of 2016 rmongodb was archived at the request of its maintainer.

As a package it was still completely functional, but the version of the c driver it shipped with is not supported by the latest version of MongoDB (any version greater than 2.6 requires some special authentication. I haven't gotten that far yet...

I was hoping to upgrade the package with the latest stable c driver, 1.4.1. It is slow going; at some point, probably around version 1.0, the libmongoc driver and libbson driver changed the nomenclature of all variables. Here's what I've done so far:

Notes: configure both libmongoc and libbson

./configure --enable-experimental-features=yes --with-libbson=bundled  --enable-ssl=no --enable-sasl=no  
? --enable-ssl=[auto/no/openssl/darwin]: prob need to find a way to do this in R for SCRAM-SHA-1 authentication.  
? --enable-sasl=[auto/yes/no] same as above

convert many \<global headers> to "local headers": Change include \<bson.h> to include "bson.h"

perl -pi -w -e 's/#include <bson.h>/#include "bson.h"/g;' $( grep -rl '#include <bson.h>' )

Change include to include "bcon.h"

perl -pi -w -e 's/#include <bcon.h>/#include "bcon.h"/g;' $( grep -rl '#include <bcon.h>' )

Change include to include "bson-string.h"

perl -pi -w -e 's/#include <bson-string.h>/#include "bson-string.h"/g;' $( grep -rl '#include <bson-string.h>' )

move src to same dir remove refs to yajl dir

perl -pi -w -e 's/<yajl\//</g;' $( grep -rl '<yajl/' )

change yajl includes to local files in:

mongoc-bson-yajl/bson-json.c:#include <yajl/yajl_parser.h>  
mongoc-bson-yajl/bson-json.c:#include <yajl/yajl_bytestack.h>  
mongoc-bson-yajl/yajl_version.c:#include <yajl/yajl_version.h>  
mongoc-bson-yajl/yajl_gen.h:#include <yajl/yajl_common.h>  
mongoc-bson-yajl/yajl_version.h:#include <yajl/yajl_common.h>  
mongoc-bson-yajl/yajl_tree.h:#include <yajl/yajl_common.h>  
mongoc-bson-yajl/yajl_parse.h:#include <yajl/yajl_common.h>

using:

perl -pi -w -e 's/#include <yajl_parser.h>/#include "yajl_parser.h"/g;' $( grep -rl '#include <yajl_parser.h>' )  
perl -pi -w -e 's/#include <yajl_bytestack.h>/#include "yajl_bytestack.h"/g;' $( grep -rl '#include <yajl_bytestack.h>' )  
perl -pi -w -e 's/#include <yajl_version.h>/#include "yajl_version.h"/g;' $( grep -rl '#include <yajl_version.h>' )  
perl -pi -w -e 's/#include <yajl_common.h>/#include "yajl_common.h"/g;' $( grep -rl '#include <yajl_common.h>' )

add vars -DMONGOC_COMPILATION -DBSON_COMPILATION to Makevars

change variables mongo -> mongoc_client_t from mongo-client.h:

/**
 * mongoc_client_t:
 *
 * The mongoc_client_t structure maintains information about a connection to
 * a MongoDB server.
*/

change variable bson -> bson_t

from bson-types.h:

/**
 * bson_t:
 *
 * This structure manages a buffer whose contents are a properly formatted
 * BSON document. You may perform various transforms on the BSON documents.
 * Additionally, it can be iterated over using bson_iter_t.
 *
 * See bson_iter_init() for iterating the contents of a bson_t.
 *
 * When building a bson_t structure using the various append functions,
 * memory allocations may occur. That is performed using power of two
 * allocations and realloc().
 *
 * See http://bsonspec.org for the BSON document spec.
 *
 * This structure is meant to fit in two sequential 64-byte cachelines.
*/

(I've started this in utility.h, api_bson.h)

R CMD build rmongodb_0.1.1 --no-build-vignettes

install to test compile:

R CMD INSTALL rmongodb_1.8.0.tar.gz

or just build shared lib:

R CMD SHLIB -o rmongodb.so a.f b.f -L/\<opt/acml3.5.0/gnu64/lib\> -l\<acml\>

view contents of dynamic shared object:

nm -D --defined-only rmongodb.so

jonkatz2/rmongodb documentation built on May 19, 2019, 7:30 p.m.