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jeroen / mongolite

Fast and Simple MongoDB Client for R
https://jeroen.github.io/mongolite/
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Installation via R failure #110

Closed nstauder2 closed 6 years ago

nstauder2 commented 6 years ago

Installation via Anaconda R fails (mongodb and mongodb-server installed, mongod service running):

> install.packages("mongolite",dependencies =TRUE,repos='http://cran.us.r-project.org')
trying URL 'http://cran.us.r-project.org/src/contrib/mongolite_1.2.tar.gz'
Content type 'application/x-gzip' length 487399 bytes (475 KB)
==================================================
downloaded 475 KB

* installing *source* package ‘mongolite’ ...
** package ‘mongolite’ successfully unpacked and MD5 sums checked
Found pkg-config cflags and libs!
Using PKG_CFLAGS= 
Using PKG_LIBS=-lsasl2 -lssl -lcrypto  
SASL has sasl_client_done.
Compiling with extra alignment.
** libs
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c bson.c -o bson.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c client.c -o client.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c collection.c -o collection.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c cursor.c -o cursor.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c hex.c -o hex.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongo_log.c -o mongo_log.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c reader.c -o reader.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c utils.c -o utils.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c bson/bcon.c -o bson/bcon.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c bson/bson-atomic.c -o bson/bson-atomic.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c bson/bson-clock.c -o bson/bson-clock.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c bson/bson-context.c -o bson/bson-context.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c bson/bson-error.c -o bson/bson-error.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c bson/bson-iso8601.c -o bson/bson-iso8601.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c bson/bson-iter.c -o bson/bson-iter.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c bson/bson-json.c -o bson/bson-json.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c bson/bson-keys.c -o bson/bson-keys.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c bson/bson-md5.c -o bson/bson-md5.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c bson/bson-memory.c -o bson/bson-memory.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c bson/bson-oid.c -o bson/bson-oid.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c bson/bson-reader.c -o bson/bson-reader.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c bson/bson-string.c -o bson/bson-string.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c bson/bson-timegm.c -o bson/bson-timegm.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c bson/bson-utf8.c -o bson/bson-utf8.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c bson/bson-value.c -o bson/bson-value.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c bson/bson-version-functions.c -o bson/bson-version-functions.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c bson/bson-writer.c -o bson/bson-writer.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c bson/bson.c -o bson/bson.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c bson/bson-decimal128.c -o bson/bson-decimal128.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c jsonsl/jsonsl.c -o jsonsl/jsonsl.o
ar rcs libbson.a bson/bcon.o bson/bson-atomic.o bson/bson-clock.o bson/bson-context.o bson/bson-error.o bson/bson-iso8601.o bson/bson-iter.o bson/bson-json.o bson/bson-keys.o bson/bson-md5.o bson/bson-memory.o bson/bson-oid.o bson/bson-reader.o bson/bson-string.o bson/bson-timegm.o bson/bson-utf8.o bson/bson-value.o bson/bson-version-functions.o bson/bson-writer.o bson/bson.o bson/bson-decimal128.o jsonsl/jsonsl.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-array.c -o mongoc/mongoc-array.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-b64.c -o mongoc/mongoc-b64.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-buffer.c -o mongoc/mongoc-buffer.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-bulk-operation.c -o mongoc/mongoc-bulk-operation.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-client-pool.c -o mongoc/mongoc-client-pool.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-client.c -o mongoc/mongoc-client.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-cluster.c -o mongoc/mongoc-cluster.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-collection.c -o mongoc/mongoc-collection.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-counters.c -o mongoc/mongoc-counters.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-cursor-array.c -o mongoc/mongoc-cursor-array.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-cursor-cursorid.c -o mongoc/mongoc-cursor-cursorid.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-cursor-transform.c -o mongoc/mongoc-cursor-transform.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-cursor.c -o mongoc/mongoc-cursor.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-database.c -o mongoc/mongoc-database.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-gridfs-file-list.c -o mongoc/mongoc-gridfs-file-list.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-gridfs-file-page.c -o mongoc/mongoc-gridfs-file-page.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-gridfs-file.c -o mongoc/mongoc-gridfs-file.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-gridfs.c -o mongoc/mongoc-gridfs.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-index.c -o mongoc/mongoc-index.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-init.c -o mongoc/mongoc-init.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-list.c -o mongoc/mongoc-list.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-log.c -o mongoc/mongoc-log.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-matcher-op.c -o mongoc/mongoc-matcher-op.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-matcher.c -o mongoc/mongoc-matcher.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-queue.c -o mongoc/mongoc-queue.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-rand-openssl.c -o mongoc/mongoc-rand-openssl.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-read-prefs.c -o mongoc/mongoc-read-prefs.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-rpc.c -o mongoc/mongoc-rpc.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-sasl.c -o mongoc/mongoc-sasl.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-scram.c -o mongoc/mongoc-scram.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-socket.c -o mongoc/mongoc-socket.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-ssl.c -o mongoc/mongoc-ssl.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-stream-buffered.c -o mongoc/mongoc-stream-buffered.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-stream-file.c -o mongoc/mongoc-stream-file.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-stream-gridfs.c -o mongoc/mongoc-stream-gridfs.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-stream-socket.c -o mongoc/mongoc-stream-socket.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-stream-tls.c -o mongoc/mongoc-stream-tls.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-stream.c -o mongoc/mongoc-stream.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-uri.c -o mongoc/mongoc-uri.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-util.c -o mongoc/mongoc-util.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-write-command.c -o mongoc/mongoc-write-command.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-write-concern.c -o mongoc/mongoc-write-concern.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-topology-description-apm.c -o mongoc/mongoc-topology-description-apm.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-async.c -o mongoc/mongoc-async.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-async-cmd.c -o mongoc/mongoc-async-cmd.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-host-list.c -o mongoc/mongoc-host-list.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-opcode.c -o mongoc/mongoc-opcode.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-server-description.c -o mongoc/mongoc-server-description.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-set.c -o mongoc/mongoc-set.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-topology-description.c -o mongoc/mongoc-topology-description.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-topology.c -o mongoc/mongoc-topology.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-topology-scanner.c -o mongoc/mongoc-topology-scanner.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-version-functions.c -o mongoc/mongoc-version-functions.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-memcmp.c -o mongoc/mongoc-memcmp.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-server-stream.c -o mongoc/mongoc-server-stream.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-find-and-modify.c -o mongoc/mongoc-find-and-modify.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-read-concern.c -o mongoc/mongoc-read-concern.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-openssl.c -o mongoc/mongoc-openssl.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-apm.c -o mongoc/mongoc-apm.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-crypto.c -o mongoc/mongoc-crypto.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-crypto-openssl.c -o mongoc/mongoc-crypto-openssl.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-handshake.c -o mongoc/mongoc-handshake.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-stream-tls-openssl.c -o mongoc/mongoc-stream-tls-openssl.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-stream-tls-openssl-bio.c -o mongoc/mongoc-stream-tls-openssl-bio.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-linux-distro-scanner.c -o mongoc/mongoc-linux-distro-scanner.o
gcc -std=gnu99 -I/usr/local/anaconda/lib/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DMONGOC_HAVE_SASL_CLIENT_DONE -DBSON_EXTRA_ALIGN  -I/usr/local/anaconda/include   -fpic  -I/usr/local/anaconda/include  -c mongoc/mongoc-cluster-sasl.c -o mongoc/mongoc-cluster-sasl.o
ar rcs libmongoc.a mongoc/mongoc-array.o mongoc/mongoc-b64.o mongoc/mongoc-buffer.o mongoc/mongoc-bulk-operation.o mongoc/mongoc-client-pool.o mongoc/mongoc-client.o mongoc/mongoc-cluster.o mongoc/mongoc-collection.o mongoc/mongoc-counters.o mongoc/mongoc-cursor-array.o mongoc/mongoc-cursor-cursorid.o mongoc/mongoc-cursor-transform.o mongoc/mongoc-cursor.o mongoc/mongoc-database.o mongoc/mongoc-gridfs-file-list.o mongoc/mongoc-gridfs-file-page.o mongoc/mongoc-gridfs-file.o mongoc/mongoc-gridfs.o mongoc/mongoc-index.o mongoc/mongoc-init.o mongoc/mongoc-list.o mongoc/mongoc-log.o mongoc/mongoc-matcher-op.o mongoc/mongoc-matcher.o mongoc/mongoc-queue.o mongoc/mongoc-rand-openssl.o mongoc/mongoc-read-prefs.o mongoc/mongoc-rpc.o mongoc/mongoc-sasl.o mongoc/mongoc-scram.o mongoc/mongoc-socket.o mongoc/mongoc-ssl.o mongoc/mongoc-stream-buffered.o mongoc/mongoc-stream-file.o mongoc/mongoc-stream-gridfs.o mongoc/mongoc-stream-socket.o mongoc/mongoc-stream-tls.o mongoc/mongoc-stream.o mongoc/mongoc-uri.o mongoc/mongoc-util.o mongoc/mongoc-write-command.o mongoc/mongoc-write-concern.o mongoc/mongoc-topology-description-apm.o mongoc/mongoc-async.o mongoc/mongoc-async-cmd.o mongoc/mongoc-host-list.o mongoc/mongoc-opcode.o mongoc/mongoc-server-description.o mongoc/mongoc-set.o mongoc/mongoc-server-description.o mongoc/mongoc-topology-description.o mongoc/mongoc-topology.o mongoc/mongoc-topology-scanner.o mongoc/mongoc-version-functions.o mongoc/mongoc-memcmp.o mongoc/mongoc-server-stream.o mongoc/mongoc-find-and-modify.o mongoc/mongoc-read-concern.o mongoc/mongoc-openssl.o mongoc/mongoc-apm.o mongoc/mongoc-crypto.o mongoc/mongoc-crypto-openssl.o mongoc/mongoc-handshake.o mongoc/mongoc-stream-tls-openssl.o mongoc/mongoc-stream-tls-openssl-bio.o mongoc/mongoc-linux-distro-scanner.o mongoc/mongoc-cluster-sasl.o
gcc -std=gnu99 -shared -L/usr/local/anaconda/lib/R/lib -L/usr/local/anaconda/lib -lgfortran -o mongolite.so bson.o client.o collection.o cursor.o hex.o mongo_log.o reader.o utils.o -L. -lmongoc -lbson -lsasl2 -lssl -lcrypto -L/usr/local/anaconda/lib/R/lib -lR
installing to /usr/local/anaconda/lib/R/library/mongolite/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error: package or namespace load failed for ‘mongolite’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/usr/local/anaconda/lib/R/library/mongolite/libs/mongolite.so':
  /usr/local/anaconda/lib/R/library/mongolite/libs/mongolite.so: undefined symbol: bson_iter_int32
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/usr/local/anaconda/lib/R/library/mongolite’

The downloaded source packages are in
    ‘/tmp/RtmpBvRVDx/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("mongolite", dependencies = TRUE, repos = "http://cran.us.r-project.org") :
  installation of package ‘mongolite’ had non-zero exit status
>
jeroen commented 6 years ago

Hmm, it works fine on regular CentOS 7 when R is installed from EPEL.Do you really need to use anaconda?

jeroen commented 6 years ago

Do you have conflicting copies of libbson or libmongoc installed in /usr/local/lib perhaps?

nstauder2 commented 6 years ago

Nothing is in /usr/local/lib, but in /usr/local/anaconda/lib there are:

libbson.a libbson.so libbson.so.0.7 libbson.so.0.7.1

and

libmongoc.a libmongoc.so libmongoc.so.0.7 libmongoc.so.0.7.1

Many of our machines use Anaconda R for ease of installation, but this could be changed if all else fails.

On Wed, Sep 27, 2017 at 3:53 PM, Jeroen Ooms notifications@github.com wrote:

Do you have conflicting copies of libbson or libmongoc installed in /usr/local/lib perhaps?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/jeroen/mongolite/issues/110#issuecomment-332636617, or mute the thread https://github.com/notifications/unsubscribe-auth/ALaHnmCCYJD84fjH2Y44DsRSEVCdMhKxks5smqfVgaJpZM4PmTTs .

jeroen commented 6 years ago

The libbson that you ship with anaconda conflicts with the one bundled one in mongolite. You somehow need to install the package without linking to -L/usr/local/anaconda/lib or remove libbson...

I can add a workaround for this in the next version of mongolite...

nstauder2 commented 6 years ago

That seems to have helped. I moved all of the libbson files out of the directory and tried again. It seems to have moved on to this error:

/usr/local/anaconda/lib/R/library/mongolite/libs/mongolite.so: undefined symbol: mongoc_read_prefs_new

jeroen commented 6 years ago

You need to do the same for libmongoc

nstauder2 commented 6 years ago

Great! That seems to have fixed it!

`** testing if installed package can be loaded

Thank you very much for helping so quickly!