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jeroen / mongolite

Fast and Simple MongoDB Client for R
https://jeroen.github.io/mongolite/
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Installation failure on Ubuntu 16.04 #129

Closed edfincham closed 6 years ago

edfincham commented 6 years ago

Been trying numerous ways to install but keep on getting the following error.

(mongodb installed and service running fine)

> install.packages("mongolite", dependencies = TRUE, repos = "http://cran.us.r-project.org")
trying URL 'http://cran.us.r-project.org/src/contrib/mongolite_1.5.tar.gz'
Content type 'application/x-gzip' length 503191 bytes (491 KB)
==================================================
downloaded 491 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 -lresolv
SASL does not have sasl_client_done.
Compiling with extra alignment.
** libs
rm -f mongolite.so mongoc/libstatmongoc.a bson/libstatbson.a bson/bcon.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.o bson/bson-decimal128.o jsonsl/jsonsl.o 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-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-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-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-cluster-sasl.o mongoc/mongoc-cmd.o mongoc/mongoc-change-stream.o mongoc/mongoc-client-session.o mongoc/mongoc-cluster-cyrus.o mongoc/mongoc-compression.o mongoc/mongoc-cyrus.o mongoc/mongoc-write-command-legacy.o mongoc/mongoc-linux-distro-scanner.o bson.o client.o collection.o cursor.o hex.o mongo_log.o reader.o utils.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bson.c -o bson.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c client.c -o client.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c collection.c -o collection.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c cursor.c -o cursor.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c hex.c -o hex.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongo_log.c -o mongo_log.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c reader.c -o reader.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c utils.c -o utils.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bson/bcon.c -o bson/bcon.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bson/bson-clock.c -o bson/bson-clock.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bson/bson-context.c -o bson/bson-context.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bson/bson-error.c -o bson/bson-error.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bson/bson-iso8601.c -o bson/bson-iso8601.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bson/bson-iter.c -o bson/bson-iter.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bson/bson-json.c -o bson/bson-json.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bson/bson-keys.c -o bson/bson-keys.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bson/bson-md5.c -o bson/bson-md5.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bson/bson-memory.c -o bson/bson-memory.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bson/bson-oid.c -o bson/bson-oid.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bson/bson-reader.c -o bson/bson-reader.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bson/bson-string.c -o bson/bson-string.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bson/bson-timegm.c -o bson/bson-timegm.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bson/bson-utf8.c -o bson/bson-utf8.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bson/bson-value.c -o bson/bson-value.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bson/bson.c -o bson/bson.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bson/bson-decimal128.c -o bson/bson-decimal128.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c jsonsl/jsonsl.c -o jsonsl/jsonsl.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-array.c -o mongoc/mongoc-array.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-b64.c -o mongoc/mongoc-b64.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-buffer.c -o mongoc/mongoc-buffer.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-bulk-operation.c -o mongoc/mongoc-bulk-operation.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-client-pool.c -o mongoc/mongoc-client-pool.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-client.c -o mongoc/mongoc-client.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-cluster.c -o mongoc/mongoc-cluster.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-collection.c -o mongoc/mongoc-collection.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-counters.c -o mongoc/mongoc-counters.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-cursor-array.c -o mongoc/mongoc-cursor-array.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-cursor-cursorid.c -o mongoc/mongoc-cursor-cursorid.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-cursor-transform.c -o mongoc/mongoc-cursor-transform.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-cursor.c -o mongoc/mongoc-cursor.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-database.c -o mongoc/mongoc-database.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-gridfs-file-list.c -o mongoc/mongoc-gridfs-file-list.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-gridfs-file-page.c -o mongoc/mongoc-gridfs-file-page.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-gridfs-file.c -o mongoc/mongoc-gridfs-file.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-gridfs.c -o mongoc/mongoc-gridfs.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-index.c -o mongoc/mongoc-index.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-init.c -o mongoc/mongoc-init.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-list.c -o mongoc/mongoc-list.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-log.c -o mongoc/mongoc-log.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-rand-openssl.c -o mongoc/mongoc-rand-openssl.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-read-prefs.c -o mongoc/mongoc-read-prefs.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-rpc.c -o mongoc/mongoc-rpc.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-sasl.c -o mongoc/mongoc-sasl.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-scram.c -o mongoc/mongoc-scram.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-socket.c -o mongoc/mongoc-socket.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-ssl.c -o mongoc/mongoc-ssl.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-stream-buffered.c -o mongoc/mongoc-stream-buffered.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-stream-socket.c -o mongoc/mongoc-stream-socket.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-stream-tls.c -o mongoc/mongoc-stream-tls.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-stream.c -o mongoc/mongoc-stream.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-uri.c -o mongoc/mongoc-uri.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-util.c -o mongoc/mongoc-util.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-write-command.c -o mongoc/mongoc-write-command.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-write-concern.c -o mongoc/mongoc-write-concern.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-topology-description-apm.c -o mongoc/mongoc-topology-description-apm.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-async.c -o mongoc/mongoc-async.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-async-cmd.c -o mongoc/mongoc-async-cmd.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-host-list.c -o mongoc/mongoc-host-list.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-set.c -o mongoc/mongoc-set.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-server-description.c -o mongoc/mongoc-server-description.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-topology-description.c -o mongoc/mongoc-topology-description.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-topology.c -o mongoc/mongoc-topology.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-topology-scanner.c -o mongoc/mongoc-topology-scanner.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-version-functions.c -o mongoc/mongoc-version-functions.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-memcmp.c -o mongoc/mongoc-memcmp.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-server-stream.c -o mongoc/mongoc-server-stream.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-find-and-modify.c -o mongoc/mongoc-find-and-modify.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-read-concern.c -o mongoc/mongoc-read-concern.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-openssl.c -o mongoc/mongoc-openssl.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-apm.c -o mongoc/mongoc-apm.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-crypto.c -o mongoc/mongoc-crypto.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-crypto-openssl.c -o mongoc/mongoc-crypto-openssl.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-handshake.c -o mongoc/mongoc-handshake.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-stream-tls-openssl.c -o mongoc/mongoc-stream-tls-openssl.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-stream-tls-openssl-bio.c -o mongoc/mongoc-stream-tls-openssl-bio.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-cluster-sasl.c -o mongoc/mongoc-cluster-sasl.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-cmd.c -o mongoc/mongoc-cmd.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-change-stream.c -o mongoc/mongoc-change-stream.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-client-session.c -o mongoc/mongoc-client-session.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-cluster-cyrus.c -o mongoc/mongoc-cluster-cyrus.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-compression.c -o mongoc/mongoc-compression.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-cyrus.c -o mongoc/mongoc-cyrus.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-write-command-legacy.c -o mongoc/mongoc-write-command-legacy.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -Ijsonsl -Ibson -Imongoc -DBSON_COMPILATION -DMONGOC_COMPILATION -DBSON_EXTRA_ALIGN     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mongoc/mongoc-linux-distro-scanner.c -o mongoc/mongoc-linux-distro-scanner.o
ar rcs bson/libstatbson.a bson/bcon.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.o bson/bson-decimal128.o jsonsl/jsonsl.o
ar rcs mongoc/libstatmongoc.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-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-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-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-cluster-sasl.o mongoc/mongoc-cmd.o mongoc/mongoc-change-stream.o mongoc/mongoc-client-session.o mongoc/mongoc-cluster-cyrus.o mongoc/mongoc-compression.o mongoc/mongoc-cyrus.o mongoc/mongoc-write-command-legacy.o mongoc/mongoc-linux-distro-scanner.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o mongolite.so bson.o client.o collection.o cursor.o hex.o mongo_log.o reader.o utils.o -Lmongoc -lstatmongoc -Lbson -lstatbson -lsasl2 -lssl -lcrypto -lresolv -lz -L/usr/lib/R/lib -lR
installing to /home/ed/R/x86_64-pc-linux-gnu-library/3.4/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 '/home/ed/R/x86_64-pc-linux-gnu-library/3.4/mongolite/libs/mongolite.so':
  libsasl2.so.3: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/ed/R/x86_64-pc-linux-gnu-library/3.4/mongolite’
Warning in install.packages :
  installation of package ‘mongolite’ had non-zero exit status
jeroen commented 6 years ago

Something is up with your installation of libsasl2-dev or libsasl2-2. Try reinstalling:

sudo apt-get remove --purge libsasl2-dev libsasl2-2
sudo apt-get install libsasl2-dev

You didn't install a custom version of sasl from source in /usr/local did you?

jeroen commented 6 years ago

Are you using ubunut's standard r-base-dev or did you get it from somewhere else?

edfincham commented 6 years ago

Thank you for the quick reply! Something is definitely up with my installation of libsasl2-dev:

Both apt-get commands return:

Unable to locate package libsasl2-dev

I'll investigate...

I'm using the standard ubuntu r-base-dev

edfincham commented 6 years ago

The absence of libsasl2-dev was tripping me up - thanks for the pointer and help :+1:

Had to manually install then it worked a treat. Closing this.

pnojai commented 4 years ago

I attempted the libsasl removal, but the warning was going to remove additionally a lot of libraries I've worked to accumulate. However, I didn't have libsasl2-dev. Just installing that resolved the mongolite installation failure on Ubuntu for me.

Seyphaton commented 4 years ago

sudo apt-get install libsasl2-dev solved the mongolite installation problem for me aswell