Error when installing RJDBC / odbc packages on RStudio Server AWS - r

Question

I am trying to install the RJDBC and odbc packages on my instance of RStudio server, which is running on AWS:
> Sys.info()
sysname release version
"Linux" "4.14.104-78.84.amzn1.x86_64" "#1 SMP Mon Mar 4 19:19:37 UTC 2019"
nodename machine login
"ip-10-0-0-170" "x86_64" "unknown"
user effective_user
"rstudio" "rstudio"
I get the same error with both installs. All other packages install without issues
I thought it may be to do with the drivers, so i downloaded them from this link: https://docs.aws.amazon.com/redshift/latest/mgmt/configure-jdbc-connection.html#download-jdbc-driver. But I still get the same error
The error message is printed below:
Installing package into ‘/home/rstudio/R/x86_64-redhat-linux-gnu-library/3.4’ (as ‘lib’ is
unspecified) also installing the dependency ‘rJava’
trying URL 'https://cran.rstudio.com/src/contrib/rJava_0.9-10.tar.gz'
Content type 'application/x-gzip' length 672577 bytes (656 KB)
================================================== downloaded 656 KB
trying URL 'https://cran.rstudio.com/src/contrib/RJDBC_0.2-7.1.tar.gz'
Content type 'application/x-gzip' length 16841 bytes (16 KB)
================================================== downloaded 16 KB
installing source package ‘rJava’ ...
** package ‘rJava’ successfully unpacked and MD5 sums checked checking for gcc... gcc -m64 -std=gnu99 checking whether the C compiler
works... yes checking for C compiler default output file name... a.out
checking for suffix of executables... checking whether we are cross
compiling... no checking for suffix of object files... o checking
whether we are using the GNU C compiler... yes checking whether gcc
-m64 -std=gnu99 accepts -g... yes checking for gcc -m64 -std=gnu99 option to accept ISO C89... none needed checking how to run the C
preprocessor... gcc -m64 -std=gnu99 -E checking for grep that handles
long lines and -e... /bin/grep checking for egrep... /bin/grep -E
checking for ANSI C header files... yes checking for sys/wait.h that
is POSIX.1 compatible... yes checking for sys/types.h... yes checking
for sys/stat.h... yes checking for stdlib.h... yes checking for
string.h... yes checking for memory.h... yes checking for strings.h...
yes checking for inttypes.h... yes checking for stdint.h... yes
checking for unistd.h... yes checking for string.h... (cached) yes
checking sys/time.h usability... yes checking sys/time.h presence...
yes checking for sys/time.h... yes checking for unistd.h... (cached)
yes checking for an ANSI C-conforming const... yes checking whether
time.h and sys/time.h may both be included... yes configure: checking
whether gcc -m64 -std=gnu99 supports static inline... yes checking
whether setjmp.h is POSIX.1 compatible... yes checking whether
sigsetjmp is declared... yes checking whether siglongjmp is
declared... yes checking Java support in R... present: interpreter :
'/usr/bin/java' archiver : '/usr/bin/jar' compiler :
'/usr/bin/javac' header prep.: '/usr/bin/javah' cpp flags :
'-I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux' java
libs : '-L/usr/lib/jvm/jre/lib/amd64/server -ljvm' checking whether
Java run-time works... yes checking whether -Xrs is supported... yes
checking whether -Xrs will be used... yes checking whether JNI
programs can be compiled... yes checking JNI data types... ok checking
whether JRI should be compiled (autodetect)... yes checking whether
debugging output should be enabled... no checking whether memory
profiling is desired... no checking whether threads support is
requested... no checking whether callbacks support is requested... no
checking whether JNI cache support is requested... no checking whether
headless init is enabled... no checking whether JRI is requested...
yes configure: creating ./config.status config.status: creating
src/Makevars config.status: creating R/zzz.R config.status: creating
src/config.h
=== configuring in jri (/tmp/RtmpYw2al0/R.INSTALL1d6d38609879/rJava/jri) configure: running
/bin/sh ./configure --disable-option-checking '--prefix=/usr/local'
--cache-file=/dev/null --srcdir=. checking build system type... x86_64-unknown-linux-gnu checking host system type...
x86_64-unknown-linux-gnu checking for gcc... gcc -m64 -std=gnu99
checking whether the C compiler works... yes checking for C compiler
default output file name... a.out checking for suffix of
executables... checking whether we are cross compiling... no checking
for suffix of object files... o checking whether we are using the GNU
C compiler... yes checking whether gcc -m64 -std=gnu99 accepts -g...
yes checking for gcc -m64 -std=gnu99 option to accept ISO C89... none
needed checking how to run the C preprocessor... gcc -m64 -std=gnu99
-E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files...
yes checking Java version... 1.7.0_201 checking whether /usr/bin/javah
actually works... yes checking for target flags... -target 1.4
-source 1.4 checking whether Java interpreter works... checking whether JNI programs can be compiled... yes checking whether JNI
programs can be run... yes checking JNI data types... ok checking
whether Rinterface.h exports R_CStackXXX variables... yes checking
whether Rinterface.h exports R_SignalHandlers... yes configure:
creating ./config.status config.status: creating src/Makefile
config.status: creating Makefile config.status: creating run
config.status: creating src/config.h
** libs gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I. -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c Rglue.c -o Rglue.o Rglue.c:860:13: warning: ‘new_jrectRef’ defined but not used
[-Wunused-function] static SEXP new_jrectRef(JNIEnv *env, jobject a,
const char *sig, SEXP dim ) {
^~~~~~~~~~~~ gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I. -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c arrayc.c -o arrayc.o gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I.
-I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c callJNI.c -o callJNI.o gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I.
-I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c callback.c -o callback.o gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I.
-I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c fields.c -o fields.o gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I.
-I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c init.c -o init.o init.c: In function ‘RinitJVM_real’: init.c:274:28: warning: unused
variable ‘add_xrs’ [-Wunused-variable]
int len = LENGTH(e), add_xrs = 1, joi = 0;
^~~~~~~ gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I. -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c jri_glue.c -o jri_glue.o gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I.
-I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c loader.c -o loader.o gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I.
-I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c otables.c -o otables.o gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I.
-I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c rJava.c -o rJava.o gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I.
-I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c tools.c -o tools.o gcc -m64 -std=gnu99 -shared -L/usr/lib64/R/lib -L/usr/local/lib64 -o
rJava.so Rglue.o arrayc.o callJNI.o callback.o fields.o init.o
jri_glue.o loader.o otables.o rJava.o tools.o
-L/usr/lib/jvm/jre/lib/amd64/server -ljvm -L/usr/lib64/R/lib -lR (cd ../jri && make) make[1]: Entering directory
/tmp/RtmpYw2al0/R.INSTALL1d6d38609879/rJava/jri' make -C src JRI.jar
make[2]: Entering directory
/tmp/RtmpYw2al0/R.INSTALL1d6d38609879/rJava/jri/src' /usr/bin/javac
-target 1.4 -source 1.4 -d . ../package-info.java ../RFactor.java ../REXP.java ../Rengine.java ../RList.java ../Mutex.java
../RConsoleOutputStream.java ../RMainLoopCallbacks.java
../RVector.java ../RBool.java warning: [options] bootstrap class path
not set in conjunction with -source 1.4 1 warning if [ -n
"/usr/bin/javah" ]; then /usr/bin/javah -d . -classpath .
org.rosuda.JRI.Rengine; fi gcc -m64 -std=gnu99 -c -o Rengine.o
Rengine.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -O2 -g
-pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -fpic -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -I/usr/include/R -I/usr/include/R gcc -m64 -std=gnu99 -c -o jri.o jri.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -O2 -g -pipe
-Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -fpic -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -I/usr/include/R -I/usr/include/R gcc -m64 -std=gnu99 -c -o Rcallbacks.o Rcallbacks.c -g -Iinclude -DRIF_HAS_CSTACK
-DRIF_HAS_RSIGHAND -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -fpic -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -I/usr/include/R -I/usr/include/R gcc -m64 -std=gnu99 -c -o Rinit.o Rinit.c -g -Iinclude
-DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -fpic -I/usr/include/R -I/usr/include/R gcc -m64 -std=gnu99 -c -o globals.o globals.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -O2 -g
-pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -fpic -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux gcc -m64 -std=gnu99 -c -o rjava.o rjava.c -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -fpic -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux rjava.c: In function ‘RJava_request_lock’: rjava.c:22:3: warning: ignoring return value of
‘write’, declared with attribute warn_unused_result [-Wunused-result]
write(ipcout, buf, sizeof(ptrlong));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rjava.c: In function
‘RJava_clear_lock’: rjava.c:30:3: warning: ignoring return value of
‘write’, declared with attribute warn_unused_result [-Wunused-result]
write(ipcout, buf, sizeof(ptrlong));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rjava.c: In function
‘RJava_request_callback’: rjava.c:39:3: warning: ignoring return value
of ‘write’, declared with attribute warn_unused_result
[-Wunused-result] write(ipcout, buf, sizeof(ptrlong) * 3);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rjava.c: In function
‘RJava_init_ctrl’: rjava.c:51:3: warning: ignoring return value of
‘write’, declared with attribute warn_unused_result [-Wunused-result]
write(ipcout, buf, sizeof(ptrlong));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rjava.c:52:3: warning: ignoring
return value of ‘read’, declared with attribute warn_unused_result
[-Wunused-result] read(resin, buf, sizeof(ptrlong) * 2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -m64 -std=gnu99 -o libjri.so
Rengine.o jri.o Rcallbacks.o Rinit.o globals.o rjava.o -shared
-L/usr/lib/jvm/jre/lib/amd64/server -ljvm -Wl,--export-dynamic -fopenmp -L/usr/local/lib64 -L/usr/lib64/R/lib -lR -ltre -lpcre -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n gcc: error: libgomp.spec: No such file or directory make[2]: * [libjri.so] Error 1 make[2]:
Leaving directory
/tmp/RtmpYw2al0/R.INSTALL1d6d38609879/rJava/jri/src' make[1]: ***
[src/JRI.jar] Error 2 make[1]: Leaving directory
/tmp/RtmpYw2al0/R.INSTALL1d6d38609879/rJava/jri' make: * [jri]
Error 2 ERROR: compilation failed for package ‘rJava’
removing ‘/home/rstudio/R/x86_64-redhat-linux-gnu-library/3.4/rJava’ Warning in install.packages : installation of package ‘rJava’ had
non-zero exit status ERROR: dependency ‘rJava’ is not available for
package ‘RJDBC’
removing ‘/home/rstudio/R/x86_64-redhat-linux-gnu-library/3.4/RJDBC’ Warning in install.packages : installation of package ‘RJDBC’ had
non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpSo7Mm5/downloaded_packages’