Fedora Install unixODBC
Encountered a problem while running the RODBC library from the R prompt as the root user, as follows:
> install.packages('RODBC') |
It failed with the following library dependency:
checking for unistd.h... yes
checking sql.h usability... no
checking sql.h presence... no
checking for sql.h... no
checking sqlext.h usability... no
checking sqlext.h presence... no
checking for sqlext.h... no
configure: error: "ODBC headers sql.h and sqlext.h not found"
ERROR: configuration failed for package ‘RODBC’
* removing ‘/usr/lib64/R/library/RODBC’
The downloaded source packages are in
‘/tmp/RtmpdT1gay/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("RODBC") :
installation of package ‘RODBC’ had non-zero exit status |
I installed unixODBC-devel and unixODBC-gui-qt libraries to fix the library dependencies with the following command as the root user:
yum install -y unixODBC* |
It should show you the following when it installs the unixODBC-devel and unixODBC-gui-qt libraries:
Loaded plugins: langpacks, refresh-packagekit You need to be root to perform this command. [student@localhost ~]$ su - root Password: Last login: Fri Apr 20 21:18:56 PDT 2018 on pts/1 [root@localhost ~]# yum install -y unixODBC* Loaded plugins: langpacks, refresh-packagekit cassandra/signature | 819 B 00:00 cassandra/signature | 2.9 kB 00:00 !!! fedora/20/x86_64/metalink | 3.3 kB 00:00 mysql-connectors-community | 2.5 kB 00:00 mysql-tools-community | 2.5 kB 00:00 mysql56-community | 2.5 kB 00:00 http://yum.postgresql.org/9.3/fedora/fedora-20-x86_64/repodata/repomd.xml: [Errno 14] HTTP Error 404 - Not Found Trying other mirror. updates/20/x86_64/metalink | 3.1 kB 00:00 Package unixODBC-2.3.2-4.fc20.x86_64 already installed and latest version Resolving Dependencies --> Running transaction check ---> Package unixODBC-devel.x86_64 0:2.3.2-4.fc20 will be installed ---> Package unixODBC-gui-qt.x86_64 0:0-0.8.20120105svn98.fc20 will be installed --> Processing Dependency: libQtNetwork.so.4()(64bit) for package: unixODBC-gui-qt-0-0.8.20120105svn98.fc20.x86_64 --> Processing Dependency: libQtGui.so.4()(64bit) for package: unixODBC-gui-qt-0-0.8.20120105svn98.fc20.x86_64 --> Processing Dependency: libQtCore.so.4()(64bit) for package: unixODBC-gui-qt-0-0.8.20120105svn98.fc20.x86_64 --> Processing Dependency: libQtAssistantClient.so.4()(64bit) for package: unixODBC-gui-qt-0-0.8.20120105svn98.fc20.x86_64 --> Running transaction check ---> Package qt.x86_64 1:4.8.6-30.fc20 will be installed --> Processing Dependency: qt-common = 1:4.8.6-30.fc20 for package: 1:qt-4.8.6-30.fc20.x86_64 --> Processing Dependency: qt-settings for package: 1:qt-4.8.6-30.fc20.x86_64 ---> Package qt-assistant-adp.x86_64 0:4.6.3-6.fc20 will be installed ---> Package qt-x11.x86_64 1:4.8.6-30.fc20 will be installed --> Processing Dependency: libmng.so.1()(64bit) for package: 1:qt-x11-4.8.6-30.fc20.x86_64 --> Processing Dependency: libclucene.so.3()(64bit) for package: 1:qt-x11-4.8.6-30.fc20.x86_64 --> Running transaction check ---> Package clucene09-core.x86_64 0:0.9.21b-13.fc20 will be installed ---> Package libmng.x86_64 0:1.0.10-12.fc20 will be installed ---> Package qt-common.noarch 1:4.8.6-30.fc20 will be installed ---> Package qt-settings.noarch 0:20-18.fc20 will be installed --> Finished Dependency Resolution Dependencies Resolved ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: unixODBC-devel x86_64 2.3.2-4.fc20 updates 55 k unixODBC-gui-qt x86_64 0-0.8.20120105svn98.fc20 fedora 624 k Installing for dependencies: clucene09-core x86_64 0.9.21b-13.fc20 updates 300 k libmng x86_64 1.0.10-12.fc20 fedora 166 k qt x86_64 1:4.8.6-30.fc20 updates 4.7 M qt-assistant-adp x86_64 4.6.3-6.fc20 fedora 257 k qt-common noarch 1:4.8.6-30.fc20 updates 5.8 k qt-settings noarch 20-18.fc20 updates 19 k qt-x11 x86_64 1:4.8.6-30.fc20 updates 12 M Transaction Summary ================================================================================ Install 2 Packages (+7 Dependent packages) Total download size: 18 M Installed size: 56 M Downloading packages: (1/9): libmng-1.0.10-12.fc20.x86_64.rpm | 166 kB 00:01 (2/9): clucene09-core-0.9.21b-13.fc20.x86_64.rpm | 300 kB 00:01 (3/9): qt-4.8.6-30.fc20.x86_64.rpm | 4.7 MB 00:00 (4/9): qt-common-4.8.6-30.fc20.noarch.rpm | 5.8 kB 00:00 (5/9): qt-settings-20-18.fc20.noarch.rpm | 19 kB 00:00 (6/9): qt-assistant-adp-4.6.3-6.fc20.x86_64.rpm | 257 kB 00:00 (7/9): qt-x11-4.8.6-30.fc20.x86_64.rpm | 12 MB 00:01 (8/9): unixODBC-devel-2.3.2-4.fc20.x86_64.rpm | 55 kB 00:00 (9/9): unixODBC-gui-qt-0-0.8.20120105svn98.fc20.x86_64.rpm | 624 kB 00:01 -------------------------------------------------------------------------------- Total 4.1 MB/s | 18 MB 00:04 Running transaction check Running transaction test Transaction test succeeded Running transaction (shutdown inhibited) Installing : libmng-1.0.10-12.fc20.x86_64 1/9 Installing : qt-settings-20-18.fc20.noarch 2/9 Installing : 1:qt-common-4.8.6-30.fc20.noarch 3/9 Installing : 1:qt-4.8.6-30.fc20.x86_64 4/9 Installing : clucene09-core-0.9.21b-13.fc20.x86_64 5/9 Installing : 1:qt-x11-4.8.6-30.fc20.x86_64 6/9 Installing : qt-assistant-adp-4.6.3-6.fc20.x86_64 7/9 Installing : unixODBC-gui-qt-0-0.8.20120105svn98.fc20.x86_64 8/9 Installing : unixODBC-devel-2.3.2-4.fc20.x86_64 9/9 Verifying : clucene09-core-0.9.21b-13.fc20.x86_64 1/9 Verifying : unixODBC-gui-qt-0-0.8.20120105svn98.fc20.x86_64 2/9 Verifying : 1:qt-x11-4.8.6-30.fc20.x86_64 3/9 Verifying : 1:qt-4.8.6-30.fc20.x86_64 4/9 Verifying : qt-settings-20-18.fc20.noarch 5/9 Verifying : 1:qt-common-4.8.6-30.fc20.noarch 6/9 Verifying : unixODBC-devel-2.3.2-4.fc20.x86_64 7/9 Verifying : qt-assistant-adp-4.6.3-6.fc20.x86_64 8/9 Verifying : libmng-1.0.10-12.fc20.x86_64 9/9 Installed: unixODBC-devel.x86_64 0:2.3.2-4.fc20 unixODBC-gui-qt.x86_64 0:0-0.8.20120105svn98.fc20 Dependency Installed: clucene09-core.x86_64 0:0.9.21b-13.fc20 libmng.x86_64 0:1.0.10-12.fc20 qt.x86_64 1:4.8.6-30.fc20 qt-assistant-adp.x86_64 0:4.6.3-6.fc20 qt-common.noarch 1:4.8.6-30.fc20 qt-settings.noarch 0:20-18.fc20 qt-x11.x86_64 1:4.8.6-30.fc20 Complete! |
After installing the unixODBC-devel and unixODBC-gui-qt libraries, I installed the RODBC library from the R prompt, having launched the R environment as the root user:
> install.packages('RODBC') |
Installing the RODBC library should install cleanly and generate the following output:
Installing package into ‘/usr/lib64/R/library’ (as ‘lib’ is unspecified) trying URL 'http://cran.cnr.berkeley.edu/src/contrib/RODBC_1.3-15.tar.gz' Content type 'application/x-gzip' length 1163967 bytes (1.1 MB) ================================================== downloaded 1.1 MB * installing *source* package ‘RODBC’ ... ** package ‘RODBC’ 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/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 sql.h usability... yes checking sql.h presence... yes checking for sql.h... yes checking sqlext.h usability... yes checking sqlext.h presence... yes checking for sqlext.h... yes checking for library containing SQLTables... -lodbc checking for SQLLEN... yes checking for SQLULEN... yes checking size of long... 8 configure: creating ./config.status config.status: creating src/Makevars config.status: creating src/config.h ** libs gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I. -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c RODBC.c -o RODBC.o gcc -m64 -std=gnu99 -shared -L/usr/lib64/R/lib -Wl,-z,relro -o RODBC.so RODBC.o -lodbc -L/usr/lib64/R/lib -lR installing to /usr/lib64/R/library/RODBC/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices converting help for package ‘RODBC’ finding HTML links ... done RODBC-internal html RODBC-package html odbc html odbcClose html odbcConnect html odbcDataSources html odbcGetInfo html odbcSetAutoCommit html setSqlTypeInfo html sqlColumns html sqlCopy html sqlDrop html sqlFetch html sqlQuery html sqlSave html sqlTables html sqlTypeInfo html ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (RODBC) Making 'packages.html' ... done The downloaded source packages are in ‘/tmp/RtmpdT1gay/downloaded_packages’ Updating HTML index of packages in '.Library' Making 'packages.html' ... done |
I hope that helps anybody who runs into the library dependency problems.
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