GeoIP C API build and patching error - patch

I have been trying to build the api in (windows 7 64bit) with msys2 using x86_64-w64-mingw32 but i keep geting errors
note that this errors wont happen when i use 32bit nmake but i need to build it in 64bit using msys2 and x86_64-w64-mingw32
Please help me fix my errors.
This log is from the build:
$ ./configure --build=x86_64-w64-mingw32 --host=x86_64-w64-mingw32
checking for x86_64-w64-mingw32-gcc... x86_64-w64-mingw32-gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.exe
checking for suffix of executables... .exe
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 x86_64-w64-mingw32-gcc accepts -g... yes
checking for x86_64-w64-mingw32-gcc option to accept ISO C89... none needed
checking whether x86_64-w64-mingw32-gcc understands -c and -o together... yes
checking how to run the C preprocessor... x86_64-w64-mingw32-gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/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 minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
/bin/sh: /home/Me/missing: No such file or directory
configure: WARNING: 'missing' script is too old or missing
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for style of include used by make... GNU
checking whether make supports nested variables... yes
checking dependency style of x86_64-w64-mingw32-gcc... gcc3
checking for x86_64-w64-mingw32-gcc... (cached) x86_64-w64-mingw32-gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether x86_64-w64-mingw32-gcc accepts -g... (cached) yes
checking for x86_64-w64-mingw32-gcc option to accept ISO C89... (cached) none needed
checking whether x86_64-w64-mingw32-gcc understands -c and -o together... (cached) yes
checking build system type... x86_64-w64-mingw32
checking host system type... x86_64-w64-mingw32
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for fgrep... /usr/bin/grep -F
checking for ld used by x86_64-w64-mingw32-gcc... c:/msys64/opt/windows_64/x86_64-w64-mingw32/bin/ld.exe
checking if the linker (c:/msys64/opt/windows_64/x86_64-w64-mingw32/bin/ld.exe) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /opt/windows_64/bin/nm -B
checking the name lister (/opt/windows_64/bin/nm -B) interface... BSD nm
checking whether ln -s works... no, using cp -pR
checking the maximum length of command line arguments... 8192
checking how to convert x86_64-w64-mingw32 file names to x86_64-w64-mingw32 format... func_convert_file_msys_to_w32
checking how to convert x86_64-w64-mingw32 file names to toolchain format... func_convert_file_msys_to_w32
checking for c:/msys64/opt/windows_64/x86_64-w64-mingw32/bin/ld.exe option to reload object files... -r
checking for x86_64-w64-mingw32-objdump... no
checking for objdump... objdump
checking how to recognize dependent libraries... file_magic ^x86 archive import|^x86 DLL
checking for x86_64-w64-mingw32-dlltool... no
checking for dlltool... dlltool
checking how to associate runtime and link libraries... func_cygming_dll_for_implib
checking for x86_64-w64-mingw32-ar... no
checking for ar... ar
checking for archiver #FILE support... #
checking for x86_64-w64-mingw32-strip... no
checking for strip... strip
checking for x86_64-w64-mingw32-ranlib... no
checking for ranlib... ranlib
checking command to parse /opt/windows_64/bin/nm -B output from x86_64-w64-mingw32-gcc object... ok
checking for sysroot... no
checking for a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for x86_64-w64-mingw32-mt... no
checking for mt... no
checking if : is a manifest tool... no
checking for dlfcn.h... no
checking for objdir... .libs
checking if x86_64-w64-mingw32-gcc supports -fno-rtti -fno-exceptions... no
checking for x86_64-w64-mingw32-gcc option to produce PIC... -DDLL_EXPORT -DPIC
checking if x86_64-w64-mingw32-gcc PIC flag -DDLL_EXPORT -DPIC works... yes
checking if x86_64-w64-mingw32-gcc static flag -static works... yes
checking if x86_64-w64-mingw32-gcc supports -c -o file.o... yes
checking if x86_64-w64-mingw32-gcc supports -c -o file.o... (cached) yes
checking whether the x86_64-w64-mingw32-gcc linker (c:/msys64/opt/windows_64/x86_64-w64-mingw32/bin/ld.exe) supports shared libraries... yes
checking whether -lc should be explicitly linked in... yes
checking dynamic linker characteristics... Win32 ld.exe
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for byte... no
checking for ushort... no
checking for ulong... no
checking for u16... no
checking for u32... no
checking for off_t... yes
checking for size_t... yes
checking for ssize_t... yes
checking for uint32_t... yes
checking for uint64_t... yes
checking whether byte ordering is bigendian... no
checking for getopt... yes
checking for gettimeofday... yes
checking for pread... no
checking for vasprintf... yes
checking for vsnprintf... yes
checking for vsprintf... yes
checking for gethostbyname... no
checking for gethostbyname in -lnsl... no
checking for gethostbyname_r... no
checking for memset... yes
checking for memchr... yes
checking for munmap... no
checking for strrchr... yes
checking for socket... no
checking for strchr... yes
checking for strdup... yes
checking for strstr... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating GeoIP.spec
config.status: creating geoip.pc
config.status: creating libGeoIP/Makefile
config.status: creating apps/Makefile
config.status: creating man/Makefile
config.status: creating test/Makefile
config.status: executing depfiles commands
config.status: executing libtool commands
$ make -i
Making all in libGeoIP
make[1]: Entering directory '/home/Me/src/geoip-api-c-1.6.3/libGeoIP'
/bin/sh ../libtool --tag=CC --mode=link x86_64-w64-mingw32-gcc -g -O2 -no-undefined -version-info 7:3:6 -o libGeoIP.la -rpath /usr/local/lib GeoIP.lo GeoIP_deprecated.lo GeoIPCity.lo regionName.lo timeZone.lo
libtool: link: rm -fr .libs/libGeoIP.dll.a
libtool: link: x86_64-w64-mingw32-gcc -shared .libs/GeoIP.o .libs/GeoIP_deprecated.o .libs/GeoIPCity.o .libs/regionName.o .libs/timeZone.o -g -O2 -o .libs/libGeoIP-1.dll -Wl,--enable-auto-image-base -Xlinker --out-implib -Xlinker .libs/libGeoIP.dll.a
.libs/GeoIP.o: In function `_check_mtime':
C:\msys64\home\Me\src\geoip-api-c-1.6.3\libGeoIP/GeoIP.c:1134: undefined reference to `pread'
C:\msys64\home\Me\src\geoip-api-c-1.6.3\libGeoIP/GeoIP.c:1172: undefined reference to `pread'
.libs/GeoIP.o: In function `_GeoIP_inet_ntop':
C:\msys64\home\Me\src\geoip-api-c-1.6.3\libGeoIP/GeoIP.c:590: undefined reference to `__imp_getnameinfo'
.libs/GeoIP.o: In function `_GeoIP_seek_record_v6_gl':
C:\msys64\home\Me\src\geoip-api-c-1.6.3\libGeoIP/GeoIP.c:1209: undefined reference to `pread'
.libs/GeoIP.o: In function `get_db_description':
C:\msys64\home\Me\src\geoip-api-c-1.6.3\libGeoIP/GeoIP.c:564: undefined reference to `__imp_GeoIPDBDescription'
.libs/GeoIP.o: In function `_get_name_v6_gl':
C:\msys64\home\Me\src\geoip-api-c-1.6.3\libGeoIP/GeoIP.c:2357: undefined reference to `pread'
.libs/GeoIP.o: In function `_GeoIP_inet_pton':
C:\msys64\home\Me\src\geoip-api-c-1.6.3\libGeoIP/GeoIP.c:606: undefined reference to `__imp_getaddrinfo'
C:\msys64\home\Me\src\geoip-api-c-1.6.3\libGeoIP/GeoIP.c:617: undefined reference to `__imp_freeaddrinfo'
.libs/GeoIP.o: In function `_GeoIP_seek_record_gl':
C:\msys64\home\Me\src\geoip-api-c-1.6.3\libGeoIP/GeoIP.c:1299: undefined reference to `pread'
.libs/GeoIP.o: In function `get_db_description':
C:\msys64\home\Me\src\geoip-api-c-1.6.3\libGeoIP/GeoIP.c:564: undefined reference to `__imp_GeoIPDBDescription'
.libs/GeoIP.o: In function `_get_name_gl':
C:\msys64\home\Me\src\geoip-api-c-1.6.3\libGeoIP/GeoIP.c:2298: undefined reference to `pread'
.libs/GeoIP.o: In function `GeoIP_open':
C:\msys64\home\Me\src\geoip-api-c-1.6.3\libGeoIP/GeoIP.c:1494: undefined reference to `pread'
C:\msys64\home\Me\src\geoip-api-c-1.6.3\libGeoIP/GeoIP.c:1547: undefined reference to `pread'
.libs/GeoIP.o: In function `_GeoIP_lookupaddress':
C:\msys64\home\Me\src\geoip-api-c-1.6.3\libGeoIP/GeoIP.c:1644: undefined reference to `__imp_inet_addr'
C:\msys64\home\Me\src\geoip-api-c-1.6.3\libGeoIP/GeoIP.c:1692: undefined reference to `__imp_ntohl'
C:\msys64\home\Me\src\geoip-api-c-1.6.3\libGeoIP/GeoIP.c:1677: undefined reference to `__imp_gethostbyname'
C:\msys64\home\Me\src\geoip-api-c-1.6.3\libGeoIP/GeoIP.c:1692: undefined reference to `__imp_ntohl'
.libs/GeoIP.o: In function `_GeoIP_lookupaddress_v6':
C:\msys64\home\Me\src\geoip-api-c-1.6.3\libGeoIP/GeoIP.c:1707: undefined reference to `__imp_getaddrinfo'
C:\msys64\home\Me\src\geoip-api-c-1.6.3\libGeoIP/GeoIP.c:1714: undefined reference to `__imp_freeaddrinfo'
.libs/GeoIP.o: In function `get_db_description':
C:\msys64\home\Me\src\geoip-api-c-1.6.3\libGeoIP/GeoIP.c:564: undefined reference to `__imp_GeoIPDBDescription'
C:\msys64\home\Me\src\geoip-api-c-1.6.3\libGeoIP/GeoIP.c:564: undefined reference to `__imp_GeoIPDBDescription'
C:\msys64\home\Me\src\geoip-api-c-1.6.3\libGeoIP/GeoIP.c:564: undefined reference to `__imp_GeoIPDBDescription'
C:\msys64\home\Me\src\geoip-api-c-1.6.3\libGeoIP/GeoIP.c:564: undefined reference to `__imp_GeoIPDBDescription'
C:\msys64\home\Me\src\geoip-api-c-1.6.3\libGeoIP/GeoIP.c:564: undefined reference to `__imp_GeoIPDBDescription'
.libs/GeoIP.o:C:\msys64\home\Me\src\geoip-api-c-1.6.3\libGeoIP/GeoIP.c:564: more undefined references to `__imp_GeoIPDBDescription' follow
.libs/GeoIP.o: In function `GeoIP_assign_region_by_inetaddr_gl':
C:\msys64\home\Me\src\geoip-api-c-1.6.3\libGeoIP/GeoIP.c:2030: undefined reference to `__imp_ntohl'
.libs/GeoIP.o: In function `_get_region_gl':
C:\msys64\home\Me\src\geoip-api-c-1.6.3\libGeoIP/GeoIP.c:2132: undefined reference to `__imp_htonl'
.libs/GeoIP.o: In function `get_db_description':
C:\msys64\home\Me\src\geoip-api-c-1.6.3\libGeoIP/GeoIP.c:564: undefined reference to `__imp_GeoIPDBDescription'
C:\msys64\home\Me\src\geoip-api-c-1.6.3\libGeoIP/GeoIP.c:564: undefined reference to `__imp_GeoIPDBDescription'
C:\msys64\home\Me\src\geoip-api-c-1.6.3\libGeoIP/GeoIP.c:564: undefined reference to `__imp_GeoIPDBDescription'
C:\msys64\home\Me\src\geoip-api-c-1.6.3\libGeoIP/GeoIP.c:564: undefined reference to `__imp_GeoIPDBDescription'
C:\msys64\home\Me\src\geoip-api-c-1.6.3\libGeoIP/GeoIP.c:564: undefined reference to `__imp_GeoIPDBDescription'
.libs/GeoIP.o:C:\msys64\home\Me\src\geoip-api-c-1.6.3\libGeoIP/GeoIP.c:564: more undefined references to `__imp_GeoIPDBDescription' follow
.libs/GeoIPCity.o: In function `_extract_record':
C:\msys64\home\Me\src\geoip-api-c-1.6.3\libGeoIP/GeoIPCity.c:97: undefined reference to `__imp_GeoIP_country_continent'
C:\msys64\home\Me\src\geoip-api-c-1.6.3\libGeoIP/GeoIPCity.c:98: undefined reference to `__imp_GeoIP_country_code'
C:\msys64\home\Me\src\geoip-api-c-1.6.3\libGeoIP/GeoIPCity.c:99: undefined reference to `__imp_GeoIP_country_code3'
C:\msys64\home\Me\src\geoip-api-c-1.6.3\libGeoIP/GeoIPCity.c:83: undefined reference to `pread'
.libs/GeoIPCity.o: In function `_get_record_gl':
C:\msys64\home\Me\src\geoip-api-c-1.6.3\libGeoIP/GeoIPCity.c:187: undefined reference to `__imp_GeoIPDBDescription'
.libs/GeoIPCity.o: In function `_get_record_v6_gl':
C:\msys64\home\Me\src\geoip-api-c-1.6.3\libGeoIP/GeoIPCity.c:217: undefined reference to `__imp_GeoIPDBDescription'
.libs/GeoIPCity.o: In function `GeoIP_record_id_by_addr':
C:\msys64\home\Me\src\geoip-api-c-1.6.3\libGeoIP/GeoIPCity.c:302: undefined reference to `__imp_GeoIPDBDescription'
.libs/GeoIPCity.o: In function `GeoIP_record_id_by_addr_v6':
C:\msys64\home\Me\src\geoip-api-c-1.6.3\libGeoIP/GeoIPCity.c:320: undefined reference to `__imp_GeoIPDBDescription'
collect2.exe: error: ld returned 1 exit status
Makefile:387: recipe for target 'libGeoIP.la' failed
make[1]: [libGeoIP.la] Error 1 (ignored)
make[1]: Leaving directory '/home/Me/src/geoip-api-c-1.6.3/libGeoIP'
Making all in apps
make[1]: Entering directory '/home/Me/src/geoip-api-c-1.6.3/apps'
x86_64-w64-mingw32-gcc -DPACKAGE_NAME=\"GeoIP\" -DPACKAGE_TARNAME=\"GeoIP\" -DPACKAGE_VERSION=\"1.6.3\" -DPACKAGE_STRING=\"GeoIP\ 1.6.3\" -DPACKAGE_BUGREPORT=\"support#maxmind.com\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__EXTENSIONS__=1 -D_ALL_SOURCE=1 -D_GNU_SOURCE=1 -D_POSIX_PTHREAD_SEMANTICS=1 -D_TANDEM_SOURCE=1 -DPACKAGE=\"GeoIP\" -DVERSION=\"1.6.3\" -DLT_OBJDIR=\".libs/\" -DLITTLE_ENDIAN_HOST=1 -DHAVE_GETOPT=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_VASPRINTF=1 -DHAVE_VSNPRINTF=1 -DHAVE_VSPRINTF=1 -DHAVE_MEMSET=1 -DHAVE_MEMCHR=1 -DHAVE_STRRCHR=1 -DHAVE_STRCHR=1 -DHAVE_STRDUP=1 -DHAVE_STRSTR=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_PARAM_H=1 -DHAVE_GETPAGESIZE=1 -I. -I../libGeoIP -DSYSCONFDIR=\"/usr/local/etc\" -Wall -g -O2 -MT geoiplookup.o -MD -MP -MF .deps/geoiplookup.Tpo -c -o geoiplookup.o geoiplookup.c
mv -f .deps/geoiplookup.Tpo .deps/geoiplookup.Po
make[1]: *** No rule to make target '../libGeoIP/libGeoIP.la', needed by 'geoiplookup.exe'. Stop.
make[1]: Leaving directory '/home/Me/src/geoip-api-c-1.6.3/apps'
Makefile:429: recipe for target 'all-recursive' failed
make: [all-recursive] Error 1 (ignored)
And this log is from patching:
$ patch -F0 -i ~/src/geoip-api-c-1.6.3/GeoIPWinDLL.patch -p0
patching file GeoIP.c
Hunk #1 FAILED at 23.
Hunk #2 FAILED at 57.
Hunk #3 FAILED at 67.
Hunk #4 FAILED at 96.
4 out of 4 hunks FAILED -- saving rejects to file GeoIP.c.rej
patching file GeoIP.h
patch: **** malformed patch at line 183:

With the help of few ppl (adrien, alexey, LRN) in irc://irc.oftc.net/#mingw-w64 i managed to fix the problems
And also i noticed that the patching wasn't needed
So here i am going say what you got to do so you can build it in msys2 using x86_64-w64-mingw32
Edit geoip-api-c-1.6.3/Makefile.am and add ACLOCAL_AMFLAGS = -I m4
Edit geoip-api-c-1.6.3/configure.ac and add AC_CONFIG_MACRO_DIRS([m4])
Edit geoip-api-c-1.6.3/libGeoIP/Makefile.am and add pread.c to libGeoIP_la_SOURCES
Once you added pread.c there you remove it from EXTRA_DIST
Run autoreconf -fiv or ./bootstrap
export "CFLAGS=-O2" export "CPPFLAGS=-DGEOIP_EXPORTS" export "LIBS=-lwsock32 -lws2_32"
or you can try export "CFLAGS=-DGEOIP_EXPORTS -O3 -I/usr/local/include" export "LDFLAGS=-L/usr/local/lib -lwsock32 -lws2_32"
./configure --build=x86_64-w64-mingw32 --host=x86_64-w64-mingw32 && make
With that i managed to build it just fine :)

Related

Rccp.h not found in Renjin when compiling package

I want to compile the units package in Renjin, which currently does not work in the online repository, see http://packages.renjin.org/package/org.renjin.cran/units/0.6-3/build/5
I created a pom.xml for the current release of udunits, see https://github.com/nuest/renjin-docker/blob/master/geospatial-packages/units/pom.xml
I built a Dockerfile for compiling packages and having the required compilers, see https://github.com/nuest/renjin-docker/blob/master/0.9.2726/Dockerfile.builder
Within a container created from an image built from that Dockerfile, I can run library('org.renjin.cran:Rcpp') in an R session, but when I run mvn clean install on units I get the following error:
[...]
Downloaded: https://nexus.bedatadriven.com/content/groups/public/org/sonatype/aether/aether-impl/1.13.1/aether-impl-1.13.1.jar (128 KB at 7.4 KB/sec)
EXECUTING: -print-file-name=plugin
EXECUTING: -shared -xc++ -I/usr/lib/gcc/x86_64-linux-gnu/4.7/plugin/include -fPIC -fno-rtti -O2 plugin.c -lstdc++ -shared-libgcc -o /packages/units/units/target/bridge.so
configure: units: 0.6-4
Warning: unsupported configuration variable CFLAGS
Warning: unsupported configuration variable CPPFLAGS
Warning: unsupported configuration variable LDFLAGS
Warning: unsupported configuration variable CXXFLAGS
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 g++-4.7 accepts -g... yes
checking how to run the C++ preprocessor... g++-4.7 -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 for stdbool.h that conforms to C99... yes
checking for _Bool... no
checking for error_at_line... yes
checking for gcc... gcc-4.7
checking whether we are using the GNU C compiler... yes
checking whether gcc-4.7 accepts -g... yes
checking for gcc-4.7 option to accept ISO C89... none needed
checking for XML_ParserCreate in -lexpat... no
checking udunits2.h usability... yes
checking udunits2.h presence... yes
checking for udunits2.h... yes
checking for ut_read_xml in -ludunits2... yes
configure: creating ./config.status
config.status: creating src/Makevars
Checking wether in Makevars CXX_STD is set to CXX11... no
g++-4.7 -I/packages/units/units/target/gnur/include -DNDEBUG -DUDUNITS2_DIR=0 -I"/packages/units/units/target/include" -fpic -m32 -fplugin=/packages/units/units/target/bridge.so -DRENJIN -fno-inline-functions -fdisable-tree-einline -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c udunits.cpp -o udunits.o
cc1plus: note: disable pass tree-einline for functions in the range of [0, 4294967295]
udunits.cpp:11:18: fatal error: Rcpp.h: No such file or directory
compilation terminated.
/packages/units/units/target/gnur/etc/Makeconf:202: recipe for target 'udunits.o' failed
make: *** [udunits.o] Error 1
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 02:20 min
[INFO] Finished at: 2019-11-15T15:27:52+00:00
[INFO] Final Memory: 17M/445M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.renjin:renjin-maven-plugin:0.9.2726:gnur-compile (gnur-compile) on project units: Compilation of GNU R sources failed: Failed to execute Makefile -> [Help 1]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
root#987c61d45fbf:/packages/units/units# exit
Anyone an idea how to tell Renjin where to find Rcpp.h ?
More details on the resources I consulted are in this GitHub issue: https://github.com/nuest/renjin-docker/issues/4
If you're using Maven to build the package, you also need to add Rcpp headers as a dependency:
<dependency>
<groupId>org.renjin.cran</groupId>
<artifactId>Rcpp</artifactId>
<version>0.12.13-renjin-15</version>
<classifier>headers</classifier>
<scope>provided</scope>
</dependency>
You can use the pom file for plyr as an example.
Note that if you just want to build a package for use with Renjin, the command line tool is far simpler:
renjin build units
This will take care of downloading the required dependencies and producing a jar file.
Do note that Renjin does not support packages which depend on external native libraries. You can see from the automated build logs that the units package will fail because of a dependency on udunits2.
That is the reason that the units packages is labeled as incompatible in our package site.

Unable to Install Older Version of R

I am trying to install and older version of R (3.2.1), and am following the instructions on this page: https://www.miskatonic.org/2015/06/23/installing-r-from-source/
As suggested by the webpage, I uninstalled R
usr#ubuntu:/usr/lib/R/R-3.2.1$ R
The program 'R' is currently not installed. You can install it by typing:
sudo apt install r-base-core
And I am fairly positive that "make" is installed:
usr#ubuntu:/usr/lib/R/R-3.2.1$ sudo apt-get install make
Reading package lists... Done
Building dependency tree
Reading state information... Done
make is already the newest version (4.1-6).
0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
When I run
$ ./configure
$ make
I get the following (I am not sure what is normal and what is an error message). In addition, the following files are created: Makeconf.in, Makefile.fw, Makefile.in
usr#ubuntu:/usr/lib/R/R-3.2.1$ sudo ./configure
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
loading site script './config.site'
loading build-specific script './config.site'
checking for pwd... /bin/pwd
checking whether builddir is srcdir... yes
checking for working aclocal... found
checking for working autoconf... found
checking for working automake... found
checking for working autoheader... found
checking for gawk... gawk
checking whether ln -s works... yes
checking for bison... no
checking for byacc... no
checking for ar... ar
checking for a BSD-compatible install... /usr/bin/install -c
checking for sed... /bin/sed
checking for which... /usr/bin/which
checking for less... /usr/bin/less
checking for gtar... no
checking for gnutar... no
checking for tar... /bin/tar
checking for tex... no
checking for pdftex... no
configure: WARNING: you cannot build PDF versions of the R manuals
checking for pdflatex... no
configure: WARNING: you cannot build PDF versions of vignettes and help pages
checking for makeindex... no
checking for texi2any... no
configure: WARNING: you cannot build info or HTML versions of the R manuals
checking for texi2dvi... no
checking for kpsewhich... no
checking for latex inconsolata package... checking for unzip... /usr/bin/unzip
checking for zip... /usr/bin/zip
checking for gzip... /bin/gzip
checking for bzip2... /bin/bzip2
checking for firefox... /usr/bin/firefox
using default browser ... /usr/bin/firefox
checking for acroread... no
checking for acroread4... no
checking for xdg-open... /usr/bin/xdg-open
checking for notangle... false
checking for realpath... /usr/bin/realpath
checking for pkg-config... /usr/bin/pkg-config
checking for gcc... gcc
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 accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking whether gcc needs -traditional... no
checking how to run the C preprocessor... gcc -E
checking for f95... f95
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether f95 accepts -g... yes
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking how to run the C++ preprocessor... g++ -E
checking whether __attribute__((visibility())) is supported... yes
checking whether gcc accepts -fvisibility... yes
checking whether f95 accepts -fvisibility... yes
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 minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking for gcc... gcc
checking whether we are using the GNU Objective C compiler... no
checking whether gcc accepts -g... no
checking for Objective C++ compiler... trying some possibilities
checking whether g++ can compile ObjC++... no
checking whether can compile ObjC++... no
no working ObjC++ compiler found
checking for a sed that does not truncate output... (cached) /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for dlfcn.h... yes
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... (cached) yes
checking how to run the C++ preprocessor... g++ -E
checking whether we are using the GNU Fortran 77 compiler... (cached) yes
checking whether f95 accepts -g... (cached) yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for ld used by g++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for f95 option to produce PIC... -fPIC
checking if f95 PIC flag -fPIC works... yes
checking if f95 static flag -static works... yes
checking if f95 supports -c -o file.o... yes
checking if f95 supports -c -o file.o... (cached) yes
checking whether the f95 linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for cos in -lm... yes
checking for sin in -lm... yes
checking for dlopen in -ldl... yes
checking readline/history.h usability... no
checking readline/history.h presence... no
checking for readline/history.h... no
checking readline/readline.h usability... no
checking readline/readline.h presence... no
checking for readline/readline.h... no
checking for rl_callback_read_char in -lreadline... no
checking for main in -lncurses... yes
checking for rl_callback_read_char in -lreadline... no
checking for history_truncate_file... no
configure: error: --with-readline=yes (default) and headers/libs are not available
usr#ubuntu:/usr/lib/R/R-3.2.1$ make
make: *** No targets specified and no makefile found. Stop.
I also tried following the instructions here: Installing older version of R, but the R version 3.2.1 is NOT listed in the directory (xenial).
Does anyone have any suggestions on how I can finish installing this version of R? I appreciate the help - ahhn
EDIT:
I am now receiving the following when I get to the "./configure" step:
usr#ubuntu:~/Downloads/R-3.2.1$ ./configure --prefix=/home/usr/Downloads/R3.2.1_VERSION --enable-R-shlib --with-blas --with-lapack
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
loading site script './config.site'
loading build-specific script './config.site'
checking for pwd... /bin/pwd
checking whether builddir is srcdir... yes
checking for working aclocal... found
checking for working autoconf... found
checking for working automake... found
checking for working autoheader... found
checking for gawk... gawk
checking whether ln -s works... yes
checking for bison... no
checking for byacc... no
checking for ar... ar
checking for a BSD-compatible install... /usr/bin/install -c
checking for sed... /bin/sed
checking for which... /usr/bin/which
checking for less... /usr/bin/less
checking for gtar... no
checking for gnutar... no
checking for tar... /bin/tar
checking for tex... no
checking for pdftex... no
configure: WARNING: you cannot build PDF versions of the R manuals
checking for pdflatex... no
configure: WARNING: you cannot build PDF versions of vignettes and help pages
checking for makeindex... no
checking for texi2any... no
configure: WARNING: you cannot build info or HTML versions of the R manuals
checking for texi2dvi... no
checking for kpsewhich... no
checking for latex inconsolata package... checking for unzip... /usr/bin/unzip
checking for zip... /usr/bin/zip
checking for gzip... /bin/gzip
checking for bzip2... /bin/bzip2
checking for firefox... /usr/bin/firefox
using default browser ... /usr/bin/firefox
checking for acroread... no
checking for acroread4... no
checking for xdg-open... /usr/bin/xdg-open
checking for notangle... false
checking for realpath... /usr/bin/realpath
checking for pkg-config... /usr/bin/pkg-config
checking for gcc... gcc
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 accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking whether gcc needs -traditional... no
checking how to run the C preprocessor... gcc -E
checking for f95... f95
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether f95 accepts -g... yes
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking how to run the C++ preprocessor... g++ -E
checking whether __attribute__((visibility())) is supported... yes
checking whether gcc accepts -fvisibility... yes
checking whether f95 accepts -fvisibility... yes
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 minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking for gcc... gcc
checking whether we are using the GNU Objective C compiler... no
checking whether gcc accepts -g... no
checking for Objective C++ compiler... trying some possibilities
checking whether g++ can compile ObjC++... no
checking whether can compile ObjC++... no
no working ObjC++ compiler found
checking for a sed that does not truncate output... (cached) /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for dlfcn.h... yes
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... (cached) yes
checking how to run the C++ preprocessor... g++ -E
checking whether we are using the GNU Fortran 77 compiler... (cached) yes
checking whether f95 accepts -g... (cached) yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for ld used by g++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for f95 option to produce PIC... -fPIC
checking if f95 PIC flag -fPIC works... yes
checking if f95 static flag -static works... yes
checking if f95 supports -c -o file.o... yes
checking if f95 supports -c -o file.o... (cached) yes
checking whether the f95 linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for cos in -lm... yes
checking for sin in -lm... yes
checking for dlopen in -ldl... yes
checking readline/history.h usability... no
checking readline/history.h presence... no
checking for readline/history.h... no
checking readline/readline.h usability... no
checking readline/readline.h presence... no
checking for readline/readline.h... no
checking for rl_callback_read_char in -lreadline... no
checking for main in -lncurses... yes
checking for rl_callback_read_char in -lreadline... no
checking for history_truncate_file... no
configure: error: --with-readline=yes (default) and headers/libs are not available
usr#ubuntu:~/Downloads/R-3.2.1$ make
make: *** No targets specified and no makefile found. Stop.
EDIT 2:
I am running into errors when I try to install readline-devel and xorg-dev:
usr#ubuntu:~$ sudo apt-get install readline-devel
Reading package lists... Done
Building dependency tree
Reading state information... Done
E: Unable to locate package readline-devel
usr#ubuntu:~$ sudo apt-get install xorg-dev
Reading package lists... Done
Building dependency tree
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:
The following packages have unmet dependencies:
xorg-dev : Depends: libxaw7-dev but it is not going to be installed
Depends: libxcursor-dev but it is not going to be installed
Depends: libxfont-dev but it is not going to be installed
Depends: libxft-dev but it is not going to be installed
Depends: libxpm-dev but it is not going to be installed
Depends: xserver-xorg-dev but it is not going to be installed
E: Unable to correct problems, you have held broken packages.
Please try the following steps:
First make sure if you have libxt-dev and jdk.
dpkg -l <package name>
If not do these following commands:
sudo apt -f install && sudo apt update && sudo apt dist-upgrade
sudo apt-get install build-essential
sudo apt-get install fort77
sudo apt-get install xorg-dev
sudo apt-get install liblzma-dev libblas-dev gfortran
sudo apt-get install gcc-multilib
sudo apt-get install gobjc++
sudo apt-get install aptitude
sudo aptitude install libreadline-dev
sudo apt-get install libxt-dev
sudo apt-get install default-jdk
Then download your preferred R version and do as follows:
wget https://cran.r-project.org/src/base/R-3/R-3.2.1.tar.gz
mkdir R-3.2.1
mv R-3.2.1.tar.gz R-3.2.1/
cd R-3.2.1/
tar -xzvf R-3.2.1.tar.gz
Next, make another folder for R's binary version and use the to that folder here:
mkdir <full path>/R3.2.1_VERSION
Build R from source, please make sure to add the full path in prefix
./configure --prefix=<full path>/R3.2.1_OLDERVERSION --enable-R-shlib --with-blas --with-lapack
make
sudo make install
Once, you are finished, please set the environment variable to make sure the right version of R is called
export PATH=<full path>/R3.2.1_VERSION/bin:$PATH
If everything went smoothly then you can see your current R version as 3.2.1 when you run R.
If you want to switch to another version of R then change the environment variable to your preferred version of R package in your account as follows:
export PATH=<full path>/R<your preferred>_VERSION/bin:$PATH

How can I install R in Linux server? When I run the ./configure command I am getting

I want to install R in Linux Server. I was going through the site: https://cran.r-project.org/doc/manuals/r-release/R-admin.html.
When I run the ./configure command I am getting the following:
[root#sd-cd1a-b9e0 R-devel]# ./configure
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
loading site script './config.site'
loading build-specific script './config.site'
checking for pwd... /bin/pwd
checking whether builddir is srcdir... yes
checking whether ln -s works... yes
checking for ar... ar
checking for a BSD-compatible install... /usr/bin/install -c
checking for sed... /bin/sed
checking for which... /usr/bin/which
checking for less... /usr/bin/less
checking for gtar... /bin/gtar
checking for tex... no
checking for pdftex... no
configure: WARNING: you cannot build PDF versions of the R manuals
checking for pdflatex... no
configure: WARNING: you cannot build PDF versions of vignettes and help pages
checking for makeindex... no
checking for texi2any... no
configure: WARNING: you cannot build info or HTML versions of the R manuals
checking for texi2dvi... no
checking for kpsewhich... no
checking for latex inconsolata package... checking for unzip...
/usr/bin/unzip
checking for zip... /usr/bin/zip
checking for gzip... /bin/gzip
checking for bzip2... /usr/bin/bzip2
checking for firefox... no
checking for mozilla... no
checking for galeon... no
checking for opera... no
checking for xdg-open... no
checking for kfmclient... no
checking for gnome-moz-remote... no
checking for open... /usr/bin/open
using default browser ... /usr/bin/open
checking for acroread... no
checking for acroread4... no
checking for xdg-open... no
checking for evince... no
checking for xpdf... no
checking for gv... no
checking for gnome-gv... no
checking for ggv... no
checking for okular... no
checking for kpdf... no
checking for open... /usr/bin/open
checking for working aclocal... missing
checking for working autoconf... missing
checking for working autoheader... missing
checking for bison... no
checking for byacc... no
checking for yacc... no
checking for notangle... false
checking for realpath... false
checking for pkg-config... /usr/bin/pkg-config
checking for gcc... gcc
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 accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking whether gcc needs -traditional... no
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 minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking how to run the C preprocessor... gcc -E
checking for gfortran... gfortran
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether gfortran accepts -g... yes
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking whether g++ -g -O2 can compile C++ code... yes
checking how to run the C++ preprocessor... g++ -E
checking whether __attribute__((visibility())) is supported... yes
checking whether gcc accepts -fvisibility... yes
checking whether gfortran accepts -fvisibility... yes
checking for gcc... gcc
checking whether we are using the GNU Objective C compiler... no
checking whether gcc accepts -g... no
checking whether g++ can compile ObjC++... no
checking whether can compile ObjC++... no
checking for Objective C++ compiler... no working ObjC++ compiler found
checking how to print strings... printf
checking for a sed that does not truncate output... (cached) /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking the maximum length of command line arguments... 1966080
checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu
format... func_convert_file_noop
checking how to convert x86_64-pc-linux-gnu file names to toolchain format...
func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for archiver #FILE support... #
checking for strip... strip
checking for ranlib... ranlib
checking for gawk... gawk
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... no
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared
libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared
libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... no
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared
libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for gfortran option to produce PIC... -fPIC
checking if gfortran PIC flag -fPIC works... yes
checking if gfortran static flag -static works... no
checking if gfortran supports -c -o file.o... yes
checking if gfortran supports -c -o file.o... (cached) yes
checking whether the gfortran linker (/usr/bin/ld -m elf_x86_64) supports
shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for cos in -lm... yes
checking for sin in -lm... yes
checking for dlopen in -ldl... yes
checking readline/history.h usability... no
checking readline/history.h presence... no
checking for readline/history.h... no
checking readline/readline.h usability... no
checking readline/readline.h presence... no
checking for readline/readline.h... no
checking for rl_callback_read_char in -lreadline... no
checking for main in -lncurses... no
checking for main in -ltermcap... no
checking for main in -ltermlib... no
checking for rl_callback_read_char in -lreadline... no
configure: error: --with-readline=yes (default) and headers/libs are not
available
When I run the make command I am getting the following issue:
[root#sd-cd1a-b9e0 R-devel]# make
make: *** No targets specified and no makefile found. Stop.
Can anyone please help how to get rid of this issue?
Your ./configure command failed as you can see at the bottom of the log:
configure: error: --with-readline=yes (default) and headers/libs are not
available
Here's SO answer to the error above:
error: --with-readline=yes (default) and headers/libs are not available
Even though I am a bit late here but I think this is still a quite common problem. What you have seen is that R is complaining about missing dependencies. You need to install A LOT OF packages before you are able to compile it. Here is a full list of them:
https://github.com/Jiefei-Wang/Painless-R-compilation-and-installation-on-Ubuntu
If you are using Ubuntu this is just a matter of copy and paste. Otherwise, you may need to take some time and figure out how to install them on your machine.

Error in NS2.35 installation on fedora 17

I'm trying to install NS2.35 on fedora 17 using allinone package.
I'm new to linux environment and have already spent many hours trying this. So far I've found out it is a problem with dependent packages. But I'm not able to figure out following error.
Please help.
===========================================================
* Build Tclcl-1.20
============================================================
No .configure file found in current directory
Continuing with default options...
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking target system type... x86_64-unknown-linux-gnu
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for g++... no
checking for c++... no
checking for gpp... no
checking for aCC... no
checking for CC... no
checking for cxx... no
checking for cc++... no
checking for cl.exe... no
checking for FCC... no
checking for KCC... no
checking for RCC... no
checking for xlC_r... no
checking for xlC... no
checking whether we are using the GNU C++ compiler... no
checking whether g++ accepts -g... no
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/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 for string.h... (cached) yes
checking for main in -lXbsd... no
checking for socket in -lsocket... no
checking for gethostbyname in -lnsl... yes
checking for dcgettext in -lintl... no
checking for getnodebyname in -ldnet_stub... no
checking that g++ can handle -O2... no
checking standard STL is available... no
checking for ranlib... ranlib
checking for snprintf... yes
checking for ANSI C header files... (cached) yes
checking for strtoq... yes
checking for strtoll... yes
checking size of long... 8
checking for strtol... yes
checking for __int64_t... no
checking for long long... yes
checking for int64_t... yes
checking which kind of 64-bit int to use... int64_t
checking for tcl.h... -I../include
checking for tclInt.h... -I../include
checking for libtcl8.5... -L../lib -ltcl8.5
checking for init.tcl... ../lib/tcl8.5
checking for http.tcl... ../lib/tcl8.5/http1.0
checking Tcl http.tcl library... yes
checking for tclsh8.5.10... no
checking for tclsh8.5... ../bin/tclsh8.5
checking for tk.h... -I../include
checking for libtk8.5... -L../lib -ltk8.5
checking for tk.tcl... ../lib/tk8.5
checking for otcl.h... -I../otcl-1.14
checking for libotcl1.14... -L../otcl-1.14 -lotcl
checking for X11 header files
checking for X11 library archive
checking for XOpenDisplay in -lX11... yes
checking for XShmAttach in -lXext... yes
checking for zlib.h... -I/usr/include
checking for libz1.1.3... no
No explicit static compilation flag; setting V_STATIC to ""
checking for dlopen in -ldl... yes
checking system version (for system-dependent libraries)... Linux-3.3.4-5.fc17.x86_64
checking for unistd.h... (cached) yes
checking for a BSD-compatible install... /usr/bin/install -c
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
config.status: config.h is unchanged
rm -f tcl2c++
g++ -o tcl2c++ tcl2c++.o
make: g++: Command not found
make: *** [tcl2c++] Error 127
tclcl-1.20 make failed! Exiting ...
See http://www.isi.edu/nsnam/ns/ns-problems.html for problems
Many many thanks
-Uday

gnu make error after successful configure

I am trying to build 'lcms2' static library which is dependent on libtiff. libtiff has again dependency on libjbig. I have successfully configured libtest with the following parameters:
CFLAGS="-fPIC" CXXFLAGS="-fPIC" LIBS="-ljbig" ./configure --prefix=/usr/local --enable-static=yes --enable-shared=no --with-zlib=yes --with-jpeg=yes --with-tiff=yes --with-pic=PIC
The configure reports no error:
checking for TIFF support ...
checking tiff.h usability... yes
checking tiff.h presence... yes
checking for tiff.h... yes
checking tiffio.h usability... yes
checking tiffio.h presence... yes
checking for tiffio.h... yes
checking for TIFFOpen in -ltiff... yes
checking for TIFFClientOpen in -ltiff... yes
checking for TIFFIsByteSwapped in -ltiff... yes
checking if TIFF package is complete... yes
checking tiffconf.h usability... yes
checking tiffconf.h presence... yes
checking for tiffconf.h... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating lcms2.pc
config.status: creating include/Makefile
config.status: creating src/Makefile
config.status: creating utils/tificc/Makefile
config.status: creating utils/transicc/Makefile
config.status: creating utils/linkicc/Makefile
config.status: creating utils/jpgicc/Makefile
config.status: creating utils/psicc/Makefile
config.status: creating testbed/Makefile
config.status: executing depfiles commands
config.status: executing libtool commands
The when I make the library it throws the following error:
/bin/sh ../../libtool --tag=CC --mode=link gcc -std=gnu99 -fPIC -o tificc tificc.o xgetopt.o vprf.o ../../src/liblcms2.la -ltiff -ljpeg -lz -lm
libtool: link: gcc -std=gnu99 -fPIC -o tificc tificc.o xgetopt.o vprf.o ../../src/.libs/liblcms2.a -ltiff -ljpeg -lz -lm
/usr/local/lib/libtiff.a(tif_jbig.o): In function `JBIGDecode':
tif_jbig.c:(.text+0xc4): undefined reference to `jbg_dec_init'
tif_jbig.c:(.text+0xe4): undefined reference to `jbg_newlen'
tif_jbig.c:(.text+0x116): undefined reference to `jbg_dec_in'
tif_jbig.c:(.text+0x12a): undefined reference to `jbg_strerror'
tif_jbig.c:(.text+0x177): undefined reference to `jbg_dec_getimage'
tif_jbig.c:(.text+0x188): undefined reference to `jbg_dec_getsize'
tif_jbig.c:(.text+0x1ac): undefined reference to `jbg_dec_free'
/usr/local/lib/libtiff.a(tif_jbig.o): In function `JBIGEncode':
tif_jbig.c:(.text+0x402): undefined reference to `jbg_enc_init'
tif_jbig.c:(.text+0x40d): undefined reference to `jbg_enc_out'
tif_jbig.c:(.text+0x418): undefined reference to `jbg_enc_free'
collect2: ld returned 1 exit status
make[1]: *** [tificc] Error 1
libtool: link: gcc -std=gnu99 -fPIC -o tificc tificc.o xgetopt.o vprf.o ../../src/.libs/liblcms2.a -ltiff -ljpeg -lz -lm
There is no reference to JBIG library in the linking command (I don't remember if it should go before or after - some libraries require both - the reference to libtiff, -ltiff), so jbg_* references can't be resolved. Having LCMS linked does not help you, since JBIG is not linked in, but only referred to, by JBIG.
Add -ljbig to the link command.
Or, manually edit the Makefile and add -ljbig to LIBS (eg. LIBS = -ljbig).

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