Hello,
I'm trying to compile dplyr on Solaris 11.2
pkg://solaris/entire@0.5.11,5.11-0.175.2.15.0.5.1:20151026T231525Z
> install.packages("dplyr");
trying URL 'http://cran.uni-muenster.de/src/contrib/dplyr_0.4.3.tar.gz'
Content type 'application/x-gzip' length 655997 bytes (640 KB)
==================================================
downloaded 640 KB
* installing *source* package 'dplyr' ...
** package 'dplyr' successfully unpacked and MD5 sums checked
** libs
/opt/solarisstudio12.4/bin/CC -m64 -I/usr/local/R/include -DNDEBUG
-I../inst/include -DCOMPILING_DPLYR -I"/usr/local/R/library/Rcpp/include"
-I"/usr/local/R/library/BH/include" -KPIC -xO3 -m64 -std=c++03 -g -c
RcppExports.cpp -o RcppExports.o
"/usr/local/R/library/Rcpp/include/Rcpp/Interrupt.h", line 60: Warning
(Anachronism): Using void(*)(void*) to initialize extern "C" void(*)(void*).
"/usr/local/R/library/Rcpp/include/Rcpp/String.h", line 67: Warning: enc
hides Rcpp::String::enc.
"/usr/local/R/library/Rcpp/include/Rcpp/String.h", line 81: Warning: enc
hides Rcpp::String::enc.
"/usr/local/R/library/Rcpp/include/Rcpp/String.h", line 95: Warning: enc
hides Rcpp::String::enc.
"/usr/local/R/library/Rcpp/include/Rcpp/String.h", line 107: Warning: enc
hides Rcpp::String::enc.
"/usr/local/R/library/BH/include/boost/exception/exception.hpp", line 140:
Error: The name exception is ambiguous, exception and Rcpp::exception.
"../inst/include/dplyr/Result/LazyGroupedSubsets.h", line 17: Warning: data
hides dplyr::LazySubsets::data.
"../inst/include/dplyr/Result/LazyRowwiseSubsets.h", line 14: Warning: data
hides dplyr::LazySubsets::data.
"../inst/include/dplyr/Collecter.h", line 303: Warning: levels hides
dplyr::FactorCollecter::levels.
1 Error(s) and 8 Warning(s) detected.
*** Error code 2
make: Fatal error: Command failed for target `RcppExports.o'
ERROR: compilation failed for package 'dplyr'
* removing '/usr/local/R/library/dplyr'
The downloaded source packages are in
'/tmp/RtmpUzD2NL/downloaded_packages'
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("dplyr") :
installation of package 'dplyr' had non-zero exit status
>
root@pkglt01 ~ [10:29:52]# more .Rprofile
local({
r <- getOption("repos")
r["CRAN"] <- "http://cran.uni-muenster.de/";
options(repos = r)
my.configure.args <- list(
"stringi" =
c("--disable-cxx11",
"--disable-pkg-config",
"--with-extra-libs='-lCrun'",
"--with-extra-libs='-lCstd'"
));
options("configure.args" = my.configure.args);
})
root@pkglt01 ~ [10:29:55]# cat .Renviron
options(internet.info = 0)
TERM=vt220
TAR=/usr/bin/tar
R_UNZIPCMD=/usr/bin/unzip
R_ZIPCMD=/usr/bin/zip
MAKE=/usr/bin/make
LD_LIBRARY_PATH=/lib:/usr/lib:/opt/solarisstudio12.4/lib/:/usr/local/R/lib:/lib:/usr/local/lib:/usr/gcc/4.8/lib/
PAGER=/usr/bin/less
R_BZIPCMD=/usr/bin/bzip2
R_GZIPCMD=/usr/bin/gzip
CXXFLAGS = -xO3 -m64 -std=c++03
CXX1XFLAGS = -xO3 -m64 -std=c++11
SHLIB_CXXLDFLAGS = -G -lstdc++ -lgcc_s -lCrunG3 -lrt -lm -lc
SHLIB_CXX1XLDFLAGS = -G -lstdc++ -lgcc_s -lCrunG3 -lrt -lm -lc
LDFLAGS = -norunpath -m64 -KPIC -DPIC -lc
-L/opt/solarisstudio12.4/lib/sparcv9 -R/opt/solarisstudio12.4/lib/sparcv9
-lsunperf -lfsu -lmtsk -lpicl -lkstat -L/usr/local/R/lib -R/usr/local/R/lib
-L/usr/include/openssl -R/usr/include/openssl
-L/usr/include/openssl/fips-140 -R/usr/include/openssl/fips-140
-L/usr/gcc/4.8/lib -R/usr/gcc/4.8/lib
CC = /opt/solarisstudio12.4/bin/cc -xc99 -m64
CXX = /opt/solarisstudio12.4/bin/CC -m64
root@pkglt01 ~ [10:33:39]# cat /usr/local/R/etc/Makeconf
# etc/Makeconf. Generated from Makeconf.in by configure.
#
# ${R_HOME}/etc/Makeconf
#
# R was configured using the following call
# (not including env. vars and site configuration)
# configure '--enable-R-shlib' '--with-blas=-xlic_lib=sunperf -lsunmath '
'--with-lapack' '--with-tcltk=no' '--with-ICU=no' '--enable-prebuilt-html'
'--with-cairo' '--with-internal-tzcode' '--disable-long-double'
'CC=/opt/SunProd/studio12u3/solarisstudio12.3/bin/cc -xc99 -m64'
'CXX=/opt/SunProd/studio12u3/solarisstudio12.3/bin/CC -m64'
'F77=/opt/SunProd/studio12u3/solarisstudio12.3/bin/f95 -m64'
'FC=/opt/SunProd/studio12u3/solarisstudio12.3/bin/f95 -m64'
'CFLAGS=-xlibmieee -DLINK_SIZE=2' 'CPPFLAGS=
## This fails if it contains spaces, or if it is quoted
include $(R_SHARE_DIR)/make/vars.mk
AR = ar
## Used by packages 'maps' and 'mapdata'
AWK = gawk
BLAS_LIBS = -xlic_lib=sunperf -lsunmath
C_VISIBILITY =
CC = /opt/solarisstudio12.4/bin/cc -xc99 -m64
CFLAGS = -O -xlibmieee -DLINK_SIZE=2 $(LTO)
CPICFLAGS = -KPIC
CPPFLAGS =
CXX = /opt/solarisstudio12.4/bin/CC -m64
CXXCPP = $(CXX) -E
CXXFLAGS = -xO3 -m64 -std=c++03 -g $(LTO)
CXXPICFLAGS = -KPIC
CXX1X =
CXX1XFLAGS = -xO3 -m64 -std=c++11
CXX1XPICFLAGS =
CXX1XSTD =
DYLIB_EXT = .so
DYLIB_LD = $(CC)
DYLIB_LDFLAGS = -G -xopenmp# $(CFLAGS) $(CPICFLAGS)
DYLIB_LINK = $(DYLIB_LD) $(DYLIB_LDFLAGS) $(LDFLAGS)
ECHO = echo
ECHO_C =
ECHO_N = -n
ECHO_T =
## NB, set FC before F77 as on Solaris make, setting FC sets F77
FC = /opt/solarisstudio12.4/bin/f95 -m64
FCFLAGS = -O -g $(LTO)
## additional libs needed when linking with $(FC), e.g. on Solaris
FCLIBS = -lfai -lfsu
F77 = /opt/solarisstudio12.4/bin/f95 -m64
F77_VISIBILITY =
FFLAGS = -O -g $(LTO)
FLIBS = -lifai -lsunimath -lfai -lfai2 -lfsumai -lfprodai -lfminlai
-lfmaxlai -lfminvai -lfmaxvai -lfui -lfsu -lsunmath -lmtsk -lm
FCPICFLAGS = -PIC
FPICFLAGS = -PIC
FOUNDATION_CPPFLAGS =
FOUNDATION_LIBS =
JAR = /usr/jdk/instances/jdk1.8.0/bin/jar
JAVA = /usr/jdk/instances/jdk1.8.0/jre/bin/java
JAVAC = /usr/jdk/instances/jdk1.8.0/bin/javac
JAVAH = /usr/jdk/instances/jdk1.8.0/include
## JAVA_HOME might be used in the next three.
## They are for packages 'JavaGD' and 'rJava'
JAVA_HOME = /usr/jdk/instances/jdk1.8.0
JAVA_CPPFLAGS = -I/usr/jdk/instances/jdk1.8.0/include
-I/usr/jdk/instances/jdk1.8.0/include/solaris
JAVA_LIBS = -L/usr/jdk/instances/jdk1.8.0/jre/lib
-L/usr/jdk/instances/jdk1.8.0/lib -L/usr/jdk/instances/jdk1.8.0/db/lib
JAVA_LD_LIBRARY_PATH =
LAPACK_LIBS =
## we only need this is if it is external, as otherwise link to R
LIBINTL=
LIBM = -lm
LIBR0 = -L$(R_HOME)/lib$(R_ARCH)
LIBR1 = -lR
LIBR = -L$(R_HOME)/lib$(R_ARCH) -lR
LIBS = -lnsl -lsocket -lrt -lsunmath -ldl -lm -liconv -lncurses -lreadline
-lbz2
## needed by R CMD config
LIBnn = lib
LIBTOOL = $(SHELL) "$(R_HOME)/bin/libtool"
#LDFLAGS =
LDFLAGS = -norunpath -m64 -KPIC -DPIC -lc
-L/opt/solarisstudio12.4/lib/sparcv9 -R/opt/solarisstudio12.4/lib/sparcv9
-lsunperf -lfsu -lmtsk -lpicl -lkstat -L/usr/local/R/lib -R/usr/local/R/lib
LTO =
## needed to build applications linking to static libR
MAIN_LD = $(CC)
MAIN_LDFLAGS = -xopenmp
MAIN_LINK = $(MAIN_LD) $(MAIN_LDFLAGS) $(LDFLAGS)
MKINSTALLDIRS = $(R_HOME)/bin/mkinstalldirs
OBJC =
OBJCFLAGS = -g -O2 $(LTO)
OBJC_LIBS =
OBJCXX =
R_ARCH =
RANLIB = ranlib
SAFE_FFLAGS = -g
SED = /usr/xpg4/bin/sed
SHELL = /bin/bash
SHLIB_CFLAGS =
SHLIB_CXXFLAGS =
SHLIB_CXXLD = $(CXX)
SHLIB_CXXLDFLAGS = -G -lstdc++ -lgcc_s -lCrunG3 -lrt -lm -lc
SHLIB_CXX1XLD = $(CXX1X) $(CXX1XSTD)
SHLIB_CXX1XLDFLAGS = -G -lstdc++ -lgcc_s -lCrunG3 -lrt -lm -lc
SHLIB_EXT = .so
SHLIB_FCLD = $(FC)
SHLIB_FCLDFLAGS = -G
SHLIB_FFLAGS =
SHLIB_LD = $(CC)
SHLIB_LDFLAGS = -G# $(CFLAGS) $(CPICFLAGS)
SHLIB_LIBADD =
## We want to ensure libR is picked up from $(R_HOME)/lib
## before e.g. /usr/local/lib if a version is already installed.
SHLIB_LINK = $(SHLIB_LD) $(SHLIB_LDFLAGS) $(LIBR0) $(LDFLAGS)
SHLIB_OPENMP_CFLAGS = -xopenmp
SHLIB_OPENMP_CXXFLAGS = -xopenmp
SHLIB_OPENMP_FCFLAGS = -xopenmp
SHLIB_OPENMP_FFLAGS = -xopenmp
STRIP_LIBS =
STRIP_STATIC_LIBS =
TCLTK_CPPFLAGS =
TCLTK_LIBS =
YACC = bison -y
## for linking to libR.a
STATIC_LIBR = # "$(R_HOME)/lib$(R_ARCH)/libR.a" $(BLAS_LIBS) $(FLIBS)
$(LIBINTL) -lreadline -lncurses $(LIBS)
R_XTRA_CFLAGS =
R_XTRA_CPPFLAGS = -I$(R_INCLUDE_DIR) -DNDEBUG
R_XTRA_CXXFLAGS =
R_XTRA_FFLAGS =
ALL_CFLAGS = $(R_XTRA_CFLAGS) $(PKG_CFLAGS) $(CPICFLAGS) $(SHLIB_CFLAGS)
$(CFLAGS)
ALL_CPPFLAGS = $(R_XTRA_CPPFLAGS) $(PKG_CPPFLAGS) $(CPPFLAGS)
$(CLINK_CPPFLAGS)
ALL_CXXFLAGS = $(R_XTRA_CXXFLAGS) $(PKG_CXXFLAGS) $(CXXPICFLAGS)
$(SHLIB_CXXFLAGS) $(CXXFLAGS)
ALL_OBJCFLAGS = $(PKG_OBJCFLAGS) $(CPICFLAGS) $(SHLIB_CFLAGS) $(OBJCFLAGS)
ALL_OBJCXXFLAGS = $(PKG_OBJCXXFLAGS) $(CXXPICFLAGS) $(SHLIB_CXXFLAGS)
$(OBJCXXFLAGS)
ALL_FFLAGS = $(R_XTRA_FFLAGS) $(PKG_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS)
$(FFLAGS)
## LIBR here as a couple of packages use this without SHLIB_LINK
ALL_LIBS = $(PKG_LIBS) $(SHLIB_LIBADD) $(LIBR)# $(LIBINTL)
.SUFFIXES:
.SUFFIXES: .c .cc .cpp .d .f .f90 .f95 .m .mm .M .o
.c.o:
$(CC) $(ALL_CPPFLAGS) $(ALL_CFLAGS) -c $< -o $@
.c.d:
@echo > $@
.m.d:
@echo > $@
.cc.o:
$(CXX) $(ALL_CPPFLAGS) $(ALL_CXXFLAGS) -c $< -o $@
.cpp.o:
$(CXX) $(ALL_CPPFLAGS) $(ALL_CXXFLAGS) -c $< -o $@
.cc.d:
@echo > $@
.cpp.d:
@echo > $@
.m.o:
$(OBJC) $(ALL_CPPFLAGS) $(ALL_OBJCFLAGS) -c $< -o $@
.mm.o:
$(OBJCXX) $(ALL_CPPFLAGS) $(ALL_OBJCXXFLAGS) -c $< -o $@
.M.o:
$(OBJCXX) $(ALL_CPPFLAGS) $(ALL_OBJCXXFLAGS) -c $< -o $@
.f.o:
$(F77) $(ALL_FFLAGS) -c $< -o $@
.f95.o:
$(FC) $(PKG_FCFLAGS) $(FCPICFLAGS) $(FCFLAGS) -c $< -o $@
.f90.o:
$(FC) $(PKG_FCFLAGS) $(FCPICFLAGS) $(FCFLAGS) -c $< -o $@
/root/.bash_profile
JAVA_HOME="/usr/jdk/instances/jdk1.8.0"
JAVAH=${JAVA_HOME}/include
PATH="/opt/solarisstudio12.4/bin:${JAVA_HOME}/bin:$PATH:/usr/sfw/bin/:/usr/xpg4/bin:/usr/xpg6/bin:/usr/gnu/bin:/usr/local/maven/bin:/usr/gnu/bin:/usr/local/texlive20150523/bin/sparc-solaris"
R_LD_LIBRARY_PATH="/lib:/usr/lib:/opt/solarisstudio12.4/lib/:/usr/local/R/lib/:/usr/gcc/4.8/lib/:/usr/jdk/instances/jdk1.8.0/lib"
LD_LIBRARY_PATH="${R_LD_LIBRARY_PATH}:${LD_LIBRARY_PATH}"
PS1="\u@\h \w [\$(date +%k:%M:%S)]# "
R_HOME=/usr/local/R
#JAVA_LD_LIBRARY_PATH=${JAVA_HOME}/jre/lib:${JAVA_HOME}/lib:${JAVA_HOME}/db/lib
JAVA_CPPFLAGS="-I${JAVA_HOME}/include -I${JAVA_HOME}/include/solaris"
JAVA_LIBS="-L${JAVA_HOME}/jre/lib -L${JAVA_HOME}/lib -L${JAVA_HOME}/db/lib"
#JAVA_LIBS=/usr/jdk/instances/jdk1.8.0/include:/usr/jdk/instances/jdk1.8.0/include/solaris
export JAVA_HOME JAVAH PATH R_LD_LIBRARY_PATH LD_LIBRARY_PATH R_HOME
JAVA_CPPFLAGS JAVA_LIBS
Any idea what should I fine tune also?
Thanks!
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