jwood000
std::make_unique compile error again
Hi Everyone,
It looks like the std::make_unique issue has returned in a new install of R 4.4.0. Any advice on how to proceed would be much appreciated.
Best, John
`
devtools::install_github('jwood000/RcppAlgos') Downloading GitHub repo jwood000/RcppAlgos@HEAD ── R CMD build ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── ✔ checking for file ‘/tmp/RtmpEpvtTp/remotes11e9563eda43e9/jwood000-RcppAlgos-c92abf9/DESCRIPTION’ (403ms) ─ preparing ‘RcppAlgos’: ✔ checking DESCRIPTION meta-information ... ─ cleaning src ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories (766ms) ─ building ‘RcppAlgos_2.8.3.tar.gz’
Installing package into ‘/home/everett/R/x86_64-pc-linux-gnu-library/4.4’ (as ‘lib’ is unspecified)
- installing source package ‘RcppAlgos’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++11 -I"/home/opt/R-4.4.0/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/everett/R/x86_64-pc-linux-gnu-library/4.4/cpp11/include' -I/usr/local/include -fpic -g -O2 -c BigComboCount.cpp -o BigComboCount.o
g++ -std=gnu++11 -I"/home/opt/R-4.4.0/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/everett/R/x86_64-pc-linux-gnu-library/4.4/cpp11/include' -I/usr/local/include -fpic -g -O2 -c BigPartsCountDistinct.cpp -o BigPartsCountDistinct.o
g++ -std=gnu++11 -I"/home/opt/R-4.4.0/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/everett/R/x86_64-pc-linux-gnu-library/4.4/cpp11/include' -I/usr/local/include -fpic -g -O2 -c BigPartsCountRep.cpp -o BigPartsCountRep.o
g++ -std=gnu++11 -I"/home/opt/R-4.4.0/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/everett/R/x86_64-pc-linux-gnu-library/4.4/cpp11/include' -I/usr/local/include -fpic -g -O2 -c BigPartsCountSection.cpp -o BigPartsCountSection.o
g++ -std=gnu++11 -I"/home/opt/R-4.4.0/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/everett/R/x86_64-pc-linux-gnu-library/4.4/cpp11/include' -I/usr/local/include -fpic -g -O2 -c BigPermuteCount.cpp -o BigPermuteCount.o
g++ -std=gnu++11 -I"/home/opt/R-4.4.0/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/everett/R/x86_64-pc-linux-gnu-library/4.4/cpp11/include' -I/usr/local/include -fpic -g -O2 -c CartesianContainer.cpp -o CartesianContainer.o
g++ -std=gnu++11 -I"/home/opt/R-4.4.0/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/everett/R/x86_64-pc-linux-gnu-library/4.4/cpp11/include' -I/usr/local/include -fpic -g -O2 -c CheckReturn.cpp -o CheckReturn.o
g++ -std=gnu++11 -I"/home/opt/R-4.4.0/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/everett/R/x86_64-pc-linux-gnu-library/4.4/cpp11/include' -I/usr/local/include -fpic -g -O2 -c ClassUtils.cpp -o ClassUtils.o
g++ -std=gnu++11 -I"/home/opt/R-4.4.0/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/everett/R/x86_64-pc-linux-gnu-library/4.4/cpp11/include' -I/usr/local/include -fpic -g -O2 -c CnstrntsSpecialClass.cpp -o CnstrntsSpecialClass.o
g++ -std=gnu++11 -I"/home/opt/R-4.4.0/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/everett/R/x86_64-pc-linux-gnu-library/4.4/cpp11/include' -I/usr/local/include -fpic -g -O2 -c CnstrntsToRClass.cpp -o CnstrntsToRClass.o
g++ -std=gnu++11 -I"/home/opt/R-4.4.0/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/everett/R/x86_64-pc-linux-gnu-library/4.4/cpp11/include' -I/usr/local/include -fpic -g -O2 -c CombinationResults.cpp -o CombinationResults.o
g++ -std=gnu++11 -I"/home/opt/R-4.4.0/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/everett/R/x86_64-pc-linux-gnu-library/4.4/cpp11/include' -I/usr/local/include -fpic -g -O2 -c CombinatoricsApply.cpp -o CombinatoricsApply.o
g++ -std=gnu++11 -I"/home/opt/R-4.4.0/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/everett/R/x86_64-pc-linux-gnu-library/4.4/cpp11/include' -I/usr/local/include -fpic -g -O2 -c CombinatoricsCount.cpp -o CombinatoricsCount.o
g++ -std=gnu++11 -I"/home/opt/R-4.4.0/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/everett/R/x86_64-pc-linux-gnu-library/4.4/cpp11/include' -I/usr/local/include -fpic -g -O2 -c CombinatoricsMain.cpp -o CombinatoricsMain.o
g++ -std=gnu++11 -I"/home/opt/R-4.4.0/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/everett/R/x86_64-pc-linux-gnu-library/4.4/cpp11/include' -I/usr/local/include -fpic -g -O2 -c ComboApplyClass.cpp -o ComboApplyClass.o
g++ -std=gnu++11 -I"/home/opt/R-4.4.0/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/everett/R/x86_64-pc-linux-gnu-library/4.4/cpp11/include' -I/usr/local/include -fpic -g -O2 -c ComboCartesian.cpp -o ComboCartesian.o
g++ -std=gnu++11 -I"/home/opt/R-4.4.0/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/everett/R/x86_64-pc-linux-gnu-library/4.4/cpp11/include' -I/usr/local/include -fpic -g -O2 -c ComboClass.cpp -o ComboClass.o
g++ -std=gnu++11 -I"/home/opt/R-4.4.0/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/everett/R/x86_64-pc-linux-gnu-library/4.4/cpp11/include' -I/usr/local/include -fpic -g -O2 -c ComboCount.cpp -o ComboCount.o
g++ -std=gnu++11 -I"/home/opt/R-4.4.0/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/everett/R/x86_64-pc-linux-gnu-library/4.4/cpp11/include' -I/usr/local/include -fpic -g -O2 -c ComboGroups.cpp -o ComboGroups.o
g++ -std=gnu++11 -I"/home/opt/R-4.4.0/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/everett/R/x86_64-pc-linux-gnu-library/4.4/cpp11/include' -I/usr/local/include -fpic -g -O2 -c ComboGroupsClass.cpp -o ComboGroupsClass.o
g++ -std=gnu++11 -I"/home/opt/R-4.4.0/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/everett/R/x86_64-pc-linux-gnu-library/4.4/cpp11/include' -I/usr/local/include -fpic -g -O2 -c ComboGroupsGeneral.cpp -o ComboGroupsGeneral.o
g++ -std=gnu++11 -I"/home/opt/R-4.4.0/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/everett/R/x86_64-pc-linux-gnu-library/4.4/cpp11/include' -I/usr/local/include -fpic -g -O2 -c ComboGroupsSame.cpp -o ComboGroupsSame.o
g++ -std=gnu++11 -I"/home/opt/R-4.4.0/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/everett/R/x86_64-pc-linux-gnu-library/4.4/cpp11/include' -I/usr/local/include -fpic -g -O2 -c ComboGroupsTemplate.cpp -o ComboGroupsTemplate.o
ComboGroupsTemplate.cpp: In function ‘std::unique_ptr<ComboGroupsTemplate> MakeComboGroup(const std::vector
&, const GroupHelper&, int, int, int, int, bool, bool, bool)’: ComboGroupsTemplate.cpp:35:21: error: ‘make_unique’ is not a member of ‘std’ 35 | return std::make_unique<ComboGroupsGeneral>( | ^~~~~~~~~~~ ComboGroupsTemplate.cpp:35:21: note: ‘std::make_unique’ is only available from C++14 onwards ComboGroupsTemplate.cpp:35:51: error: expected primary-expression before ‘>’ token 35 | return std::make_unique<ComboGroupsGeneral>( | ^ ComboGroupsTemplate.cpp:39:21: error: ‘make_unique’ is not a member of ‘std’ 39 | return std::make_unique<ComboGroupsUnique>(n, r, i1, i2, bnd, vGrpSize); | ^~~~~~~~~~~ ComboGroupsTemplate.cpp:39:21: note: ‘std::make_unique’ is only available from C++14 onwards ComboGroupsTemplate.cpp:39:50: error: expected primary-expression before ‘>’ token 39 | return std::make_unique<ComboGroupsUnique>(n, r, i1, i2, bnd, vGrpSize); | ^ ComboGroupsTemplate.cpp:41:21: error: ‘make_unique’ is not a member of ‘std’ 41 | return std::make_unique<ComboGroupsSame>( | ^~~~~~~~~~~ ComboGroupsTemplate.cpp:41:21: note: ‘std::make_unique’ is only available from C++14 onwards ComboGroupsTemplate.cpp:41:48: error: expected primary-expression before ‘>’ token 41 | return std::make_unique<ComboGroupsSame>( | ^ make: *** [/home/opt/R-4.4.0/lib/R/etc/Makeconf:204: ComboGroupsTemplate.o] Error 1 ERROR: compilation failed for package ‘RcppAlgos’ - removing ‘/home/everett/R/x86_64-pc-linux-gnu-library/4.4/RcppAlgos’ Warning message: In i.p(...) : installation of package ‘/tmp/RtmpEpvtTp/file11e956686cc6ab/RcppAlgos_2.8.3.tar.gz’ had non-zero exit status `
`
sessionInfo() R version 4.4.0 (2024-04-24) Platform: x86_64-pc-linux-gnu Running under: Ubuntu 22.04.4 LTS
Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3 LAPACK: /home/opt/R-4.4.0/lib/R/lib/libRlapack.so; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8
[8] LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: America/New_York tzcode source: system (glibc)
attached base packages: [1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached): [1] compiler_4.4.0 tools_4.4.0 `
This looks like you need to enable a more recent c++ standard. I see you have g++ -std=gnu++11, where you need at least c++ 14 support. As of c++ 14, std::make_unique is defined in the memory header.
You may need to upgrade your compiler if it doesn't support a later standard.
Also, I don't see anything from the current checks: https://cran.r-project.org/web/checks/check_results_RcppAlgos.html
Please let me know what you find.
Thanks
Thanks ! Great observation. Curious though because CXX is set to C++ 17 (below). Perhaps something in the MakeFile is calling for 11. I will dig deeper.
Best, John
(base) @.***:~$ R CMD config CXX g++ -std=gnu++17
(base) @.***:~$ grep ^CXX $(R RHOME)/etc/Makeconf CXX = g++ -std=gnu++17 CXXFLAGS = -g -O2 -ffile-prefix-map=/build/r-base-H8urij/r-base-4.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 $(LTO) CXXPICFLAGS = -fpic CXX11 = g++ CXX11FLAGS = -g -O2 -ffile-prefix-map=/build/r-base-H8urij/r-base-4.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 $(LTO) CXX11PICFLAGS = -fpic CXX11STD = -std=gnu++11 CXX14 = g++ CXX14FLAGS = -g -O2 -ffile-prefix-map=/build/r-base-H8urij/r-base-4.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 $(LTO) CXX14PICFLAGS = -fpic CXX14STD = -std=gnu++14 CXX17 = g++ CXX17FLAGS = -g -O2 -ffile-prefix-map=/build/r-base-H8urij/r-base-4.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 $(LTO) CXX17PICFLAGS = -fpic CXX17STD = -std=gnu++17 CXX20 = g++ CXX20FLAGS = -g -O2 -ffile-prefix-map=/build/r-base-H8urij/r-base-4.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 $(LTO) CXX20PICFLAGS = -fpic CXX20STD = -std=gnu++20 CXX23 = g++ CXX23FLAGS = -g -O2 -ffile-prefix-map=/build/r-base-H8urij/r-base-4.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 $(LTO) CXX23PICFLAGS = -fpic CXX23STD = -std=gnu++23 CXX_VISIBILITY = -fvisibility=hidden
On Fri, May 24, 2024 at 1:57 PM Joseph Wood @.***> wrote:
This looks like you need to enable a more recent c++ standard. I see you have g++ -std=gnu++11, where you need at least c++ 14 support. As of c++ 14, std::make_unique is defined in the memory header.
You may need to upgrade your compiler if it doesn't support a later standard.
Also, I don't see anything from the current checks: https://cran.r-project.org/web/checks/check_results_RcppAlgos.html
Please let me know what you find.
Thanks
— Reply to this email directly, view it on GitHub https://github.com/jwood000/RcppAlgos/issues/51#issuecomment-2130089420, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB2ISQ2P7FRIOVJBV4W57JTZD55PPAVCNFSM6AAAAABIHYXUUGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMZQGA4DSNBSGA . You are receiving this because you authored the thread.Message ID: @.***>
-- John K. Everett, Ph.D. http://www.linkedin.com/in/JohnEverettPhD
... before I start digging, my default R compiler configurations are below. C++ settings look good. Kindly let me know where in your package compilation initiates, eg. MakeFile(s). Perhaps there is something that is pushing my system to use -std=gnu++11.
Best, John
(base) @.***:~$ more /etc/R/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 '--prefix=/usr' '--with-cairo' '--with-jpeglib'
'--with-readline' '--with-tcltk' '--mandir=/usr/share/man' '--infodir=/usr/share/info' '--datadir=/usr/share/R/share' '--includedir=/usr/share/R/include' '--with-blas' '--with-lap ack' '--enable-long-double' '--enable-R-profiling' '--enable-R-shlib' '--enable-memory-profiling' '--without-recommended-packages' '--build' 'x86_64-linux-gnu' 'build_alias=x86_64-linux-gnu' 'R_PRINTCMD=/usr/bin/lpr' 'R_PAPERSIZE=letter' 'T AR=/bin/tar' 'R_BROWSER=xdg-open' 'LIBnn=lib' 'JAVA_HOME=/usr/lib/jvm/default-java' 'R_SHELL=/bin/bash' 'CC=gcc' 'CFLAGS=-g -O2 -ffile-prefix-map=/build/r-base-H8urij/r-base-4.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2' 'LDFLAGS=-Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro' 'CPPFLAGS=' 'FC=gfortran' 'FCFLAGS=-g -O2 -ffile-prefix-map=/build/r-base-H8urij/r-base-4.4.0=. -fstack-protector-stron g' 'CXX=g++' 'CXXFLAGS=-g -O2 -ffile-prefix-map=/build/r-base-H8urij/r-base-4.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2'
This fails if it contains spaces, or if it is quoted
include $(R_SHARE_DIR)/make/vars.mk
AR = ar BLAS_LIBS = -lblas
C compilers
CC = gcc CFLAGS = -g -O2 -ffile-prefix-map=/build/r-base-H8urij/r-base-4.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 $(LTO) CC17 = gcc -std=gnu17 C17FLAGS = -g -O2 -ffile-prefix-map=/build/r-base-H8urij/r-base-4.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 $(LTO) CC23 = gcc -std=gnu2x C23FLAGS = -g -O2 -ffile-prefix-map=/build/r-base-H8urij/r-base-4.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 $(LTO) CC90 = gcc -std=gnu90 C90FLAGS = -g -O2 -ffile-prefix-map=/build/r-base-H8urij/r-base-4.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 $(LTO) CC99 = gcc -std=gnu99 C99FLAGS = -g -O2 -ffile-prefix-map=/build/r-base-H8urij/r-base-4.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 $(LTO) CPICFLAGS = -fpic CPPFLAGS = C_VISIBILITY = -fvisibility=hidden
C++ compilers
CXX = g++ -std=gnu++17 CXXFLAGS = -g -O2 -ffile-prefix-map=/build/r-base-H8urij/r-base-4.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 $(LTO) CXXPICFLAGS = -fpic CXX11 = g++ CXX11FLAGS = -g -O2 -ffile-prefix-map=/build/r-base-H8urij/r-base-4.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 $(LTO) CXX11PICFLAGS = -fpic CXX11STD = -std=gnu++11 CXX14 = g++ CXX14FLAGS = -g -O2 -ffile-prefix-map=/build/r-base-H8urij/r-base-4.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 $(LTO) CXX14PICFLAGS = -fpic CXX14STD = -std=gnu++14 CXX17 = g++ CXX17FLAGS = -g -O2 -ffile-prefix-map=/build/r-base-H8urij/r-base-4.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 $(LTO) CXX17PICFLAGS = -fpic CXX17STD = -std=gnu++17 CXX20 = g++ CXX20FLAGS = -g -O2 -ffile-prefix-map=/build/r-base-H8urij/r-base-4.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 $(LTO) CXX20PICFLAGS = -fpic CXX20STD = -std=gnu++20 CXX23 = g++ CXX23FLAGS = -g -O2 -ffile-prefix-map=/build/r-base-H8urij/r-base-4.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 $(LTO) CXX23PICFLAGS = -fpic CXX23STD = -std=gnu++23 CXX_VISIBILITY = -fvisibility=hidden
DYLIB_EXT = .so DYLIB_LD = $(CC) DYLIB_LDFLAGS = -shared -fopenmp# $(CFLAGS) $(CPICFLAGS)
should be used by packages for dylibs, but at the time of writing was not
DYLIB_LINK = $(DYLIB_LD) $(DYLIB_LDFLAGS) $(LDFLAGS) ECHO = echo ECHO_C = ECHO_N = -n ECHO_T =
Fortran
FC = gfortran FCFLAGS = -g -O2 -ffile-prefix-map=/build/r-base-H8urij/r-base-4.4.0=. -fstack-protector-strong $(LTO_FC)
additional libs needed when linking with $(FC), e.g. on some Oracle
compilers FCLIBS_XTRA = FFLAGS = -g -O2 -ffile-prefix-map=/build/r-base-H8urij/r-base-4.4.0=. -fstack-protector-strong $(LTO_FC) FLIBS = -lgfortran -lm -lquadmath FPICFLAGS = -fpic FPIEFLAGS = -fPIE F_VISIBILITY = -fvisibility=hidden
FOUNDATION_CPPFLAGS = FOUNDATION_LIBS = JAR = /usr/lib/jvm/default-java/bin/jar JAVA = /usr/lib/jvm/default-java/bin/java JAVAC = /usr/lib/jvm/default-java/bin/javac JAVAH =
JAVA_HOME might be used in the next three.
They are for packages 'JavaGD' and 'rJava'
JAVA_HOME = /usr/lib/jvm/default-java JAVA_CPPFLAGS = -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux JAVA_LIBS = -L$(JAVA_HOME)/lib/server -ljvm JAVA_LD_LIBRARY_PATH = $(JAVA_HOME)/lib/server LAPACK_LIBS = -llapack LDFLAGS = -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro
we only need this is if it is external, as otherwise link to R
LIBINTL= LIBM = -lm LIBR0 = -L"$(R_HOME)/lib$(R_ARCH)" LIBR1 = -lR LIBR = -L"$(R_HOME)/lib$(R_ARCH)" -lR LIBS = -lpcre2-8 -ldeflate -llzma -lbz2 -lz -ltirpc -lrt -ldl -lm -licuuc -licui18n
needed by R CMD config
LIBnn = lib LIBTOOL = $(SHELL) "$(R_HOME)/bin/libtool"
set for --enable-lto, --enable-lto=check
LTO = LTO_FC = LTO_LD =
set for --enable-lto=R, used in INSTALL
LTO_OPT = LTO_FC_OPT =
needed to build applications linking to static libR
MAIN_LD = $(CC) MAIN_LDFLAGS = -Wl,--export-dynamic -fopenmp MAIN_LINK = $(MAIN_LD) $(MAIN_LDFLAGS) $(LDFLAGS) MKINSTALLDIRS = "$(R_HOME)/bin/mkinstalldirs" NM = /usr/bin/nm -B OBJC = OBJCFLAGS = $(LTO) OBJC_LIBS = OBJCXX = R_ARCH = RANLIB = ranlib SAFE_FFLAGS = -g -O2 -ffile-prefix-map=/build/r-base-H8urij/r-base-4.4.0=. -fstack-protector-strong -msse2 -mfpmath=sse
A version of SHLIB_LIBADD not overridden in install.R.
SAN_LIBS = SED = /bin/sed SHELL = /bin/bash SHLIB_CFLAGS = SHLIB_CXXFLAGS = SHLIB_CXXLD = $(CXX) SHLIB_CXXLDFLAGS = -shared# $(CXXFLAGS) $(CXXPICFLAGS) $(LTO_LD) SHLIB_CXX11LD = $(CXX11) $(CXX11STD) SHLIB_CXX11LDFLAGS = -shared# $(CXX11FLAGS) $(CXX11PICFLAGS) $(LTO_LD) SHLIB_CXX14LD = $(CXX14) $(CXX14STD) SHLIB_CXX14LDFLAGS = -shared# $(CXX14FLAGS) $(CXX14PICFLAGS) $(LTO_LD) SHLIB_CXX17LD = $(CXX17) $(CXX17STD) SHLIB_CXX17LDFLAGS = -shared# $(CXX17FLAGS) $(CXX17PICFLAGS) $(LTO_LD) SHLIB_CXX20LD = $(CXX20) $(CXX20STD) SHLIB_CXX20LDFLAGS = -shared# $(CXX20FLAGS) $(CXX20PICFLAGS) $(LTO_LD) SHLIB_CXX23LD = $(CXX23) $(CXX23STD) SHLIB_CXX23LDFLAGS = -shared# $(CXX23FLAGS) $(CXX23PICFLAGS) $(LTO_LD) SHLIB_EXT = .so SHLIB_FCLD = $(FC) SHLIB_FCLDFLAGS = -shared# $(FCFLAGS) $(FPICFLAGS) SHLIB_FFLAGS = SHLIB_LD = $(CC)
used for add-on packages linked by C
SHLIB_LDFLAGS = -shared# $(CFLAGS) $(CPICFLAGS) $(LTO_LD)
used for standard packages
SHLIB_LDFLAGS_R = -shared# $(CFLAGS) $(CPICFLAGS) $(LTO_LD)
used in install.R to add OBJC_LIBS, FLIBS ....
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) $(LDFLAGS) SHLIB_OPENMP_CFLAGS = -fopenmp SHLIB_OPENMP_CXXFLAGS = -fopenmp SHLIB_OPENMP_FFLAGS = -fopenmp STRIP_STATIC_LIB = strip --strip-debug STRIP_SHARED_LIB = strip --strip-unneeded TCLTK_CPPFLAGS = -I/usr/include/tcl8.6 -I/usr/include/tcl8.6 TCLTK_LIBS = -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -L/usr/lib/x86_64-linux-gnu -ltk8.6 -lX11 -lXss -lXext YACC = bison -y
for linking to libR.a
STATIC_LIBR = # -Wl,--whole-archive "$(R_HOME)/lib$(R_ARCH)/libR.a" -Wl,--no-whole-archive $(BLAS_LIBS) $(FLIBS) $(LIBINTL) -lreadline $(LIBS)
These are recorded as macros for legacy use in packages
set on AIX, formerly for old glibc (-D__NO_MATH_INLINES)
R_XTRA_CFLAGS =
was formerly set on HP-UX
R_XTRA_CPPFLAGS = -I"$(R_INCLUDE_DIR)" -DNDEBUG
currently unset
R_XTRA_CXXFLAGS =
used for gfortran >= 7 in R 3.6.1 - 4.2.x
R_XTRA_FFLAGS =
SHLIB_CFLAGS SHLIB_CXXFLAGS SHLIB_FFLAGS are apparently currently unused
SHLIB_CXXFLAGS is undocumented, there is no SHLIB_FCFLAGS
ALL_CFLAGS = $(PKG_CFLAGS) $(CPICFLAGS) $(SHLIB_CFLAGS) $(CFLAGS)
XDEFS was a temporary measure for use by R CMD INSTALL
ALL_CPPFLAGS = -I"$(R_INCLUDE_DIR)" -DNDEBUG $(PKG_CPPFLAGS) $(CLINK_CPPFLAGS) $(CPPFLAGS) $(XDEFS)
CXX_DEFS allows adding defines only for C++, e.g. -DR_NO_REMAP
ALL_CXXFLAGS = $(PKG_CXXFLAGS) $(CXXPICFLAGS) $(SHLIB_CXXFLAGS) $(CXXFLAGS) $(CXX_DEFS) ALL_OBJCFLAGS = $(PKG_OBJCFLAGS) $(CPICFLAGS) $(SHLIB_CFLAGS) $(OBJCFLAGS) ALL_OBJCXXFLAGS = $(PKG_OBJCXXFLAGS) $(CXXPICFLAGS) $(SHLIB_CXXFLAGS) $(OBJCXXFLAGS) ALL_FFLAGS = $(PKG_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(FFLAGS)
can be overridden by R CMD SHLIB
P_FCFLAGS = $(PKG_FFLAGS) ALL_FCFLAGS = $(P_FCFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(FCFLAGS)
LIBR here as a couple of packages use this without SHLIB_LINK
ALL_LIBS = $(PKG_LIBS) $(SHLIB_LIBADD) $(SAN_LIBS) $(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 "making $@ from $<" @$(CC) -MM $(ALL_CPPFLAGS) $< > $@ .m.d: @echo > $@ .cc.o: $(CXX) $(ALL_CPPFLAGS) $(ALL_CXXFLAGS) -c $< -o $@ .cpp.o: $(CXX) $(ALL_CPPFLAGS) $(ALL_CXXFLAGS) -c $< -o $@ .cc.d: @echo "making $@ from $<" @$(CXX) -M $(ALL_CPPFLAGS) $< > $@ .cpp.d: @echo "making $@ from $<" @$(CXX) -M $(ALL_CPPFLAGS) $< > $@ .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: $(FC) $(ALL_FFLAGS) -c $< -o $@ .f95.o: $(FC) $(ALL_FCFLAGS) -c $< -o $@ .f90.o: $(FC) $(ALL_FCFLAGS) -c $< -o $@
On Fri, May 24, 2024 at 8:50 PM John Everett @.***> wrote:
Thanks ! Great observation. Curious though because CXX is set to C++ 17 (below). Perhaps something in the MakeFile is calling for 11. I will dig deeper.
Best, John
(base) @.***:~$ R CMD config CXX g++ -std=gnu++17
(base) @.***:~$ grep ^CXX $(R RHOME)/etc/Makeconf CXX = g++ -std=gnu++17 CXXFLAGS = -g -O2 -ffile-prefix-map=/build/r-base-H8urij/r-base-4.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 $(LTO) CXXPICFLAGS = -fpic CXX11 = g++ CXX11FLAGS = -g -O2 -ffile-prefix-map=/build/r-base-H8urij/r-base-4.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 $(LTO) CXX11PICFLAGS = -fpic CXX11STD = -std=gnu++11 CXX14 = g++ CXX14FLAGS = -g -O2 -ffile-prefix-map=/build/r-base-H8urij/r-base-4.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 $(LTO) CXX14PICFLAGS = -fpic CXX14STD = -std=gnu++14 CXX17 = g++ CXX17FLAGS = -g -O2 -ffile-prefix-map=/build/r-base-H8urij/r-base-4.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 $(LTO) CXX17PICFLAGS = -fpic CXX17STD = -std=gnu++17 CXX20 = g++ CXX20FLAGS = -g -O2 -ffile-prefix-map=/build/r-base-H8urij/r-base-4.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 $(LTO) CXX20PICFLAGS = -fpic CXX20STD = -std=gnu++20 CXX23 = g++ CXX23FLAGS = -g -O2 -ffile-prefix-map=/build/r-base-H8urij/r-base-4.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 $(LTO) CXX23PICFLAGS = -fpic CXX23STD = -std=gnu++23 CXX_VISIBILITY = -fvisibility=hidden
On Fri, May 24, 2024 at 1:57 PM Joseph Wood @.***> wrote:
This looks like you need to enable a more recent c++ standard. I see you have g++ -std=gnu++11, where you need at least c++ 14 support. As of c++ 14, std::make_unique is defined in the memory header.
You may need to upgrade your compiler if it doesn't support a later standard.
Also, I don't see anything from the current checks: https://cran.r-project.org/web/checks/check_results_RcppAlgos.html
Please let me know what you find.
Thanks
— Reply to this email directly, view it on GitHub https://github.com/jwood000/RcppAlgos/issues/51#issuecomment-2130089420, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB2ISQ2P7FRIOVJBV4W57JTZD55PPAVCNFSM6AAAAABIHYXUUGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMZQGA4DSNBSGA . You are receiving this because you authored the thread.Message ID: @.***>
-- John K. Everett, Ph.D. http://www.linkedin.com/in/JohnEverettPhD
-- John K. Everett, Ph.D. http://www.linkedin.com/in/JohnEverettPhD
@helixscript,
Before spending too much time on your setup, let me point out a few things:
- There is a Makevars file and a DESCRIPTION that could possibly affect compilation.
- For the current
Makevarsfile there is no specification for C++ standard nor is there anything in theSystemRequirementsfield of theDESCRIPTIONfile. - Given the two points above, the base C++ standard employed is dependent on the R version you are using. Since R 4.0.0, the standard is C++17.
- Finally, there is an INSTALL.md file that has some guidelines for installation. It says there that a modern compiler is required. We know that compilation fails for gcc 4.8.5 whereas compilation was successful for gcc 5.3.1.
- It looks like you are using gcc compiler. You can find what version of gcc you have by typing
gcc -von the command line.
Please let me know what you find.
Thanks
@helixscript I am closing this issue as there has been no reply for some time. If you have any further information or questions, please don't hesitate to reach out.