Error in if (nzchar(SHLIB_LIBADD)) SHLIB_LIBADD else character() : argument is of length zero
可能原因：多数出现在anaconda下安装R，R目录下的R/etc/Makeconf为空
- 解决办法：
复制一份非空的Makeconf 文件过来
- Makeconf 是什么
默认情况下，configure在C、Fortran和CXX源的编译标志中添加一个标志(通常是-g)。这会降低R和包的编译速度，增加对象的大小，所以改变这些标志(在config中设置' CFLAGS '等)可能是个好主意。网站之前配置，或编辑文件Makeconf和etc/Makeconf之间运行配置和make)。
$ miniconda3/envs/scrna/lib/R/etc
$ls
javaconf ldpaths Makeconf Renviron repositories
$ cat 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=/miniconda3/envs/tcga' '--host=x86_64-conda_cos6-linux-gnu' '--build=x86_64-conda_cos6-linux-gnu' '--enable-shared' '--enable-R-shlib' '--with-blas=-lblas' '--with-lapack=-llapack' '--disable-prebuilt-html' '--enable-memory-profiling' '--with-tk-config=/miniconda3/envs/tcga/lib/tkConfig.sh' '--with-tcl-config=/miniconda3/envs/tcga/lib/tclConfig.sh' '--with-x' '--with-pic' '--with-cairo' '--with-readline' '--with-recommended-packages=no' '--without-libintl-prefix' 'LIBnn=lib' 'build_alias=x86_64-conda_cos6-linux-gnu' 'host_alias=x86_64-conda_cos6-linux-gnu' 'PKG_CONFIG_PATH=/miniconda3/envs/tcga/lib/pkgconfig' 'CC=x86_64-conda_cos6-linux-gnu-cc' 'CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /miniconda3/envs/tcga/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1595316670215/work=/usr/local/src/conda/r-base-4.0.2 -fdebug-prefix-map=/miniconda3/envs/tcga=/usr/local/src/conda-prefix' 'LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/miniconda3/envs/tcga/lib -Wl,-rpath-link,/miniconda3/envs/tcga/lib -L/miniconda3/envs/tcga/lib -Wl,-rpath-link,/miniconda3/envs/tcga/lib' 'CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /miniconda3/envs/tcga/include -I/miniconda3/envs/tcga/include -Wl,-rpath-link,/miniconda3/envs/tcga/lib' 'CPP=/home/conda/feedstock_root/build_artifacts/r-base_1595316670215/_build_env/bin/x86_64-conda_cos6-linux-gnu-cpp' 'FC=x86_64-conda_cos6-linux-gnu-gfortran' 'CXX=x86_64-conda_cos6-linux-gnu-c++' 'CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /miniconda3/envs/tcga/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1595316670215/work=/usr/local/src/conda/r-base-4.0.2 -fdebug-prefix-map=/miniconda3/envs/tcga=/usr/local/src/conda-prefix' 'OBJC=x86_64-conda_cos6-linux-gnu-cc'
## This fails if it contains spaces, or if it is quoted
include $(R_SHARE_DIR)/make/vars.mk
AR = x86_64-conda_cos6-linux-gnu-ar
BLAS_LIBS = -lblas
C_VISIBILITY = -fvisibility=hidden
CC = x86_64-conda_cos6-linux-gnu-cc
CFLAGS = -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /miniconda3/envs/tcga/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1595316670215/work=/usr/local/src/conda/r-base-4.0.2 -fdebug-prefix-map=/miniconda3/envs/tcga=/usr/local/src/conda-prefix $(LTO)
CPICFLAGS = -fpic
CPPFLAGS = -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /miniconda3/envs/tcga/include -I/miniconda3/envs/tcga/include -Wl,-rpath-link,/miniconda3/envs/tcga/lib
CXX = x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11
## Not used by anything in R, in particular not for the .cc.d rule
## but used via R CMD config by several packages
CXXCPP = $(CXX) -E
CXXFLAGS = -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /miniconda3/envs/tcga/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1595316670215/work=/usr/local/src/conda/r-base-4.0.2 -fdebug-prefix-map=/miniconda3/envs/tcga=/usr/local/src/conda-prefix $(LTO)
CXXPICFLAGS = -fpic
CXX11 = x86_64-conda_cos6-linux-gnu-c++
CXX11FLAGS = -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /miniconda3/envs/tcga/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1595316670215/work=/usr/local/src/conda/r-base-4.0.2 -fdebug-prefix-map=/miniconda3/envs/tcga=/usr/local/src/conda-prefix $(LTO)
CXX11PICFLAGS = -fpic
CXX11STD = -std=gnu++11
CXX14 = x86_64-conda_cos6-linux-gnu-c++
CXX14FLAGS = -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /miniconda3/envs/tcga/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1595316670215/work=/usr/local/src/conda/r-base-4.0.2 -fdebug-prefix-map=/miniconda3/envs/tcga=/usr/local/src/conda-prefix $(LTO)
CXX14PICFLAGS = -fpic
CXX14STD = -std=gnu++14
CXX17 = x86_64-conda_cos6-linux-gnu-c++
CXX17FLAGS = -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /miniconda3/envs/tcga/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1595316670215/work=/usr/local/src/conda/r-base-4.0.2 -fdebug-prefix-map=/miniconda3/envs/tcga=/usr/local/src/conda-prefix $(LTO)
CXX17PICFLAGS = -fpic
CXX17STD = -std=gnu++17
CXX20 =
CXX20FLAGS = $(LTO)
CXX20PICFLAGS =
CXX20STD =
CXX_VISIBILITY = -fvisibility=hidden
DYLIB_EXT = .so
DYLIB_LD = $(CC)
DYLIB_LDFLAGS = -shared -fopenmp# $(CFLAGS) $(CPICFLAGS)
DYLIB_LINK = $(DYLIB_LD) $(DYLIB_LDFLAGS) $(LDFLAGS)
ECHO = echo
ECHO_C =
ECHO_N = -n
ECHO_T =
F_VISIBILITY = -fvisibility=hidden
## FC is the compiler used for all Fortran as from R 3.6.0
FC = x86_64-conda_cos6-linux-gnu-gfortran
FCFLAGS = -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /miniconda3/envs/tcga/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1595316670215/work=/usr/local/src/conda/r-base-4.0.2 -fdebug-prefix-map=/miniconda3/envs/tcga=/usr/local/src/conda-prefix $(LTO)
## additional libs needed when linking with $(FC), e.g. on some Oracle compilers
FCLIBS_XTRA =
FFLAGS = -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /miniconda3/envs/tcga/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1595316670215/work=/usr/local/src/conda/r-base-4.0.2 -fdebug-prefix-map=/miniconda3/envs/tcga=/usr/local/src/conda-prefix $(LTO)
FLIBS = -lgfortran -lm -lgomp -lquadmath -lpthread
FPICFLAGS = -fpic
FOUNDATION_CPPFLAGS =
FOUNDATION_LIBS =
JAR = /usr/bin/jar
JAVA = /usr/bin/java
JAVAC = /usr/bin/javac
JAVAH = /usr/bin/javah
## JAVA_HOME might be used in the next three.
## They are for packages 'JavaGD' and 'rJava'
JAVA_HOME = /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.181-7.b13.el7.x86_64/jre
JAVA_CPPFLAGS = -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux
JAVA_LIBS = -L$(JAVA_HOME)/lib/amd64/server -ljvm
JAVA_LD_LIBRARY_PATH = $(JAVA_HOME)/lib/amd64/server
LAPACK_LIBS = -llapack
LDFLAGS = -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/miniconda3/envs/tcga/lib -Wl,-rpath-link,/miniconda3/envs/tcga/lib -L/miniconda3/envs/tcga/lib -Wl,-rpath-link,/miniconda3/envs/tcga/lib
## we only need this is if it is external, as otherwise link to R
LIBINTL=
LIBM = -lm
LIBR0 = -L"$(R_HOME)/lib$(R_ARCH)"
LIBR1 = -lR
LIBR = -L"$(R_HOME)/lib$(R_ARCH)" -lR
LIBS = -L/miniconda3/envs/tcga/lib -lpcre2-8 -llzma -lbz2 -lz -lrt -ldl -lm -liconv -licuuc -licui18n
## needed by R CMD config
LIBnn = lib
LIBTOOL = $(SHELL) "$(R_HOME)/bin/libtool"
LTO =
## needed to build applications linking to static libR
MAIN_LD = $(CC)
MAIN_LDFLAGS = -Wl,--export-dynamic -fopenmp
RPATH_LDFLAGS = -Wl,-rpath,$(abs_top_builddir)/lib -Wl,-rpath,/miniconda3/envs/tcga/lib
MAIN_LINK = $(MAIN_LD) $(MAIN_LDFLAGS) $(LDFLAGS) $(RPATH_LDFLAGS)
MKINSTALLDIRS = "$(R_HOME)/bin/mkinstalldirs"
OBJC = x86_64-conda_cos6-linux-gnu-cc
OBJCFLAGS = -g -O2 -fobjc-exceptions $(LTO)
OBJC_LIBS =
OBJCXX =
R_ARCH =
RANLIB = x86_64-conda_cos6-linux-gnu-ranlib
SAFE_FFLAGS = -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /miniconda3/envs/tcga/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1595316670215/work=/usr/local/src/conda/r-base-4.0.2 -fdebug-prefix-map=/miniconda3/envs/tcga=/usr/local/src/conda-prefix -msse2 -mfpmath=sse
SED = /miniconda3/envs/tcga/bin/sed
SHELL = /bin/sh
SHLIB_CFLAGS =
SHLIB_CXXFLAGS =
SHLIB_CXXLD = $(CXX)
SHLIB_CXXLDFLAGS = -shared
SHLIB_CXX11LD = $(CXX11) $(CXX11STD)
SHLIB_CXX11LDFLAGS = -shared
SHLIB_CXX14LD = $(CXX14) $(CXX14STD)
SHLIB_CXX14LDFLAGS = -shared
SHLIB_CXX17LD = $(CXX17) $(CXX17STD)
SHLIB_CXX17LDFLAGS = -shared
SHLIB_CXX20LD = $(CXX20) $(CXX20STD)
SHLIB_CXX20LDFLAGS = -shared
SHLIB_EXT = .so
SHLIB_FFLAGS =
SHLIB_LD = $(CC)
SHLIB_LDFLAGS = -shared# $(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 = -fopenmp
SHLIB_OPENMP_CXXFLAGS = -fopenmp
SHLIB_OPENMP_FFLAGS =
STRIP_STATIC_LIB = x86_64-conda_cos6-linux-gnu-strip --strip-debug
STRIP_SHARED_LIB = x86_64-conda_cos6-linux-gnu-strip --strip-unneeded
TCLTK_CPPFLAGS = -I/miniconda3/envs/tcga/include -I/miniconda3/envs/tcga/include
TCLTK_LIBS = -L/miniconda3/envs/tcga/lib -ltcl8.6 -L/miniconda3/envs/tcga/lib -ltk8.6 -lX11
YACC = yacc
## Legacy settings: these might be used in a src/Makefile
SHLIB_FCLD = $(FC)
SHLIB_FCLDFLAGS = -shared
## for linking to libR.a
STATIC_LIBR = # -Wl,--whole-archive "$(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 in R > 3.6.0
R_XTRA_FFLAGS = -fno-optimize-sibling-calls
## CXX98 is no longer supported, but packages may use it.
SHLIB_CXX98LD = @SHLIB_CXX98LD@
SHLIB_CXX98LDFLAGS = @SHLIB_CXX98LDFLAGS@
## 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) $(CFLAGS)
ALL_CPPFLAGS = -I"$(R_INCLUDE_DIR)" -DNDEBUG $(PKG_CPPFLAGS) $(CLINK_CPPFLAGS) $(CPPFLAGS)
ALL_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 = -fno-optimize-sibling-calls $(PKG_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(FFLAGS)
## can be overridden by R CMD SHLIB
P_FCFLAGS = $(PKG_FFLAGS)
ALL_FCFLAGS = -fno-optimize-sibling-calls $(P_FCFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(FCFLAGS)
## 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 "making $@ from $<"
@$(CC) -MM $(ALL_CPPFLAGS) $< > $@
.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 $@
.m.d:
@echo "making $@ from $<"
@$(OBJC) -MM $(ALL_CPPFLAGS) $< > $@
.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 $@
## @FCFLAGS_f9x@ are flags needed to recognise the extensions
.f95.o:
$(FC) $(ALL_FCFLAGS) -c $< -o $@
.f90.o:
$(FC) $(ALL_FCFLAGS) -c $< -o $@
- Makeconf 为什么会变成空的
R CMD javareconf --help
Usage: R CMD javareconf [options]
Detect current Java setup and update the corresponding configuration in R.
Options:
-h, --help print this help message and exit
-v, --version print version info and exit
-n, --dry-run perform Java detection, but don't touch any
configuration files
-e <prog> same as -n but exports all detected variables
and runs <prog>. If -e is the last argument
or <prog> is '' then a shell is used instead
xxx=yyy evaluate the corresponding expression
(e.g. JAVA_HOME=/usr/lib/java)
Environment variables that can be used to influence the detection:
JAVA path to a Java interpreter executable
By default first 'java' command found on the PATH
is taken (unless JAVA_HOME is also specified).
JAVA_HOME home of the Java environment. If not specified,
it will be detected automatically from the Java
interpreter.
JAVAC path to a Java compiler
JAVAH path to a Java header/stub generator
JAR path to a Java archive tool
Values specified when R was configured will be used unless overridden.
The following variables should be used with extreme caution. They
must all match, so use only if you have a very special setup that
javareconf cannot detect automatically:
JAVA_LD_LIBRARY_PATH library path necessary at run-time
JAVA_CPPFLAGS C preprocessor flags necessary to compile JNI programs
JAVA_LIBS libraries (as linker flags) necessary to compile
JNI programs
Report bugs at <https://bugs.R-project.org>.
https://www.yuque.com/dream-north/r_statistics/is4tsa?language=en-us
https://stackoverflow.com/questions/53813323/installing-r-packages-in-macos-mojave-error-in-if-nzcharshlib-libadd
https://rdrr.io/cran/rstan/man/makeconf_path.html
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html
https://stackoverflow.com/questions/22452826/customize-package-compilation-option-r
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