HenrikBengtsson
commented
2 years ago … I'm using macOS for Monterey 12.3.1, R 4.1.3, gcc 11.2.0. …
Searching for "error" in your compilation output, I see:
fusion/file/CELFileData.h: At global scope:
fusion/file/CELFileData.h:91:23: warning: malformed '#pragma options align={mac68k|power|reset}', ignoring [-Wpragmas]
91 | #pragma options align=packed
| ^~~~~~
fusion/file/CELFileData.h:127:23: error: too many '#pragma options align=reset'
127 | #pragma options align=reset
| ^~~~~This looks like a macOS problem to me(*). Sorry, I don't have access to macOS, so I cannot help here. Someone else with a macOS needs to step in.
(*) FWIW, I've verified that affxparser 1.66.0 installs out of the box on CentOS 7 Linux running R 4.1.3. I've verified this with both GCC 8.3.1 and GCC 11.2.1. Details below. So, I think we can rule out the modern GCC 11.2.1 to be the problem.
$ gcc --version
gcc (GCC) 11.2.1 20210728 (Red Hat 11.2.1-1)and
$ gcc --version
gcc (GCC) 8.3.1 20190311 (Red Hat 8.3.1-3)$ R CMD config --all
CC = gcc
CFLAGS = -g -O2
CPICFLAGS = -fpic
CPPFLAGS = -I/usr/local/include
CXX = g++ -std=gnu++14
CXXFLAGS = -g -O2
CXXPICFLAGS = -fpic
CXX11 = g++
CXX11STD = -std=gnu++11
CXX11FLAGS = -g -O2
CXX11PICFLAGS = -fpic
CXX14 = g++
CXX14STD = -std=gnu++14
CXX14FLAGS = -g -O2
CXX14PICFLAGS = -fpic
CXX17 = g++
CXX17STD = -std=gnu++17
CXX17FLAGS = -g -O2
CXX17PICFLAGS = -fpic
CXX20 = g++
CXX20STD = -std=gnu++2a
CXX20FLAGS = -g -O2
CXX20PICFLAGS = -fpic
DYLIB_EXT = .so
DYLIB_LD = gcc
DYLIB_LDFLAGS = -shared -fopenmp
FC = gfortran
FFLAGS = -g -O2
FPICFLAGS = -fpic
FLIBS = -lgfortran -lm -lquadmath
FCFLAGS = -g -O2
SAFE_FFLAGS = -g -O2 -msse2 -mfpmath=sse
OBJC =
OBJCFLAGS =
JAVA = /usr/lib/jvm/java-1.8.0/jre/bin/java
JAVAC = /usr/lib/jvm/java-1.8.0/bin/javac
JAVAH = /usr/lib/jvm/java-1.8.0/bin/javah
JAR = /usr/lib/jvm/java-1.8.0/bin/jar
JAVA_HOME = /usr/lib/jvm/java-1.8.0
JAVA_LIBS = -L/usr/lib/jvm/java-1.8.0/jre/lib/amd64/server -ljvm
JAVA_CPPFLAGS = -I/usr/lib/jvm/java-1.8.0/include -I/usr/lib/jvm/java-1.8.0/include/linux
LDFLAGS = -L/usr/local/lib64
SHLIB_CFLAGS =
SHLIB_CXXFLAGS =
SHLIB_CXXLD = g++ -std=gnu++14
SHLIB_CXXLDFLAGS = -shared
SHLIB_CXX11LD = g++ -std=gnu++11
SHLIB_CXX11LDFLAGS = -shared
SHLIB_CXX14LD = g++ -std=gnu++14
SHLIB_CXX14LDFLAGS = -shared
SHLIB_CXX17LD = g++ -std=gnu++17
SHLIB_CXX17LDFLAGS = -shared
SHLIB_CXX20LD = g++ -std=gnu++2a
SHLIB_CXX20LDFLAGS = -shared
SHLIB_EXT = .so
SHLIB_FFLAGS =
SHLIB_LD = gcc
SHLIB_LDFLAGS = -shared
TCLTK_CPPFLAGS = -I/usr/include -I/usr/include
TCLTK_LIBS = -L/usr/lib64 -ltcl8.5 -L/usr/lib64 -ltk8.5 -lX11
BLAS_LIBS = -L/software/c4/cbi/software/R-4.1.3-gcc8/lib64/R/lib -lRblas
LAPACK_LIBS = -L/software/c4/cbi/software/R-4.1.3-gcc8/lib64/R/lib -lRlapack
MAKE = make
LIBnn = lib64
AR = ar
NM = /opt/rh/devtoolset-8/root/usr/bin/nm -B
RANLIB = ranlib
LTO =
LTO_FC =
LTO_LD =
## The following variables are defunct
CPP CXXCPP> library(affxparser)
> sessionInfo()
R version 4.1.3 (2022-03-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS: /software/c4/cbi/software/R-4.1.3-gcc8/lib64/R/lib/libRblas.so
LAPACK: /software/c4/cbi/software/R-4.1.3-gcc8/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=C
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] affxparser_1.66.0
loaded via a namespace (and not attached):
[1] compiler_4.1.3PS. @Christopher-Yang-Chq, please format your code/log output using Markdown code blocks (https://docs.github.com/en/get-started/writing-on-github/getting-started-with-writing-and-formatting-on-github/basic-writing-and-formatting-syntax#quoting-code); makes it easier to skim and parse.
PS2. Please also avoid @:ing people in issues, unless you think it's only that person who can respond. By @:ing someone, there's a risk that other's who follow this repo will ignore the posted issue.
Christopher-Yang-Chq
kasperdanielhansen
Hello everyone, here is my problems with installing affxparser package. I'm using macOS for Monterey 12.3.1, R 4.1.3, gcc 11.2.0. The error shows below.
Hope for requests. Thanks!