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jean997 / cause

R package for CAUSE
https://jean997.github.io/cause/
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Cannot install the cause #11

Closed whecrane closed 3 years ago

whecrane commented 3 years ago

Hi Jean, I try to install the package used the code : devtools::install_github("jean997/cause@v1.2.0") and the develpment vesion (devtools::install_github("jean997/cause"), neither failed. They got the same error:

That will be so nice if you can give me some help. Thank you!

Best wishes, Crane

jean997 commented 3 years ago

Wow I've never seen anything like this error before. My guess is that it is something to do with your conda environment and compiling the c++ code. I will see if I can figure it out. Does it install outside of the conda environment?

whecrane commented 3 years ago

I installed it in the conda environment, the version of R is 4.0.

王鹤

邮箱：whe930102@163.com | On 12/05/2020 00:15, Jean Morrison wrote:

Wow I've never seen anything like this error before. My guess is that it is something to do with your conda environment and compiling the c++ code. I will see if I can figure it out. Does it install outside of the conda environment?

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CreRecombinase commented 3 years ago

Can you post the output of the R command sessionInfo()?

CreRecombinase commented 3 years ago

Please also post the output of the shell command R CMD config --all

whecrane commented 3 years ago

This is the outputs: $R CMD config --all 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 /media/EXTend2018/Wanghe2019/.conda/envs/r_4/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1591949865905/work=/usr/local/src/conda/r-base-4.0.1 -fdebug-prefix-map=/media/EXTend2018/Wanghe2019/.conda/envs/r_4=/usr/local/src/conda-prefix CPICFLAGS = -fpic CPPFLAGS = -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /media/EXTend2018/Wanghe2019/.conda/envs/r_4/include -I/media/EXTend2018/Wanghe2019/.conda/envs/r_4/include -Wl,-rpath-link,/media/EXTend2018/Wanghe2019/.conda/envs/r_4/lib CXX = x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11 CXXFLAGS = -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /media/EXTend2018/Wanghe2019/.conda/envs/r_4/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1591949865905/work=/usr/local/src/conda/r-base-4.0.1 -fdebug-prefix-map=/media/EXTend2018/Wanghe2019/.conda/envs/r_4=/usr/local/src/conda-prefix CXXPICFLAGS = -fpic CXX11 = x86_64-conda_cos6-linux-gnu-c++ CXX11STD = -std=gnu++11 CXX11FLAGS = -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /media/EXTend2018/Wanghe2019/.conda/envs/r_4/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1591949865905/work=/usr/local/src/conda/r-base-4.0.1 -fdebug-prefix-map=/media/EXTend2018/Wanghe2019/.conda/envs/r_4=/usr/local/src/conda-prefix CXX11PICFLAGS = -fpic CXX14 = x86_64-conda_cos6-linux-gnu-c++ CXX14STD = -std=gnu++14 CXX14FLAGS = -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /media/EXTend2018/Wanghe2019/.conda/envs/r_4/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1591949865905/work=/usr/local/src/conda/r-base-4.0.1 -fdebug-prefix-map=/media/EXTend2018/Wanghe2019/.conda/envs/r_4=/usr/local/src/conda-prefix CXX14PICFLAGS = -fpic CXX17 = x86_64-conda_cos6-linux-gnu-c++ CXX17STD = -std=gnu++17 CXX17FLAGS = -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /media/EXTend2018/Wanghe2019/.conda/envs/r_4/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1591949865905/work=/usr/local/src/conda/r-base-4.0.1 -fdebug-prefix-map=/media/EXTend2018/Wanghe2019/.conda/envs/r_4=/usr/local/src/conda-prefix CXX17PICFLAGS = -fpic CXX20 = CXX20STD = CXX20FLAGS = CXX20PICFLAGS = DYLIB_EXT = .so DYLIB_LD = x86_64-conda_cos6-linux-gnu-cc DYLIB_LDFLAGS = -shared -fopenmp FC = x86_64-conda_cos6-linux-gnu-gfortran FFLAGS = -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /media/EXTend2018/Wanghe2019/.conda/envs/r_4/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1591949865905/work=/usr/local/src/conda/r-base-4.0.1 -fdebug-prefix-map=/media/EXTend2018/Wanghe2019/.conda/envs/r_4=/usr/local/src/conda-prefix FPICFLAGS = -fpic FLIBS = -lgfortran -lm -lgomp -lquadmath -lpthread FCFLAGS = -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /media/EXTend2018/Wanghe2019/.conda/envs/r_4/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1591949865905/work=/usr/local/src/conda/r-base-4.0.1 -fdebug-prefix-map=/media/EXTend2018/Wanghe2019/.conda/envs/r_4=/usr/local/src/conda-prefix SAFE_FFLAGS = -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /media/EXTend2018/Wanghe2019/.conda/envs/r_4/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1591949865905/work=/usr/local/src/conda/r-base-4.0.1 -fdebug-prefix-map=/media/EXTend2018/Wanghe2019/.conda/envs/r_4=/usr/local/src/conda-prefix -msse2 -mfpmath=sse OBJC = x86_64-conda_cos6-linux-gnu-cc OBJCFLAGS = -g -O2 -fobjc-exceptions JAVA = /media/EXTend2018/Wanghe2019/miniconda3/bin/java JAVAC = /media/EXTend2018/Wanghe2019/miniconda3/bin/javac JAVAH = /media/EXTend2018/Wanghe2019/miniconda3/bin/javah JAR = /media/EXTend2018/Wanghe2019/miniconda3/bin/jar JAVA_HOME = /media/EXTend2018/Wanghe2019/miniconda3/jre JAVA_LIBS = -L/media/EXTend2018/Wanghe2019/miniconda3/jre/lib/amd64/server -ljvm JAVA_CPPFLAGS = -I/media/EXTend2018/Wanghe2019/miniconda3/jre/../include -I/media/EXTend2018/Wanghe2019/miniconda3/jre/../include/linux LDFLAGS = -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/media/EXTend2018/Wanghe2019/.conda/envs/r_4/lib -Wl,-rpath-link,/media/EXTend2018/Wanghe2019/.conda/envs/r_4/lib -L/media/EXTend2018/Wanghe2019/.conda/envs/r_4/lib -Wl,-rpath-link,/media/EXTend2018/Wanghe2019/.conda/envs/r_4/lib SHLIB_CFLAGS = SHLIB_CXXFLAGS = SHLIB_CXXLD = x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11 SHLIB_CXXLDFLAGS = -shared SHLIB_CXX11LD = x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11 SHLIB_CXX11LDFLAGS = -shared SHLIB_CXX14LD = x86_64-conda_cos6-linux-gnu-c++ -std=gnu++14 SHLIB_CXX14LDFLAGS = -shared SHLIB_CXX17LD = x86_64-conda_cos6-linux-gnu-c++ -std=gnu++17 SHLIB_CXX17LDFLAGS = -shared SHLIB_CXX20LD = SHLIB_CXX20LDFLAGS = -shared SHLIB_EXT = .so SHLIB_FFLAGS = SHLIB_LD = x86_64-conda_cos6-linux-gnu-cc SHLIB_LDFLAGS = -shared TCLTK_CPPFLAGS = -I/media/EXTend2018/Wanghe2019/.conda/envs/r_4/include -I/media/EXTend2018/Wanghe2019/.conda/envs/r_4/include TCLTK_LIBS = -L/media/EXTend2018/Wanghe2019/.conda/envs/r_4/lib -ltcl8.6 -L/media/EXTend2018/Wanghe2019/.conda/envs/r_4/lib -ltk8.6 -lX11 BLAS_LIBS = -lblas LAPACK_LIBS = -llapack MAKE = make LIBnn = lib AR = x86_64-conda_cos6-linux-gnu-ar RANLIB = x86_64-conda_cos6-linux-gnu-ranlib

The following variables are deprecated

CPP = /media/EXTend2018/Wanghe2019/.conda/envs/r_4/bin/x86_64-conda_cos6-linux-gnu-cpp CXXCPP = x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11 -E

sessionInfo() R version 4.0.1 (2020-06-06) Platform: x86_64-conda_cos6-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS/LAPACK: /media/EXTend2018/Wanghe2019/.conda/envs/r_4/lib/libopenblasp-r0.3.10.so

locale: [1] LC_CTYPE=zh_CN.UTF-8 LC_NUMERIC=C [3] LC_TIME=zh_CN.UTF-8 LC_COLLATE=zh_CN.UTF-8 [5] LC_MONETARY=zh_CN.UTF-8 LC_MESSAGES=zh_CN.UTF-8 [7] LC_PAPER=zh_CN.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached): [1] compiler_4.0.1

Best wishes, Crane

在 2020-12-05 00:53:59，"Nicholas Knoblauch" notifications@github.com 写道：

Please also post the output of the shell command R CMD config --all

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CreRecombinase commented 3 years ago

My best guess is that there's something missing from your conda environment, which isn't allowing you to build packages from source. Can you verify that you are able to install any packages from source? What happens if you try, for example, devtools::install_github("dangerzig/tipitaka")? Could you also try removing the conda environment and reinstalling it?

whecrane commented 3 years ago

Thank you for your help. I used another conda environment and it worked. You are so nice, thanks!

王鹤

邮箱：whe930102@163.com | On 12/05/2020 05:17, Nicholas Knoblauch wrote:

My best guess is that there's something missing from your conda environment, which isn't allowing you to build packages from source. Can you verify that you are able to install any packages from source? What happens if you try, for example, devtools::install_github("dangerzig/tipitaka")? Could you also try removing the conda environment and reinstalling it?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.