Closed hzongyao closed 3 years ago
jgabry
commented
4 years ago I'm not sure what's going on here. @bgoodri any ideas? Looks like R 3.6 with Debian.
@hzongyao You could also try asking on the Stan forums (https://discourse.mc-stan.org/) where you'll get more eyes on your question.
bgoodri
commented
4 years ago We need to see more of the error message, specifically the part that starts with "error:".
On Mon, Oct 12, 2020 at 2:44 PM Jonah Gabry notifications@github.com wrote:
I'm not sure what's going on here. @bgoodri https://github.com/bgoodri any ideas? Looks like R 3.6 with Debian.
@hzongyao https://github.com/hzongyao You could also try asking on the Stan forums (https://discourse.mc-stan.org/) where you'll get more eyes on your question.
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bgoodri
commented
4 years ago Your ~/.Rprofile file seems to be printing out the mirrors that R would use, which messes everything up. Either delete that or start R with the --vanilla option.
On Tue, Oct 13, 2020 at 8:27 AM zi纵笑yao notifications@github.com wrote:
Using library: /mnt/raid/huangzongyao/lib/Rlib/R36 Using temp directory: /mnt/raid/huangzongyao/tmp/Rtmp g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -DSTAN_THREADS NULL CRAN "https://mirrors.tuna.tsinghua.edu.cn/CRAN/" [1] "https://mirrors.tuna.tsinghua.edu.cn/bioconductor" -I"/mnt/raid/huangzongyao/lib/Rlib/R36/Rcpp/include" -I"/mnt/raid/huangzongyao/lib/Rlib/R36/RcppEigen/include" -I"/mnt/raid/huangzongyao/lib/Rlib/R36/BH/include" -I"/mnt/raid/huangzongyao/lib/Rlib/R36/StanHeaders/include" -I"/mnt/raid/huangzongyao/lib/Rlib/R36/RcppParallel/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-V28x5H/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c chains.cpp -o chains.o g++: error: NULL: No such file or directory g++: error: CRAN: No such file or directory g++: error: https://mirrors.tuna.tsinghua.edu.cn/CRAN/: No such file or directory g++: error: [1]: No such file or directory g++: error: https://mirrors.tuna.tsinghua.edu.cn/bioconductor: No such file or directory /usr/lib/R/etc/Makeconf:177: recipe for target 'chains.o' failed make: *** [chains.o] Error 1 ERROR: compilation failed for package ‘rstan’
- removing ‘/mnt/raid/huangzongyao/lib/Rlib/R36/rstan’
The downloaded source packages are in ‘/mnt/raid/huangzongyao/tmp/Rtmp/RtmpyOec3m/downloaded_packages’ Warning message: In install.packages("rstan") : installation of package ‘rstan’ had non-zero exit status
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jgabry
commented
3 years ago Going to close this but @hzongyao if this is still unresolved we can reopen
Summary:
Please provide a short summary (no more than a sentence or two). /usr/local/lib/R/etc/Makeconf:176: recipe for target 'chains.o' failed make: *** [chains.o] Error 1 ERROR: compilation failed for package ‘rstan’
Description:
Describe the issue as clearly as possible.
Reproducible Steps:
Please report steps to reproduce the issue. If it's not possible to reproduce, please include a description of how you discovered the issue.
If you have a reproducible example, please include it.
Current Output:
If applicable, any relevant output from RStan. /usr/local/lib/R/etc/Makeconf:176: recipe for target 'chains.o' failed make: *** [chains.o] Error 1 ERROR: compilation failed for package ‘rstan’
Expected Output:
If applicable, the output you expected from RStan.
RStan Version:
The version of RStan you are running (e.g., from
packageVersion("rstan")) 3.6R Version:
The version of R you are running (e.g., from
R.version.string)Operating System:
Your operating system (e.g., OS X 10.11.3)
Matrix products: default BLAS/LAPACK: /usr/lib/libopenblasp-r0.2.19.so
locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=C
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.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_3.6.1 tools_3.6.1