I wanted to install stringi and RcppDist package at first.install.packages("stringi")
But I get some problems with C++ compiler, it doesn't work properly although I've searched for almost every solutions I can find online.
Installing package into '/data/gongyixi/R/x86_64-conda-linux-gnu-library/4.0'
(as 'lib' is unspecified)
URL’https://cran.rstudio.com/src/contrib/stringi_1.8.3.tar.gz'
Content type 'application/x-gzip' length 11917752 bytes (11.4 MB)
==================================================
downloaded 11.4 MB
* installing *source* package ‘stringi’ ...
** successfully ‘stringi’ MD5 checked
** using staged installation
checking for R_HOME... /public/home/maintain/miniconda3/lib/R
checking for R... /public/home/maintain/miniconda3/lib/R/bin/R
checking for endianness... little
checking for cat... /usr/bin/cat
checking whether the C++ compiler works... no
configure: error: in `/tmp/RtmpPkzeqM/R.INSTALL3fa654dfb9ee6/stringi':
configure: error: C++ compiler cannot create executables
See `config.log' for more details
ERROR: configuration failed for package ‘stringi’
* removing ‘/data/gongyixi/R/x86_64-conda-linux-gnu-library/4.0/stringi’
Warning in install.packages :
installation of package 'stringi' had non-zero exit status
The downloaded source packages are in
'/tmp/Rtmpmip14o/downloaded_packages'
I checked the config.log to see what's wrong.
## ----------- ##
## Core tests. ##
## ----------- ##
configure:2395: checking for R_HOME
configure:2406: result: /public/home/maintain/miniconda3/lib/R
configure:2412: checking for R
configure:2422: result: /public/home/maintain/miniconda3/lib/R/bin/R
configure:2426: checking for endianness
configure:2435: result: little
configure:2446: checking for cat
configure:2469: found /usr/bin/cat
configure:2481: result: /usr/bin/cat
configure:2677: checking for C++ compiler version
configure:2686: x86_64-conda-linux-gnu-c++ -std=gnu++11 --version >&5
x86_64-conda-linux-gnu-c++ (conda-forge gcc 9.4.0-16) 9.4.0
Copyright (C) 2019 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
configure:2697: $? = 0
configure:2686: x86_64-conda-linux-gnu-c++ -std=gnu++11 -v >&5
Reading specs from /public/home/maintain/miniconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.4.0/specs
could not find specs file conda.specs
COLLECT_GCC=x86_64-conda-linux-gnu-c++
COLLECT_LTO_WRAPPER=/public/home/maintain/miniconda3/bin/../libexec/gcc/x86_64-conda-linux-gnu/9.4.0/lto-wrapper
Target: x86_64-conda-linux-gnu
Configured with: ../configure --prefix=/home/conda/feedstock_root/build_artifacts/gcc_compilers_1650668900000/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho --with-slibdir=/home/conda/feedstock_root/build_artifacts/gcc_compilers_1650668900000/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib --libdir=/home/conda/feedstock_root/build_artifacts/gcc_compilers_1650668900000/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib --mandir=/home/conda/feedstock_root/build_artifacts/gcc_compilers_1650668900000/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/man --build=x86_64-conda-linux-gnu --host=x86_64-conda-linux-gnu --target=x86_64-conda-linux-gnu --enable-default-pie --enable-languages=c,c++,fortran,objc,obj-c++ --enable-__cxa_atexit --disable-libmudflap --enable-libgomp --disable-libssp --enable-libquadmath --enable-libquadmath-support --enable-libsanitizer --enable-lto --enable-threads=posix --enable-target-optspace --enable-plugin --enable-gold --disable-nls --disable-bootstrap --disable-multilib --enable-long-long --with-sysroot=/home/conda/feedstock_root/build_artifacts/gcc_compilers_1650668900000/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/x86_64-conda-linux-gnu/sysroot --with-build-sysroot=/home/conda/feedstock_root/build_artifacts/gcc_compilers_1650668900000/_build_env/x86_64-conda-linux-gnu/sysroot --with-gxx-include-dir=/home/conda/feedstock_root/build_artifacts/gcc_compilers_1650668900000/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/x86_64-conda-linux-gnu/include/c++/9.4.0 --with-pkgversion='conda-forge gcc 9.4.0-16' --with-bugurl=https://github.com/conda-forge/ctng-compilers-feedstock/issues/new/choose
Thread model: posix
gcc version 9.4.0 (conda-forge gcc 9.4.0-16)
configure:2697: $? = 0
configure:2686: x86_64-conda-linux-gnu-c++ -std=gnu++11 -V >&5
x86_64-conda-linux-gnu-c++: error: unrecognized command line option '-V'
x86_64-conda-linux-gnu-c++: fatal error: no input files
compilation terminated.
configure:2697: $? = 1
configure:2686: x86_64-conda-linux-gnu-c++ -std=gnu++11 -qversion >&5
x86_64-conda-linux-gnu-c++: error: unrecognized command line option '-qversion'; did you mean '--version'?
x86_64-conda-linux-gnu-c++: fatal error: no input files
compilation terminated.
configure:2697: $? = 1
configure:2717: checking whether the C++ compiler works
configure:2739: x86_64-conda-linux-gnu-c++ -std=gnu++11 ...
collect2: error: ld returned 1 exit status
configure:2743: $? = 1
configure:2783: result: no
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "stringi"
| #define PACKAGE_TARNAME "stringi"
| #define PACKAGE_VERSION "1.8"
| #define PACKAGE_STRING "stringi 1.8"
| #define PACKAGE_BUGREPORT "https://stringi.gagolewski.com/"
| #define PACKAGE_URL ""
| /* end confdefs.h. */
|
| int
| main (void)
| {
|
| ;
| return 0;
| }
configure:2788: error: in `/tmp/Rtmpmip14o/downloaded_packages/stringi':
configure:2790: error: C++ compiler cannot create executables
See `config.log' for more details
I notice that there're error related with 'gcc -V' 'gcc -qversion',but I still don't know how to solve it.
What's more, the gcc compiler works fine when I do compilation manually. Here's my sessioninfo:
R version 4.0.5 (2021-03-31)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /public/home/maintain/miniconda3/lib/libopenblasp-r0.3.20.so
locale:
[1] LC_CTYPE=zh_CN.UTF-8 LC_NUMERIC=C LC_TIME=zh_CN.UTF-8
[4] LC_COLLATE=zh_CN.UTF-8 LC_MONETARY=zh_CN.UTF-8 LC_MESSAGES=zh_CN.UTF-8
[7] LC_PAPER=zh_CN.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] RcppDist_0.1.1.9000
loaded via a namespace (and not attached):
[1] Rcpp_1.0.12 compiler_4.0.5 later_1.3.2 BiocManager_1.30.18
[5] urlchecker_1.0.1 prettyunits_1.1.1 profvis_0.3.8 remotes_2.5.0
[9] tools_4.0.5 digest_0.6.35 pkgbuild_1.3.1 pkgload_1.3.4
[13] memoise_2.0.1 lifecycle_1.0.4 rlang_1.1.3 shiny_1.7.1
[17] cli_3.6.2 rstudioapi_0.13 curl_5.2.1 fastmap_1.1.1
[21] withr_3.0.0 stringr_1.5.1 fs_1.6.3 htmlwidgets_1.6.4
[25] vctrs_0.6.5 devtools_2.4.5 rprojroot_2.0.3 glue_1.7.0
[29] R6_2.5.1 processx_3.8.3 sessioninfo_1.2.2 callr_3.7.5
[33] purrr_1.0.2 magrittr_2.0.3 ps_1.7.6 promises_1.3.0
[37] ellipsis_0.3.2 htmltools_0.5.8.1 usethis_2.1.6 mime_0.12
[41] xtable_1.8-4 httpuv_1.6.15 stringi_1.7.6 miniUI_0.1.1.1
[45] cachem_1.0.8 crayon_1.5.2
My gcc version:gcc version 9.3.0 (GCC)
If you manage your R environment by anaconda, try conda install conda-forge::gcc_linux-64 before installing stringi.