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October 15, 2019 05:14
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classInt installation error
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[docker@a715cb8d440c /]$ R | |
> install.packages("classInt") | |
trying URL 'https://cran.cnr.berkeley.edu/src/contrib/e1071_1.7-2.tar.gz' | |
Content type 'application/x-gzip' length 583003 bytes (569 KB) | |
================================================== | |
downloaded 569 KB | |
trying URL 'https://cran.cnr.berkeley.edu/src/contrib/classInt_0.4-1.tar.gz' | |
Content type 'application/x-gzip' length 19048 bytes (18 KB) | |
================================================== | |
downloaded 18 KB | |
* installing *source* package ‘e1071’ ... | |
** package ‘e1071’ successfully unpacked and MD5 sums checked | |
* installing *source* package ‘e1071’ ... [0/11770] | |
** package ‘e1071’ successfully unpacked and MD5 sums checked | |
** using staged installation | |
checking for C++ compiler default output file name... a.out | |
checking whether the C++ compiler works... yes | |
checking whether we are cross compiling... no | |
checking for suffix of executables... | |
checking for suffix of object files... o | |
checking whether we are using the GNU C++ compiler... yes | |
checking whether g++ -std=gnu++11 accepts -g... yes | |
** libs | |
gcc -I"/usr/include/R/" -DNDEBUG -D_FORTIFY_SOURCE=2 -fpic -m64 -I/opt/intel/compilers_and_libraries_2019.4.243/linux/mkl/include -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -c Rsvm.c -o Rsvm.o | |
gcc -I"/usr/include/R/" -DNDEBUG -D_FORTIFY_SOURCE=2 -fpic -m64 -I/opt/intel/compilers_and_libraries_2019.4.243/linux/mkl/include -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -c cmeans.c -o cmeans.o | |
gcc -I"/usr/include/R/" -DNDEBUG -D_FORTIFY_SOURCE=2 -fpic -m64 -I/opt/intel/compilers_and_libraries_2019.4.243/linux/mkl/include -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -c cshell.c -o cshell.o | |
gcc -I"/usr/include/R/" -DNDEBUG -D_FORTIFY_SOURCE=2 -fpic -m64 -I/opt/intel/compilers_and_libraries_2019.4.243/linux/mkl/include -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -c floyd.c -o floyd.o | |
gcc -I"/usr/include/R/" -DNDEBUG -D_FORTIFY_SOURCE=2 -fpic -m64 -I/opt/intel/compilers_and_libraries_2019.4.243/linux/mkl/include -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -c init.c -o init.o | |
g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG -D_FORTIFY_SOURCE=2 -fpic -m64 -I/opt/intel/compilers_and_libraries_2019.4.243/linux/mkl/include -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -c svm.cpp -o svm.o | |
g++ -std=gnu++11 -shared -L/usr/lib64/R/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o e1071.so Rsvm.o cmeans.o cshell.o floyd.o init.o svm.o -L/usr/lib64/R/lib -lR | |
installing to /home/docker/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-e1071/00new/e1071/libs | |
** R | |
** inst | |
** byte-compile and prepare package for lazy loading | |
** help | |
*** installing help indices | |
** building package indices | |
** installing vignettes | |
** testing if installed package can be loaded from temporary location | |
** checking absolute paths in shared objects and dynamic libraries | |
** testing if installed package can be loaded from final location | |
** testing if installed package keeps a record of temporary installation path | |
* DONE (e1071) | |
* installing *source* package ‘classInt’ ... | |
** package ‘classInt’ successfully unpacked and MD5 sums checked | |
** using staged installation | |
** libs | |
gfortran -fno-optimize-sibling-calls -fpic -m64 -I/opt/intel/compilers_and_libraries_2019.4.243/linux/mkl/include -c fish1.f -o fish1.o | |
f951: Warning: Nonexistent include directory ‘/opt/intel/compilers_and_libraries_2019.4.243/linux/mkl/include’ [-Wmissing-include-dirs] | |
fish1.f:100:72: | |
100 | DO 10 I=1,M | |
| 1 | |
Warning: Fortran 2018 deleted feature: Shared DO termination label 10 at (1) | |
fish1.f:132:72: | |
132 | 40 IWORK(I,1)=1 | |
| 1 | |
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 40 at (1) | |
gcc -I"/usr/include/R/" -DNDEBUG -D_FORTIFY_SOURCE=2 -fpic -m64 -I/opt/intel/compilers_and_libraries_2019.4.243/linux/mkl/include -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -c init.c -o init.o | |
gcc -shared -L/usr/lib64/R/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o classInt.so fish1.o init.o -lgfortran -limf -lm -lquadmath -L/usr/lib64/R/lib -lR | |
/usr/sbin/ld: cannot find -limf | |
collect2: error: ld returned 1 exit status | |
make: *** [/usr/share/R//make/shlib.mk:6: classInt.so] Error 1 | |
ERROR: compilation failed for package ‘classInt’ | |
* removing ‘/home/docker/R/x86_64-pc-linux-gnu-library/3.6/classInt’ | |
The downloaded source packages are in | |
‘/tmp/RtmpaL1yoI/downloaded_packages’ | |
Warning message: | |
In install.packages("classInt") : | |
installation of package ‘classInt’ had non-zero exit status | |
> sessionInfo() | |
R version 3.6.1 (2019-07-05) | |
Platform: x86_64-pc-linux-gnu (64-bit) | |
Running under: Arch Linux | |
Matrix products: default | |
BLAS/LAPACK: /opt/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64_lin/libmkl_gf_lp64.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=en_US.UTF-8 | |
[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 | |
[docker@a715cb8d440c /]$ cd /opt/intel/lib | |
[docker@a715cb8d440c lib]$ ls -la | |
total 112468 | |
drwxr-xr-x 3 root root 4096 Oct 14 21:44 . | |
drwxr-xr-x 3 root root 4096 Oct 14 21:44 .. | |
-rwxr-xr-x 1 root root 1656 Sep 18 09:11 init.o | |
-rwxr-xr-x 1 root root 206796 Sep 18 09:11 libbfp754.a | |
-rwxr-xr-x 1 root root 35064 Sep 18 09:11 libchkp.so | |
-rwxr-xr-x 1 root root 117792 Sep 18 09:11 libchkpwrap.a | |
-rwxr-xr-x 1 root root 64170 Sep 18 09:11 libchkpwrap_h.a | |
-rwxr-xr-x 1 root root 45508 Sep 18 09:11 libchkpwrap_h_w.a | |
-rwxr-xr-x 1 root root 85818 Sep 18 09:11 libchkpwrap_w.a | |
-rwxr-xr-x 1 root root 24 Sep 18 09:11 libcilkrts.so | |
-rwxr-xr-x 1 root root 244784 Sep 18 09:11 libcilkrts.so.5 | |
-rwxr-xr-x 1 root root 4961742 Sep 18 09:11 libdecimal.a | |
-rwxr-xr-x 1 root root 8476308 Sep 18 09:11 libimf.a | |
-rwxr-xr-x 1 root root 4738096 Sep 18 09:11 libimf.so | |
-rwxr-xr-x 1 root root 22 Sep 18 09:11 libintlc.so | |
-rwxr-xr-x 1 root root 459024 Sep 18 09:11 libintlc.so.5 | |
-rwxr-xr-x 1 root root 197734 Sep 18 09:11 libipgo.a | |
-rwxr-xr-x 1 root root 761134 Sep 18 09:11 libirc.a | |
-rwxr-xr-x 1 root root 7968 Sep 18 09:11 libirc_s.a | |
-rwxr-xr-x 1 root root 458864 Sep 18 09:11 libirc.so | |
-rwxr-xr-x 1 root root 2809658 Sep 18 09:11 libirng.a | |
-rwxr-xr-x 1 root root 1487600 Sep 18 09:11 libirng.so | |
-rwxr-xr-x 1 root root 9446158 Sep 18 09:11 libmatmul.a | |
-rwxr-xr-x 1 root root 102472 Sep 18 09:11 libmpx.so | |
-rwxr-xr-x 1 root root 216858 Sep 18 09:11 libpdbx.a | |
-rwxr-xr-x 1 root root 17456 Sep 18 09:11 libpdbxinst.a | |
-rwxr-xr-x 1 root root 22 Sep 18 09:11 libpdbx.so | |
-rwxr-xr-x 1 root root 129064 Sep 18 09:11 libpdbx.so.5 | |
-rwxr-xr-x 1 root root 112672 Sep 18 09:11 libqkmalloc.so | |
-rwxr-xr-x 1 root root 54168358 Sep 18 09:11 libsvml.a | |
-rwxr-xr-x 1 root root 25737072 Sep 18 09:11 libsvml.so | |
drwxr-xr-x 3 root root 4096 Oct 14 21:44 locale |
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