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Created October 15, 2019 05:14
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classInt installation error
[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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