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Error with package loading

Open AntKirill opened this issue 6 years ago • 2 comments

Hi, I was trying to install the Hexbin but came across this error. It is compiled successfully, but unable to be loaded. Is there any way to overcome this?

> install.packages('hexbin')
Installing package into ‘/home/kirant/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/hexbin_1.27.2.tar.gz'
Content type 'application/x-gzip' length 491560 bytes (480 KB)
==================================================
downloaded 480 KB

* installing *source* package ‘hexbin’ ...
** package ‘hexbin’ successfully unpacked and MD5 sums checked
** libs
gfortran   -fpic  -g -O2 -fstack-protector-strong  -c hbin.f -o hbin.o
gfortran   -fpic  -g -O2 -fstack-protector-strong  -c hcell.f -o hcell.o
gfortran   -fpic  -g -O2 -fstack-protector-strong  -c herode.f -o herode.o
gfortran   -fpic  -g -O2 -fstack-protector-strong  -c hsm.f -o hsm.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c reg.c -o reg.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o hexbin.so hbin.o hcell.o herode.o hsm.o reg.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
installing to /home/kirant/R/x86_64-pc-linux-gnu-library/3.4/hexbin/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error: package or namespace load failed for ‘hexbin’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/kirant/R/x86_64-pc-linux-gnu-library/3.4/hexbin/libs/hexbin.so':
  libgfortran.so.4: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/kirant/R/x86_64-pc-linux-gnu-library/3.4/hexbin’

The downloaded source packages are in
	‘/tmp/Rtmp2whtdX/downloaded_packages’
Warning message:
In install.packages("hexbin") :
  installation of package ‘hexbin’ had non-zero exit status

My sessionInfo() is:

> sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.6 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=ru_RU.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=ru_RU.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=ru_RU.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=ru_RU.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_3.4.4 tools_3.4.4   

AntKirill avatar Mar 19 '19 06:03 AntKirill

See #8.

edzer avatar Apr 28 '19 17:04 edzer

I solved this by installing gcc-fortran on Manjaro. Error was similar:

gfortran -fno-optimize-sibling-calls  -fpic  -g -O2  -c hbin.f -o hbin.o
make: gfortran: No such file or directory
make: *** [/usr/lib64/R/etc/Makeconf:191: hbin.o] Error 127
ERROR: compilation failed for package ‘hexbin’
* removing ‘/home/mundo/R/x86_64-pc-linux-gnu-library/3.6/hexbin’

this might be the answer for ubuntu 16.06 https://stackoverflow.com/questions/46516394/how-to-install-libgfortran-so-4-on-ubuntu-16-06/46516499

heyeddi avatar Mar 14 '20 04:03 heyeddi