ChemmineOB.cpp:1569:10: fatal error: openbabel/obutil.h: No such file or directory
1569 | #include <openbabel/obutil.h>
| ^~~~~~~~~~~~~~~~~~~~
compilation terminated.
make: *** [/usr/lib/R/etc/Makeconf:177: ChemmineOB.o] Error 1
ERROR: compilation failed for package ‘ChemmineOB’
* removing ‘/home/mamata/R/x86_64-pc-linux-gnu-library/4.2/ChemmineOB’
The downloaded source packages are in
‘/tmp/Rtmpzscekt/downloaded_packages’
Warning message:
In install.packages(...) :
installation of package ‘ChemmineOB’ had non-zero exit status
i am trying to install ChemmineOB and I get the this error. I have openbabel installed in the system already. Can anyone help?
Related
I'm using RStudio on Ubuntu 18 and I'm trying to install the htslib package from the Bioconductor repo, but I'm stuck now.
This is what I get:
* installing *source* package ‘Rhtslib’ ...
** using non-staged installation via StagedInstall field
** libs
cd "htslib-1.7" && make -f "/usr/lib/R/etc/Makeconf" -f "Makefile.Rhtslib"
make[1]: Entering directory '/tmp/RtmpbL8Yil/R.INSTALL1664f5019f4/Rhtslib/src/htslib-1.7'
Makefile.Rhtslib:128: warning: overriding recipe for target '.c.o'
/usr/lib/R/etc/Makeconf:168: warning: ignoring old recipe for target '.c.o'
...
cram/cram_io.c:61:10: fatal error: lzma.h: No such file or directory
#include <lzma.h>
^~~~~~~~
compilation terminated.
Makefile.Rhtslib:128: recipe for target 'cram/cram_io.o' failed
make[1]: Leaving directory '/tmp/RtmpbL8Yil/R.INSTALL1664f5019f4/Rhtslib/src/htslib-1.7'
Makevars.common:24: recipe for target 'htslib' failed
make[1]: *** [cram/cram_io.o] Error 1
make: *** [htslib] Error 2
ERROR: compilation failed for package ‘Rhtslib’
* removing ‘/home/thiago/R/x86_64-pc-linux-gnu-library/4.1/Rhtslib’
The downloaded source packages are in
‘/tmp/RtmpL0DYph/downloaded_packages’
Installation paths not writeable, unable to update packages
path: /usr/lib/R/library
packages:
spatial
Warning message:
In .inet_warning(msg) :
installation of package ‘Rhtslib’ had non-zero exit status
What can I do in order to properly install the package?
I am trying to install rJava, as it's a dependency of OpenStreetMap (I want to create some maps).
However, when trying to install, I get the following error:
/usr/bin/ld: cannot find -lpcre2-8
collect2: error: ld returned 1 exit status
make[2]: Leaving directory '/tmp/RtmplfpzAZ/R.INSTALL2958202af052/rJava/jri/src'
make[2]: *** [Makefile.all:35: libjri.so] Error 1
make[1]: Leaving directory '/tmp/RtmplfpzAZ/R.INSTALL2958202af052/rJava/jri'
make[1]: *** [Makefile.all:19: src/JRI.jar] Error 2
make: *** [Makevars:14: jri] Error 2
ERROR: compilation failed for package ‘rJava’
* removing ‘/home/maanan/R/x86_64-pc-linux-gnu-library/4.0/rJava’
Warning in install.packages :
installation of package ‘rJava’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpRkgFko/downloaded_packages’
Could someone please tell me what I did wrong? I have JDK and JRE installed.
Thanks.
apt install libpcre2-8-0 libpcre2-dev
That will (should) get you past the error at the very top. Of course I don't know what else you might be missing. Please google future errors you may get ...
I am installing lme4 in R, but the mentioned problem occurred. I saw answers for Linux and Ubuntu. I am running on Windows, and I receive a fatal error message as shown. Can someone help, pls?
compilation terminated.
make: *** [C:/PROGRA~1/R/R-36~1.1/etc/i386/Makeconf:208: init_nloptr.o] Error 1
ERROR: compilation failed for package 'nloptr'
* removing 'C:/Users/Admin/Documents/R/win-library/3.6/nloptr'
Warning in install.packages :
installation of package ‘C:/Users/Admin/Desktop/MARK'S~1/SURP/Thesis/Software/R/Packages/nloptr_1.2.1.tar.gz’ had non-zero exit status
I'm currently unable to install the ez package in R studio 1.1.456 on macbook. Here is what I am getting:
/bin/sh: x86_64-apple-darwin13.4.0-clang: command not found
make: *** [init.o] Error 127
ERROR: compilation failed for package 'zip'
* removing '/anaconda3/lib/R/library/zip'
Warning in install.packages :
installation of package 'zip' had non-zero exit status
ERROR: compilation failed for package 'SparseM'
* removing '/anaconda3/lib/R/library/SparseM'
Warning in install.packages :
installation of package 'SparseM' had non-zero exit status
Warning in install.packages :
installation of package 'ez' had non-zero exit status
When trying to install the pcalg package, I am getting the following error:
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [pcalg.so] Error 1
ERROR: compilation failed for package ‘pcalg’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/pcalg’
The downloaded source packages are in
‘/private/var/folders/54/nwpr9hkn49b1m4h3hjmwph6r0000gn/T/RtmpREqD5T/downloaded_packages’
Warning message:
In install.packages("pcalg") :
installation of package ‘pcalg’ had non-zero exit status
I'm assuming this is because the gfortan package now in gcc, but I don't know how to point it to the right place. Does anybody know how to fix this?