I am trying to install nagios on nginx.
I have done with Nagios core without any errors but when am trying to install plugins I am having errors
I am using "make" to do it & getting the below error:
libtool: link: gcc -DNP_VERSION=\"2.1.1\" -g -O2 -o check_dummy check_dummy.o -L. libnpcommon.a ../lib/libnagiosplug.a ../gl/libgnu.a -lpthread -ldl
gcc -DLOCALEDIR=\"/usr/local/nagios/share/locale\" -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib -I../gl -I../intl -I/usr/include -DNP_VERSION='"2.1.1"' -g -O2 -MT check_http.o -MD -MP -MF .deps/check_http.Tpo -c -o check_http.o check_http.c
mv -f .deps/check_http.Tpo .deps/check_http.Po
/bin/bash ../libtool --tag=CC --mode=link gcc -DNP_VERSION='"2.1.1"' -g -O2 -L. -o check_http check_http.o libnpcommon.a ../lib/libnagiosplug.a ../gl/libgnu.a libnpcommon.a ../lib/libnagiosplug.a ../gl/libgnu.a -lnsl -lresolv -lssl -lcrypto -lpthread -ldl
libtool: link: gcc -DNP_VERSION=\"2.1.1\" -g -O2 -o check_http check_http.o -L. libnpcommon.a ../lib/libnagiosplug.a ../gl/libgnu.a -lnsl -lresolv -lssl -lcrypto -lpthread -ldl
libnpcommon.a(sslutils.o): In function `np_net_ssl_init_with_hostname_version_and_cert':
/usr/local/src/nagios-plugins-2.1.1/plugins/sslutils.c:73: undefined reference to `SSLv3_client_method'
collect2: error: ld returned 1 exit status
make[2]: *** [check_http] Error 1
make[2]: Leaving directory `/usr/local/src/nagios-plugins-2.1.1/plugins'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/usr/local/src/nagios-plugins-2.1.1'
make: *** [all] Error 2
So can anyone tell why am getting this error?
This link is slove your problem
https://support.nagios.com/forum/viewtopic.php?f=35&t=36601&p=168235&hilit=SSLv3#p168235
Close your TOPIC
Related
For some odd reason, the latest version of Microsoft R Open is failing to compile various packages, because of something (Rcpp I think) that spawns multiple R sessions, and the repeated calls to clear the terminal window are introducing line breaks in the middle of the compiler commands. See below. There doesn't seem to be a reliable way to completely suppress the verbose startup message, which appears to be causing this error.
Note the same happens with /opt/microsoft/ropen/4.0.2/lib64/R/bin/R CMD INSTALL as well as /opt/microsoft/ropen/4.0.2/lib64/R/bin/Rscript
Ideas? Suggestions?
$ /opt/microsoft/ropen/4.0.2/lib64/R/bin/R -q
> install.packages('minqa')
Installing package into ‘/raid/users/g-socsldap/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 53548 100 53548 0 0 247k 0 --:--:-- --:--:-- --:--:-- 247k
Microsoft R Open 4.0.2
The enhanced R distribution from Microsoft
Microsoft packages Copyright (C) 2020 Microsoft Corporation
Using the Intel MKL for parallel mathematical computing (using 44 cores).
Default CRAN mirror snapshot taken on 2020-07-16.
See: https://mran.microsoft.com/.
* installing *source* package ‘minqa’ ...
** package ‘minqa’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gfortran -fpic -g -O2 -c altmov.f -o altmov.o
gfortran -fpic -g -O2 -c bigden.f -o bigden.o
gfortran -fpic -g -O2 -c biglag.f -o biglag.o
gfortran -fpic -g -O2 -c bobyqa.f -o bobyqa.o
gfortran -fpic -g -O2 -c bobyqb.f -o bobyqb.o
gfortran -fpic -g -O2 -c lagmax.f -o lagmax.o
g++ -I/opt/microsoft/ropen/4.0.2/lib64/R/include -DNDEBUG -I'/opt/microsoft/ropen/4.0.2/lib64/R/library/Rcpp/include' -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -O2 -g -c minqa.cpp -o minqa.o
gfortran -fpic -g -O2 -c newuoa.f -o newuoa.o
gfortran -fpic -g -O2 -c newuob.f -o newuob.o
gfortran -fpic -g -O2 -c prelim.f -o prelim.o
gfortran -fpic -g -O2 -c rescue.f -o rescue.o
gfortran -fpic -g -O2 -c trsapp.f -o trsapp.o
gfortran -fpic -g -O2 -c trsbox.f -o trsbox.o
gfortran -fpic -g -O2 -c trstep.f -o trstep.o
gfortran -fpic -g -O2 -c uobyqa.f -o uobyqa.o
gfortran -fpic -g -O2 -c uobyqb.f -o uobyqb.o
gfortran -fpic -g -O2 -c update.f -o update.o
gfortran -fpic -g -O2 -c updatebobyqa.f -o updatebobyqa.o
g++ -shared -L/opt/microsoft/ropen/4.0.2/lib64/R/lib -o minqa.so altmov.o bigden.o biglag.o bobyqa.o bobyqb.o lagmax.o minqa.o newuoa.o newuob.o prelim.o rescue.o trsapp.o trsbox.o trstep.o uobyqa.o uobyqb.o update.o updatebobyqa.o Microsoft R Open 4.0.2 The enhanced R distribution from Microsoft Microsoft packages Copyright (C) 2020 Microsoft Corporation Using the Intel MKL for parallel mathematical computing (using 44 cores). Default CRAN mirror snapshot taken on 2020-07-16. See: https://mran.microsoft.com/. -lgfortran -lm -L/opt/microsoft/ropen/4.0.2/lib64/R/lib -lR
g++: error: Microsoft: No such file or directory
g++: error: R: No such file or directory
g++: error: Open: No such file or directory
g++: error: 4.0.2: No such file or directory
g++: error: The: No such file or directory
g++: error: enhanced: No such file or directory
g++: error: R: No such file or directory
g++: error: distribution: No such file or directory
g++: error: from: No such file or directory
g++: error: Microsoft: No such file or directory
g++: error: Microsoft: No such file or directory
g++: error: packages: No such file or directory
g++: error: Copyright: No such file or directory
g++: error: (C): No such file or directory
g++: error: 2020: No such file or directory
g++: error: Microsoft: No such file or directory
g++: error: Corporation: No such file or directory
g++: error: Using: No such file or directory
g++: error: the: No such file or directory
g++: error: Intel: No such file or directory
g++: error: MKL: No such file or directory
g++: error: for: No such file or directory
g++: error: parallel: No such file or directory
g++: error: mathematical: No such file or directory
g++: error: computing: No such file or directory
g++: error: (using: No such file or directory
g++: error: 44: No such file or directory
g++: error: cores).: No such file or directory
g++: error: Default: No such file or directory
g++: error: CRAN: No such file or directory
g++: error: mirror: No such file or directory
g++: error: snapshot: No such file or directory
g++: error: taken: No such file or directory
g++: error: on: No such file or directory
g++: error: 2020-07-16.: No such file or directory
g++: error: See:: No such file or directory
g++: error: https://mran.microsoft.com/.: No such file or directory
make: *** [/opt/microsoft/ropen/4.0.2/lib64/R/share/make/shlib.mk:6: minqa.so] Error 1
ERROR: compilation failed for package ‘minqa’
* removing ‘/raid/users/g-socsldap/R/x86_64-pc-linux-gnu-library/4.0/minqa’
The downloaded source packages are in
‘/tmp/RtmpMlXevk/downloaded_packages’
Warning message:
In install.packages("minqa") :
installation of package ‘minqa’ had non-zero exit status
I figured this problem with running R in --vanilla mode (this mode ignores .Rprofile.site located in /opt/microsoft/ropen/4.0.2/lib64/R/etc/Rprofile.site):
R --vanilla
install.packages("minqa")
// select any link you want
I've been attempting to install R-3.1.3 from source on
# cat /etc/*release*
NAME="Amazon Linux AMI"
VERSION="2015.09"
ID="amzn"
ID_LIKE="rhel fedora"
VERSION_ID="2015.09"
PRETTY_NAME="Amazon Linux AMI 2015.09"
ANSI_COLOR="0;33"
CPE_NAME="cpe:/o:amazon:linux:2015.09:ga"
HOME_URL="http://aws.amazon.com/amazon-linux-ami/"
Amazon Linux AMI release 2015.09
cpe:/o:amazon:linux:2015.09:ga
And after ./configure && make installation fails with the following error
gcc -std=gnu99 -shared -fopenmp -L/usr/local/lib64 -o libRlapack.so
dlamch.o dlapack.o cmplx.o -L../../../lib -lRblas -lgfortran -lm -lquadmath
/usr/bin/ld: /usr/lib/gcc/x86_64-amazon-linux/4.8.3/libgfortran.a(string_intrinsics.o): relocation R_X86_64_32S against `.bss.zero_length_string' can not be used when making a shared object; recompile with -fPIC
/usr/lib/gcc/x86_64-amazon-linux/4.8.3/libgfortran.a: could not read symbols: Bad value
collect2: error: ld returned 1 exit status
make[4]: *** [libRlapack.so] Error 1
Naturally I learn about -fPIC on how to recompile with -fPIC and R_X86_64_32S on What do R_X86_64_32S and R_X86_64_64 relocation mean?
I then make the change in the CFLAGS
# ./configure 'CFLAGS=-g -O2 -fPIC' --with-x=no --enable-shared
I know it worked because configure prints the values it set,
C compiler: gcc -std=gnu99 -g -O2 -fPIC
Fortran 77 compiler: gfortran -g -O2
Nevertheless same error occurs.
I've tested this on Centos65, and Centos71 and Ubuntu1404 all work, but my VPC won't, please help
I am able to use my existing versions of R and RStudio just fine, but I cannot seem to sync the version I have in /Applications with the Terminal in El Capitan, which means I cannot use ESS in emacs.
shermmac:~ brandonsherman$ brew install R
==> Installing r from homebrew/homebrew-science
==> Using Homebrew-provided fortran compiler.
This may be changed by setting the FC environment variable.
==> Downloading http://cran.rstudio.com/src/base/R-3/R-3.2.2.tar.gz
Already downloaded: /Library/Caches/Homebrew/r-3.2.2.tar.gz
==> Patching
patching file src/modules/lapack/vecLibg95c.c
==> ./configure --prefix=/usr/local/Cellar/r/3.2.2_1 --with-libintl-
==> make
Last 15 lines from /Users/brandonsherman/Library/Logs/Homebrew/r/02.make:
5: In as.POSIXlt.POSIXct(x, tz) : unknown timezone 'America/New_York'
clang -I../../../../include -DNDEBUG -I/usr/local/include -I/usr/local/include -I/usr/X11/include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -fPIC -g -O2 -c init.c -o init.o
clang -I../../../../include -DNDEBUG -I/usr/local/include -I/usr/local/include -I/usr/X11/include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -fPIC -g -O2 -c tcltk.c -o tcltk.o
clang -I../../../../include -DNDEBUG -I/usr/local/include -I/usr/local/include -I/usr/X11/include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -fPIC -g -O2 -c tcltk_unix.c -o tcltk_unix.o
making tcltk.d from tcltk.c
making init.d from init.c
making tcltk_unix.d from tcltk_unix.c
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L../../../../lib -L/usr/local/opt/gettext/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/openssl/lib -o tcltk.so init.o tcltk.o tcltk_unix.o -L/usr/local/lib -ltcl8.6 -L/usr/local/lib -ltk8.6 -L/usr/X11/lib -lX11 -Wl,-weak-lXss -lXext -L../../../../lib -lR -lintl -Wl,-framework -Wl,CoreFoundation
ld: library not found for -lX11
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[4]: *** [tcltk.so] Error 1
make[3]: *** [all] Error 1
make[2]: *** [R] Error 1
make[1]: *** [R] Error 1
make: *** [R] Error 1
READ THIS: https://git.io/brew-troubleshooting
If reporting this issue please do so at (not Homebrew/homebrew):
https://github.com/homebrew/homebrew-science/issues
Warning:
Note that there is nothing after Warning:.
I reinstalled Command Line Tools for 10.10 and rebooted. I then installed R 3.2.2 via Homebrew as in the original question. It gave me the following error regarding my gfortran compiler:
dyld: Library not loaded: /usr/local/lib/gcc/5/libgfortran.3.dylib
Referenced from: /usr/local/Cellar/r/3.2.2_1/R.framework/Versions/3.2/Resources/lib/libR.dylib
Reason: image not found
dyld: Library not loaded: /usr/local/lib/gcc/5/libgfortran.3.dylib
Referenced from: /usr/local/Cellar/r/3.2.2_1/R.framework/Versions/3.2/Resources/lib/libR.dylib
Reason: image not found
brew link gcc got rid of this error. R now works fine.
I'm trying to install the deldir package in R via install.packages("deldir",type = 'source') but am getting the following error message (this is OSX Mavericks):
* installing *source* package ‘deldir’ ...
** package ‘deldir’ successfully unpacked and MD5 sums checked
** libs
gfortran-4.8 -fPIC -g -O2 -c acchk.f -o acchk.o
make: gfortran-4.8: No such file or directory
make: *** [acchk.o] Error 1
ERROR: compilation failed for package ‘deldir’
gfortran 4.8 does seem to be available on my system, however:
> gfortran -v
Using built-in specs.
COLLECT_GCC=gfortran
COLLECT_LTO_WRAPPER=/usr/local/gfortran/libexec/gcc/x86_64-apple-darwin13/4.8.2/lto-wrapper
Target: x86_64-apple-darwin13
Configured with: ../gcc-4.8.2/configure --prefix=/usr/local/gfortran --with-gmp=/Users/fx/devel/gcc/deps-static/x86_64 --enable-languages=c,c++,fortran,objc,obj-c++ --build=x86_64-apple-darwin13
Thread model: posix
gcc version 4.8.2 (GCC)
After symlinking gfortran-4.8 to gfortran I get a bit further but fail nonetheless:
* installing *source* package ‘deldir’ ...
** package ‘deldir’ successfully unpacked and MD5 sums checked
** libs
gfortran-4.8 -fPIC -g -O2 -c acchk.f -o acchk.o
gfortran-4.8 -fPIC -g -O2 -c addpt.f -o addpt.o
gfortran-4.8 -fPIC -g -O2 -c adjchk.f -o adjchk.o
gfortran-4.8 -fPIC -g -O2 -c binsrt.f -o binsrt.o
gfortran-4.8 -fPIC -g -O2 -c circen.f -o circen.o
gfortran-4.8 -fPIC -g -O2 -c cross.f -o cross.o
gfortran-4.8 -fPIC -g -O2 -c delet.f -o delet.o
gfortran-4.8 -fPIC -g -O2 -c delet1.f -o delet1.o
gfortran-4.8 -fPIC -g -O2 -c delout.f -o delout.o
gfortran-4.8 -fPIC -g -O2 -c delseg.f -o delseg.o
gfortran-4.8 -fPIC -g -O2 -c dirout.f -o dirout.o
gfortran-4.8 -fPIC -g -O2 -c dirseg.f -o dirseg.o
gfortran-4.8 -fPIC -g -O2 -c dldins.f -o dldins.o
gfortran-4.8 -fPIC -g -O2 -c initad.f -o initad.o
gfortran-4.8 -fPIC -g -O2 -c insrt.f -o insrt.o
gfortran-4.8 -fPIC -g -O2 -c insrt1.f -o insrt1.o
gfortran-4.8 -fPIC -g -O2 -c intri.f -o intri.o
gfortran-4.8 -fPIC -g -O2 -c locn.f -o locn.o
gfortran-4.8 -fPIC -g -O2 -c master.f -o master.o
gfortran-4.8 -fPIC -g -O2 -c mnnd.f -o mnnd.o
gfortran-4.8 -fPIC -g -O2 -c pred.f -o pred.o
gfortran-4.8 -fPIC -g -O2 -c qtest.f -o qtest.o
gfortran-4.8 -fPIC -g -O2 -c qtest1.f -o qtest1.o
gfortran-4.8 -fPIC -g -O2 -c stoke.f -o stoke.o
gfortran-4.8 -fPIC -g -O2 -c succ.f -o succ.o
gfortran-4.8 -fPIC -g -O2 -c swap.f -o swap.o
gfortran-4.8 -fPIC -g -O2 -c testeq.f -o testeq.o
gfortran-4.8 -fPIC -g -O2 -c triar.f -o triar.o
gfortran-4.8 -fPIC -g -O2 -c trifnd.f -o trifnd.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o deldir.so acchk.o addpt.o adjchk.o binsrt.o circen.o cross.o delet.o delet1.o delout .o delseg.o dirout.o dirseg.o dldins.o initad.o insrt.o insrt1.o intri.o locn.o master.o mnnd.o pred.o qtest.o qtest1.o stoke.o succ.o swap.o testeq.o triar.o trifnd.o -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 - lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [deldir.so] Error 1
ERROR: compilation failed for package ‘deldir’
Note that /usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.3 exists, /usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 does not
sessionInfo():
> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-apple-darwin13.1.0 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
Sys.getenv():
> Sys.getenv()
__CF_USER_TEXT_ENCODING
"0x1F5:0:0"
__CHECKFIX1436934
"1"
Apple_PubSub_Socket_Render
"/tmp/launch-jCxLku/Render"
DISPLAY
":0"
DYLD_FALLBACK_LIBRARY_PATH
"/Users/<myusername>/lib:/usr/local/lib:/usr/lib::/Library/Frameworks/R.framework/Resources/lib"
EDITOR
"vi"
GIT_ASKPASS
"rpostback-askpass"
HOME
"/Users/<myusername>"
LANG
"en_US.UTF-8"
LC_CTYPE
"en_US.UTF-8"
LN_S
"ln -s"
LOGNAME
"<myusername>"
MAKE
"make"
PAGER
"/usr/bin/less"
PATH
"/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/texbin"
R_BROWSER
"/usr/bin/open"
R_BZIPCMD
"/usr/bin/bzip2"
R_DOC_DIR
"/Library/Frameworks/R.framework/Resources/doc"
R_GZIPCMD
"/usr/bin/gzip"
R_HOME
"/Library/Frameworks/R.framework/Resources"
R_INCLUDE_DIR
"/Library/Frameworks/R.framework/Resources/include"
R_LIBS_SITE
""
R_LIBS_USER
"~/Library/R/3.1/library"
R_PAPERSIZE
"a4"
R_PDFVIEWER
"/usr/bin/open"
R_PLATFORM
"x86_64-apple-darwin13.1.0"
R_PRINTCMD
"lpr"
R_QPDF
"/Library/Frameworks/R.framework/Resources/bin/qpdf"
R_RD4PDF
"times,inconsolata,hyper"
R_SESSION_TMPDIR
"/var/folders/jf/ds4sdyys44xckz_7f9zhrvsh0000gn/T//RtmpXaPpYF"
R_SHARE_DIR
"/Library/Frameworks/R.framework/Resources/share"
R_SYSTEM_ABI
"osx,gcc,gxx,gfortran,?"
R_TEXI2DVICMD
"/usr/bin/texi2dvi"
R_UNZIPCMD
"/usr/bin/unzip"
R_ZIPCMD
"/usr/bin/zip"
RS_RPOSTBACK_PATH
"/Applications/RStudio.app/Contents/MacOS/rpostback"
RS_SHARED_SECRET
<removed>
RSTUDIO
"1"
RSTUDIO_PANDOC
"/Applications/RStudio.app/Contents/MacOS/pandoc"
RSTUDIO_SESSION_PORT
"10153"
RSTUDIO_USER_IDENTITY
"<myusername>"
SED
"/usr/bin/sed"
SHELL
"/bin/bash"
SSH_AUTH_SOCK
"/tmp/launch-Shnu2H/Listeners"
TAR
"/usr/bin/tar"
TMPDIR
"/var/folders/jf/ds4sdyys44xckz_7f9zhrvsh0000gn/T/"
USER
"<myusername>"
I was getting the same error when installing the igraph package in R on Manjaro Linux.
It was due to the absence of a Fortran compiler (gfortran I think). I found out that gfortran package is named as gcc-fortran in Manjaro repo and many other (GNU) Linux repos. So, I just installed gcc-fortran package and then restarted RStudio and igraph package installed without any issues.
I found a solution here: https://support.rstudio.com/hc/communities/public/questions/201688563-Problem-with-Mac-Yosemite-Beta-and-RStudio-not-finding-TeX-distribution
It turns out that Adam Maxwell noted that Yosemite beta has a significant bug in passing environment variables to subprocesses.
After installing gfortran as in OS X package installation depends on gfortran-4.8 .
This works: create an alias in your .bash_profile
alias fixrs="launchctl setenv PATH /usr/texbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin"
Then close and open the terminal.
And execute the fixrs command in the terminal before launching RStudio.
Then I could build igraph successfully.
I was using a linux machine and RStudio server. I had a similar problem. I knew already that gfortran was on the machine thanks to the system administrator.
To solve, in the shell, I typed which gfortran, which gave me a path.
Then, following this SO posting, I entered the following in the shell to create a new Makevars file
# create a file called ~/.R/Makevars:
mkdir -p ~/.R
touch ~/.R/Makevars
Then, in that new file, I wrote the following
F77 = /usr/local/bin/gfortran #this was the path that I got from typing which gfortran in the shell
FC = $F77
FLIBS = -L/usr/local/bin/gfortran
From there, I was able to install the package that wasn't compiling properly (in my case vegan instead of igraph using install.packages("vegan")
I had your same problem (in OS X Yosemite), and (unfortunately) painstakingly recreated your symlink "partial solution". Finally, I was able to solve the issue by forgetting about linking or aliasing and just downgrading to gfortran-4.8.
I had installed the newer version with brew, so for me this entailed uninstalling
brew uninstall gcc
and then following the instructions here to install 4.8.2, i.e.
curl -O http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2
sudo tar fvxz gfortran-4.8.2-darwin13.tar.bz2 -C /
It still threw up some warnings but at least I got a successful installation of deldir, which I needed to run pgirmess.
I am installing lme4 using the README.md file on their github account and I fail during installing the dependencies. I tried to install them separately and still crash at installing the minqa package. I'm using R/3.0.2 on RHEL6. During the build the compiler argues about RScript not existing which as I check it is in the R/bin folder.
Here is the log to the R INSTALL:
$ R CMD INSTALL minqa_1.2.2.tar.gz
* installing to library ‘/gpfs/apps/x86_64-rhel6/R/3.0.2/R/library’
* installing *source* package ‘minqa’ ...
** package ‘minqa’ successfully unpacked and MD5 sums checked
** libs
gfortran -fpic -g -O2 -c altmov.f -o altmov.o
gfortran -fpic -g -O2 -c bigden.f -o bigden.o
gfortran -fpic -g -O2 -c biglag.f -o biglag.o
gfortran -fpic -g -O2 -c bobyqa.f -o bobyqa.o
gfortran -fpic -g -O2 -c bobyqb.f -o bobyqb.o
gfortran -fpic -g -O2 -c lagmax.f -o lagmax.o
g++ -I/gpfs/apps/x86_64-rhel6/R/3.0.2/R/include -DNDEBUG -I/usr/local/include -I"/gpfs/apps/x86_64-rhel6/R/3.0.2/R/library/Rcpp/include" -fpic -g -O2 -c minqa.cpp -o minqa.o
gfortran -fpic -g -O2 -c newuoa.f -o newuoa.o
gfortran -fpic -g -O2 -c newuob.f -o newuob.o
gfortran -fpic -g -O2 -c prelim.f -o prelim.o
gfortran -fpic -g -O2 -c rescue.f -o rescue.o
gfortran -fpic -g -O2 -c trsapp.f -o trsapp.o
gfortran -fpic -g -O2 -c trsbox.f -o trsbox.o
gfortran -fpic -g -O2 -c trstep.f -o trstep.o
gfortran -fpic -g -O2 -c uobyqa.f -o uobyqa.o
gfortran -fpic -g -O2 -c uobyqb.f -o uobyqb.o
gfortran -fpic -g -O2 -c update.f -o update.o
gfortran -fpic -g -O2 -c updatebobyqa.f -o updatebobyqa.o
Rscript execution error: No such file or directory
g++ -shared -L/usr/local/lib64 -o minqa.so altmov.o bigden.o biglag.o bobyqa.o bobyqb.o lagmax.o minqa.o newuoa.o newuob.o prelim.o rescue.o trsapp.o trsbox.o trstep.o uobyqa.o uobyqb.o update.o updatebobyqa.o -lgfortran -lm -L/gpfs/apps/x86_64-rhel6/R/3.0.2/R/lib -lR
Rscript execution error: No such file or directory
installing to /gpfs/apps/x86_64-rhel6/R/3.0.2/R/library/minqa/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/gpfs/apps/x86_64-rhel6/R/3.0.2/R/library/minqa/libs/minqa.so':
/gpfs/apps/x86_64-rhel6/R/3.0.2/R/library/minqa/libs/minqa.so: undefined symbol: _ZTIN4Rcpp7RObjectE
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/gpfs/apps/x86_64-rhel6/R/3.0.2/R/library/minqa’
A similar error also occurs when trying to upgrade lme4 from 1.0-5 to 1.0-6. The error message is something like:
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/usr/local/lib/R/site-library/minqa/libs/minqa.so':
libRcpp.so: cannot open shared object file: No such file or directory
ERROR: lazy loading failed for package ‘lme4’
To resolve this install the packages in the order below:
install.packages('Rcpp')
install.packages('RcppEigen')
install.packages('minqa')
install.packages('lme4')
I guess it's related to RCpp; just upgrade the version from 0.10.6 to 0.11.0 and some ABI break change happens?
Credit from dmbates
/usr/share/R/share/make/shlib.mk:6: recipe for target 'minqa.so' failed make: *** [minqa.so] Error 1
I got the same error when installing minqa (needed for lme4). It was due to modify .First() in /etc/R/Rprofile.site
Desactive .First or use R --vanilla.