I am trying to install locfit R package, but not able to install on Red Hat Enterprise Linux Server 7.4 (Maipo). It works fine on my local machine. I get the following error.
lf_adap.c(132) (col. 34): internal error: 04010026_1450
icc: error #10014: problem during multi-file optimization compilation (code 4)
make: *** [locfit.so] Error 4
ERROR: compilation failed for package 'locfit'
* removing '/home/a/ahwani/R/x86_64-pc-linux-gnu-library/3.6/locfit'
The downloaded source packages are in
'/tmp/Rtmp9zRFVC/downloaded_packages'
Warning message:
In install.packages("locfit") :
installation of package 'locfit' had non-zero exit status
sessionInfo():
version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.4 (Maipo)
Matrix products: default
BLAS/LAPACK: /apps/intel/2019/compilers_and_libraries_2019.1.144/linux/mkl/lib/intel64_lin/libmkl_intel_lp64.so
locale:
[1] LC_CTYPE=C 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_3.6.0
Related
I have upgraded Ubuntu from 18.04 to 20.04 and now some of my R packages fail to compile/load. One example is shown below:
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for 'myPackage' in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/usr/local/lib/R/site-library/00LOCK-my_package/00new/myPackage/libs/myPackage.so':
/usr/local/lib/R/site-library/00LOCK-my_package/00new/myPackge/libs/myPackage.so: undefined symbol: dgesvx_
Error: loading failed
Execution halted
ERROR: loading failed
This dgesvx_ looks like a LAPACK problem (https://www.netlib.org/lapack/explore-html/d7/d3b/group__double_g_esolve_ga9d90ccf6e340cacd08b7bbbb502ceb21.html#ga9d90ccf6e340cacd08b7bbbb502ceb21).
And I have latest LAPACK version available in Ubuntu 20.04 installed (3.9.0-1build1).
What can I do here to resolve the problem?
My sessionInfo():
> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.1 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C 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_4.0.2 tools_4.0.2
I try installing some required packages in R, which I just installed on a Linux machine. I am unable to install any package and get the below warning:
> install.packages("mongolite", repos="https://cran.r-project.org", lib="/opt/app/workload/deployments/installables/R-3.5.0/Rpackages")
^C
^CWarning: unable to access index for repository https://cran.r-project.org/src/contrib:
'wget' call had nonzero exit status
Warning message:
package ‘mongolite’ is not available (for R version 3.5.0)
I had to press ^+c after waiting for about 30 mins.
The same is the case with 'curl', but without the wait of 30 mins.
The following is the output of sessionInfo():
> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.4 (Maipo)
Matrix products: default
BLAS: /.../R-3.5.0/lib/libRblas.so
LAPACK: /.../R-3.5.0/lib/libRlapack.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_3.5.0 tools_3.5.0
>
I am unable to understand what is blocking the packages to be installed. Please help.
Thank you
I have installed a package in our server already and was working properly.
After a few hourse, once I wanted to load it again, I'm getting the following error:
library("SPONGE")
Error: package or namespace load failed for ‘SPONGE’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/adinfo/R/x86_64-pc-linux-gnu-library/3.4/gRbase/libs/gRbase.so':
/usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /home/adinfo/R/x86_64-pc-linux-gnu-library/3.4/gRbase/libs/gRbase.so)
I've also tried to install it again using
source("https://bioconductor.org/biocLite.R")
biocLite("SPONGE")
But I've got again the error that "Installation has zero exit"
Can someone help me with that?
> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)
Matrix products: default
BLAS: /TL/opt/R-3.4.0/lib/libRblas.so
LAPACK: /TL/opt/R-3.4.0/lib/libRlapack.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_3.4.0 tools_3.4.0
>
I try running:
install.packages("MonetDBLite")
in R. However, I get the following error:
cc1: error: -Wformat-security ignored without -Wformat [-Werror=format-security]
cc1: some warnings being treated as errors
Makevars:194: recipe for target 'build/objects/monetdblite/common/stream.o' failed
make: *** [build/objects/monetdblite/common/stream.o] Error 1
ERROR: compilation failed for package ‘MonetDBLite’
Does anyone know why this isn't working?
Output from sessionInfo() below:
R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 17.10
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
LC_TELEPHONE=C 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_3.4.2 tools_3.4.2 yaml_2.1.15
This should be resolved with the latest version of MonetDBLite on CRAN, 0.5.1.
I recently installed rSymPy to perform some symbolic calculations in R. This step also installed some dependencies (“rJava”, “rjson” and “rJython”). After the installation was complete, I loaded the library and ran a very simple command which gave me an error:
> library("rSymPy")
Loading required package: rJython
Loading required package: rJava
Loading required package: rjson
> x <- Var("x")
Error in .jcheck() : No running JVM detected. Maybe .jinit() would help.
Here is my sessionInfo(), just in case you need it:
> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.7 (Final)
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
other attached packages:
[1] rSymPy_0.2-1.1 rJython_0.0-4 rjson_0.2.15 rJava_0.9-8
loaded via a namespace (and not attached):
[1] tools_3.2.2 tcltk_3.2.2
I have tried to install different versions of required packages, but I always get this error. I would really appreciate any help.
Thanks,
Aashish
Thanks to Gabor Grothendieck (developer of rSymPy) for pointing out that sometimes one needs to manually initialize JVM. One can simply use "sympyStart()" at the beginning of the code, and that fixes the error.