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.
Related
Almost the time the app works find but the error occurs randomly, and I cannot find the error trace in the apps log(/var/log/shiny-server):
An error has occurred
The application exited unexpectedly.
read ECONNRESET
The sessionInfo() is as below:
R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux buster/sid
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
[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_3.4.3
And there's not much info about this issue with R shiny app, maybe it's about node.js?
Thanks for any advise in advance.
Finally I solved it by adding below code in server.r
onStop(function() {
odbcClose(conn)
})
I query data from database frequently but I did not close it.
After adding the code to close connection the error seldom occurs.
And I also adjust the app_idle_timeout to 0 in the /etc/shiny-server/shiny-server.conf
I am trying to install some packages (quite basic ones actually) for R 3.6, but I'm getting a fairly strange error message from BiocManager::install():
BiocManager::install("XML", destdir = "/my/dir/R/x86_64-pc-linux-gnu-library/3.6/")
error: could not load shared object '/my/dir/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-XML/00new/XML/libs/XML.so':
libicui18n.so.58: Could not open shared object file: No such file or directory
(Translated from french - could be approximate)
Does this mean that R can't write in /my/dir/R/x86_64-pc-linux-gnu-library/3.6/? That would be my first idea but I really don't know.
EDIT:
Here is my session info:
R version 3.6.2 (2019-12-12)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 10 (buster)
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.8.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.8.0
locale:
[1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C LC_TIME=C
[4] LC_COLLATE=fr_FR.UTF-8 LC_MONETARY=C LC_MESSAGES=fr_FR.UTF-8
[7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocManager_1.30.10
loaded via a namespace (and not attached):
[1] compiler_3.6.2 tools_3.6.2
This is a configuration problem, there is a fix available at github.com/r-lib/xml2/issues/219.
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
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
>