Hello,
Referring to Hydrating packages • Hydra, I created an PLE package (“estimationxxxxxx”) from a json file according to Hydra’s instructions.
The first time I successfully obtained estimation results.
I’ve been trying to execute another PLE package since then, but I do not know what are the problems.
I saw these messages.
- Project ‘~/estimationxxxxxx’ loaded. [renv 0.15.4]
- The project may be out of sync – use
renv::status()for more details.
2.** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
- DONE (estimationxxxxxx)
After executing renv::status(), renv::snapshot(), renv:restore(), etc., and installing necessary packages,
“execute(connectionDetails = connectionDetails,
cdmDatabaseSchema = cdmDatabaseSchema,
cohortDatabaseSchema = cohortDatabaseSchema,
cohortTable = cohortTable,
oracleTempSchema = oracleTempSchema,
outputFolder = outputFolder,
databaseId = databaseId,
databaseName = databaseName,
databaseDescription = databaseDescription,
createCohort = TRUE;
runAnalyses = TRUE;
packageResults = TRUE;
maxCores = maxCores)”
but I have met various kinds of errors.
One of those errors is as follows
start of the error message ++++++++++++++++++++++++++++++++++++++
Warning message:
In i.p(…) : installation of package ‘sodium’ had non-zero exit status
install.packages(“sodium”)
Retrieving ‘https://cloud.r-project.org/src/contrib/sodium_1.2.1.tar.gz’ …
OK [downloaded 457.1 Kb in 0 secs]
Installing sodium [1.2.1] …
FAILED
Error installing package ‘sodium’:
==================================
- installing source package ‘sodium’ …
** package ‘sodium’ successfully unpacked and MD5 sums checked
** using staged installation
Package libsodium was not found in the pkg-config search path.
Perhaps you should add the directory containing `libsodium.pc’
to the PKG_CONFIG_PATH environment variable
No package ‘libsodium’ found
Using PKG_CFLAGS=
Using PKG_LIBS=-lsodium
--------------------------- [ANTICONF] --------------------------------
Configuration failed because libsodium was not found. Try installing: - deb: libsodium-dev (Debian, Ubuntu, etc)
- rpm: libsodium-devel (Fedora, EPEL)
- csw: libsodium_dev (Solaris)
- brew: libsodium (OSX)
If libsodium is already installed, check that ‘pkg-config’ is in your
PATH and PKG_CONFIG_PATH contains a libsodium.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars=‘INCLUDE_DIR=… LIB_DIR=…’
-------------------------- [ERROR MESSAGE] ---------------------------
:1:10: fatal error: sodium.h: No such file or directory
compilation terminated.
ERROR: configuration failed for package ‘sodium’
- removing ‘/home/ohdsi/estimation221124/renv/staging/1/sodium’
Error: install of package ‘sodium’ failed [error code 1]
end of the error message ++++++++++++++++++++++++++++++++++++++
I guess the reason why it happened is a version conflict between the required packages or a problem with the installation order.
I wonder where I can check the exact version of the package to be installed for population level estimation and the repository where those packages are located. I already checked the “renv.lock” and “readme.md.”
I’m waiting anyone could give an advice or a solution?
my system is
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS
ATLAS 2.7.8