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Using the hydra package


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.

  1. 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

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] …
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