I run debian stable on several boxes. This morning I installed some security updates affecting Java on different boxes. The problem is that now I have some issues in using RJSDMX on one of them, despite they all having similar configurations.
https://github.com/amattioc/SDMX
which is a tool (available in many languages) to download statistical data from different providers. Part of the discussion is available here
https://github.com/amattioc/SDMX/issues/222
(including the suggestion to resort to the development version of RJSDMX). The situation is the following: if I install the development version of RJSDMX with
require(devtools)
install_github(repo = "amattioc/SDMX", subdir = "RJSDMX")
and then I try running the following short script
library(tidyverse)
library(RJSDMX)
estat_retrieval <- function(dataset_query){
res <- getTimeSeriesTable('EUROSTAT', dataset_query
) |> as_tibble()
return(res)
}
query <- "ert_bil_eur_a/A.AVG.NAC.RON"
all_rates_ini <- estat_retrieval(query)
all_rates_ini
sessionInfo()
I get this output
── Attaching packages ─────────────────────────────────────── tidyverse 1.3.2 ──
✔ ggplot2 3.4.0 ✔ purrr 1.0.1
✔ tibble 3.1.8 ✔ dplyr 1.1.0
✔ tidyr 1.3.0 ✔ stringr 1.5.0
✔ readr 2.1.3 ✔ forcats 0.5.2
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()
Loading required package: rJava
Loading required package: zoo
Attaching package: ‘zoo’
The following objects are masked from ‘package:base’:
as.Date, as.Date.numeric
2023-01-30T15:40:23.983 INFO [it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery] Contacting web service with query: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/dataflow/ESTAT/ert_bil_eur_a/latest
2023-01-30T15:40:24.448 SEVERE [it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery] Exception. Class: javax.net.ssl.SSLHandshakeException - Message: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, :
it.bancaditalia.oss.sdmx.exceptions.SdmxIOException: Connection problems while talking to endpoint: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
> sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 11 (bullseye)
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.13.so
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=en_GB.UTF-8
[9] LC_ADDRESS=en_GB.UTF-8 LC_TELEPHONE=en_GB.UTF-8
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=en_GB.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] RJSDMX_3.0-4 zoo_1.8-11 rJava_1.0-6 forcats_0.5.2
[5] stringr_1.5.0 dplyr_1.1.0 purrr_1.0.1 readr_2.1.3
[9] tidyr_1.3.0 tibble_3.1.8 ggplot2_3.4.0 tidyverse_1.3.2
loaded via a namespace (and not attached):
[1] pillar_1.8.1 compiler_4.2.2 cellranger_1.1.0
[4] dbplyr_2.2.1 tools_4.2.2 lattice_0.20-45
[7] timechange_0.1.1 googledrive_2.0.0 jsonlite_1.8.4
[10] lubridate_1.9.0 lifecycle_1.0.3 gargle_1.2.1
[13] gtable_0.3.1 pkgconfig_2.0.3 rlang_1.0.6
[16] reprex_2.0.2 DBI_1.1.3 cli_3.6.0
[19] haven_2.5.1 xml2_1.3.3 withr_2.5.0
[22] httr_1.4.4 generics_0.1.3 vctrs_0.5.2
[25] fs_1.5.2 hms_1.1.2 googlesheets4_1.0.1
[28] grid_4.2.2 tidyselect_1.2.0 glue_1.6.2
[31] R6_2.5.1 fansi_1.0.4 readxl_1.4.1
[34] tzdb_0.3.0 modelr_0.1.9 magrittr_2.0.3
[37] backports_1.4.1 scales_1.2.1 ellipsis_0.3.2
[40] rvest_1.0.3 assertthat_0.2.1 colorspace_2.0-3
[43] utf8_1.2.2 stringi_1.7.8 munsell_0.5.0
[46] broom_1.0.1 crayon_1.5.2
Apparently it is an issue with updating some Java certificates, but I have no idea about how to do that. Running
$ sudo R CMD javareconf
Java interpreter : /usr/lib/jvm/default-java/bin/java
Java version : 11.0.18
Java home path : /usr/lib/jvm/default-java
Java compiler : /usr/lib/jvm/default-java/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/lib/jvm/default-java/bin/jar
trying to compile and link a JNI program
detected JNI cpp flags : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -fpic -g -O2 -ffile-prefix-map=/home/jranke/git/r-backports/bullseye/r-base-4.2.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c conftest.c -o conftest.o
gcc -shared -L/usr/lib/R/lib -Wl,-z,relro -o conftest.so conftest.o -L/usr/lib/jvm/default-java/lib/server -ljvm -L/usr/lib/R/lib -lR
JAVA_HOME : /usr/lib/jvm/default-java
Java library path: $(JAVA_HOME)/lib/server
JNI cpp flags : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
Updating Java configuration in /usr/lib/R
Done.
did not help. Any suggestion is really appreciated!
