* using log directory ‘/data/gannet/ripley/R/packages/tests-ATLAS/phreeqc.Rcheck’
* using R Under development (unstable) (2025-05-13 r88200)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-15 (GCC) 15.1.0
    GNU Fortran (GCC) 15.1.0
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘phreeqc/DESCRIPTION’ ... OK
* this is package ‘phreeqc’ version ‘3.8.7’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘phreeqc’ can be installed ... [14m/20m] WARNING
Found the following significant warnings:
  /usr/include/bits/stdio2.h:54:35: warning: null destination pointer [-Wformat-truncation=]
See ‘/data/gannet/ripley/R/packages/tests-ATLAS/phreeqc.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-15 (GCC) 15.1.0’
* used C++ compiler: ‘g++-15 (GCC) 15.1.0’
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking examples ... [9s/13s] ERROR
Running examples in ‘phreeqc-Ex.R’ failed
The error most likely occurred in:

> ### Name: ex7
> ### Title: Example 7-Gas-Phase Calculations
> ### Aliases: ex7
> ### Keywords: dataset
> 
> ### ** Examples
> 
> 
> phrLoadDatabaseString(phreeqc.dat)

 *** caught segfault ***
address (nil), cause 'unknown'

Traceback:
 1: phrLoadDatabaseString(phreeqc.dat)
An irrecoverable exception occurred. R is aborting now ...
* checking PDF version of manual ... [12s/16s] OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR, 1 WARNING
See
  ‘/data/gannet/ripley/R/packages/tests-ATLAS/phreeqc.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 21:10.71, 850.07 + 58.98