* using log directory ‘/data/gannet/ripley/R/packages/tests-OpenBLAS/phreeqc.Rcheck’
* using R Under development (unstable) (2023-01-02 r83548)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)
GNU Fortran (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)
* running under: Fedora Linux 36 (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 ‘3.7.4’
* 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 ... [563s/246s] OK
* used C compiler: ‘gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
* used C++ compiler: ‘g++ (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
* 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 R 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 ... WARNING
File ‘phreeqc/libs/phreeqc.so’:
Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
Objects: ‘IPhreeqc.o’, ‘R.o’, ‘phreeqcpp/basicsubs.o’,
‘phreeqcpp/inverse.o’, ‘phreeqcpp/kinetics.o’,
‘phreeqcpp/mainsubs.o’, ‘phreeqcpp/parse.o’,
‘phreeqcpp/PBasic.o’, ‘phreeqcpp/PHRQ_io_output.o’,
‘phreeqcpp/pitzer.o’, ‘phreeqcpp/print.o’,
‘phreeqcpp/ReadClass.o’, ‘phreeqcpp/readtr.o’,
‘phreeqcpp/transport.o’, ‘phreeqcpp/utilities.o’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking examples ... 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)
corrupted double-linked list
* checking PDF version of manual ... [11s/11s] 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-OpenBLAS/phreeqc.Rcheck/00check.log’
for details.
Command exited with non-zero status 1
Time 4:59.34, 567.24 + 43.38
Note: this link no longer exists from https://www.stats.ox.ac.uk/pub/bdr/Rblas/OpenBLAS/phreeqc.out