* using log directory ‘/home/hornik/tmp/CRAN_special_valgrind/mpactr.Rcheck’ * using R Under development (unstable) (2025-09-14 r88832) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc-14 (Debian 14.2.0-19) 14.2.0 GNU Fortran (Debian 14.2.0-19) 14.2.0 * running under: Debian GNU/Linux forky/sid * using session charset: UTF-8 * using option ‘--use-valgrind’ * checking for file ‘mpactr/DESCRIPTION’ ... OK * this is package ‘mpactr’ version ‘0.3.1’ * 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 ‘mpactr’ can be installed ... [16s/16s] OK * used C++ compiler: ‘g++-14 (Debian 14.3.0-7) 14.3.0’ * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ 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 ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] 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 ... [6s/6s] OK * checking Rd files ... [0s/0s] 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 ... [1s/1s] 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [13m/12m] OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed import_data 64.133 3.996 67.889 filter_mispicked_ions 58.659 5.219 62.249 get_group_averages 56.704 3.756 59.360 filter_summary 55.290 4.838 58.362 plot_qc_tree 54.040 4.289 56.599 filter_group 51.844 3.250 54.442 qc_summary 49.036 4.499 51.816 get_similar_ions 47.902 3.980 50.220 filter_insource_ions 48.411 2.208 50.391 filter_cv 46.294 2.393 48.251 get_cv_data 36.114 2.466 38.143 get_meta_data 32.623 2.125 34.615 get_peak_table 32.475 1.935 34.290 get_raw_data 32.108 2.008 33.993 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [31m/30m] ERROR Running ‘testthat.R’ [31m/30m] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(mpactr) > > limit_cores() > test_check("mpactr") i Checking 1303 peaks for mispicked peaks. i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum. v 70 ions failed the mispicked filter, 1233 ions remain. i Checking 1303 peaks for mispicked peaks. i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum. v 70 ions failed the mispicked filter, 1233 ions remain. i Checking 1303 peaks for mispicked peaks. i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum. v 70 ions failed the mispicked filter, 1233 ions remain. i Checking 1303 peaks for mispicked peaks. i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum. v 70 ions failed the mispicked filter, 1233 ions remain. i Checking 1303 peaks for mispicked peaks. i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum. v 70 ions failed the mispicked filter, 1233 ions remain. i Parsing 1233 peaks based on the sample group: Blanks. i Argument remove_ions is: TRUE.Removing peaks from Blanks. v 749 ions failed the Blanks filter, 484 ions remain. i Parsing 484 peaks for replicability across technical replicates. v 33 ions failed the cv_filter filter, 451 ions remain. i Checking 1303 peaks for mispicked peaks. i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum. v 70 ions failed the mispicked filter, 1233 ions remain. i Parsing 1303 peaks based on the sample group: Blanks. i Argument remove_ions is: TRUE.Removing peaks from Blanks. v 796 ions failed the Blanks filter, 507 ions remain. i Checking 1303 peaks for mispicked peaks. i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum. v 70 ions failed the mispicked filter, 1233 ions remain. i Checking 1303 peaks for mispicked peaks. i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum. v 70 ions failed the mispicked filter, 1233 ions remain. i Checking 1303 peaks for mispicked peaks. i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum. v 70 ions failed the mispicked filter, 1233 ions remain. i Parsing 1233 peaks based on the sample group: Blanks. i Argument remove_ions is: TRUE.Removing peaks from Blanks. v 749 ions failed the Blanks filter, 484 ions remain. i Checking 1303 peaks for mispicked peaks. i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum. v 70 ions failed the mispicked filter, 1233 ions remain. i Parsing 1233 peaks based on the sample group: Blanks. i Argument remove_ions is: TRUE.Removing peaks from Blanks. v 749 ions failed the Blanks filter, 484 ions remain. i Parsing 484 peaks for replicability across technical replicates. v 33 ions failed the cv_filter filter, 451 ions remain. i Checking 1303 peaks for mispicked peaks. i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum. v 70 ions failed the mispicked filter, 1233 ions remain. i Parsing 1233 peaks based on the sample group: Blanks. i Argument remove_ions is: TRUE.Removing peaks from Blanks. v 749 ions failed the Blanks filter, 484 ions remain. i Checking 1303 peaks for mispicked peaks. i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum. v 70 ions failed the mispicked filter, 1233 ions remain. i Checking 1303 peaks for mispicked peaks. i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum. v 70 ions failed the mispicked filter, 1233 ions remain. i Checking 1303 peaks for mispicked peaks. i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum. v 70 ions failed the mispicked filter, 1233 ions remain. i Checking 1303 peaks for mispicked peaks. i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum. v 70 ions failed the mispicked filter, 1233 ions remain. i Parsing 1233 peaks based on the sample group: Blanks. i Argument remove_ions is: TRUE.Removing peaks from Blanks. v 749 ions failed the Blanks filter, 484 ions remain. i Checking 1303 peaks for mispicked peaks. i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum. v 70 ions failed the mispicked filter, 1233 ions remain. i Parsing 1233 peaks based on the sample group: Blanks. i Argument remove_ions is: TRUE.Removing peaks from Blanks. v 749 ions failed the Blanks filter, 484 ions remain. i Parsing 484 peaks for replicability across technical replicates. v 33 ions failed the cv_filter filter, 451 ions remain. i Checking 1303 peaks for mispicked peaks. i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum. v 70 ions failed the mispicked filter, 1233 ions remain. i Checking 1303 peaks for mispicked peaks. i Argument merge_peaks is: TRUE. Merging mispicked peaks with method . i Checking 1303 peaks for mispicked peaks. i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum. v 70 ions failed the mispicked filter, 1233 ions remain. i Checking 1303 peaks for mispicked peaks. i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum. v 70 ions failed the mispicked filter, 1233 ions remain. i Checking 1303 peaks for mispicked peaks. i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum. v 70 ions failed the mispicked filter, 1233 ions remain. i Parsing 1233 peaks based on the sample group: Blanks. ! Argument remove_ions is FALSE. Peaks from Blanks will not be removed. i Parsing 1233 peaks based on the sample group: Blanks. i Argument remove_ions is: TRUE.Removing peaks from Blanks. v 749 ions failed the Blanks filter, 484 ions remain. i Checking 1303 peaks for mispicked peaks. i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum. v 70 ions failed the mispicked filter, 1233 ions remain. i Parsing 1233 peaks based on the sample group: Blanks. i Argument remove_ions is: TRUE.Removing peaks from Blanks. v 749 ions failed the Blanks filter, 484 ions remain. i Parsing 484 peaks for replicability across technical replicates. v 33 ions failed the cv_filter filter, 451 ions remain. i Checking 1303 peaks for mispicked peaks. i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum. Execution halted ==3386971== ==3386971== HEAP SUMMARY: ==3386971== in use at exit: 188,116,945 bytes in 36,353 blocks ==3386971== total heap usage: 4,648,463 allocs, 4,612,110 frees, 3,233,759,242 bytes allocated ==3386971== ==3386971== LEAK SUMMARY: ==3386971== definitely lost: 0 bytes in 0 blocks ==3386971== indirectly lost: 0 bytes in 0 blocks ==3386971== possibly lost: 384 bytes in 1 blocks ==3386971== still reachable: 188,116,561 bytes in 36,352 blocks ==3386971== suppressed: 0 bytes in 0 blocks ==3386971== Rerun with --leak-check=full to see details of leaked memory ==3386971== ==3386971== For lists of detected and suppressed errors, rerun with: -s ==3386971== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0) * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [51s/48s] OK * checking PDF version of manual ... [4s/4s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR