* using log directory ‘/srv/hornik/tmp/CRAN_pretest/CorMID.Rcheck’ * using R Under development (unstable) (2025-01-07 r87537) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.6 (1) Debian flang-new version 19.1.6 (1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘CorMID/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CorMID’ version ‘0.3.1’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/6s] OK * 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 ‘CorMID’ can be installed ... [7s/7s] WARNING Found the following significant warnings: poss_local.cpp:44:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value] poss_local.cpp:46:22: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value] poss_local.cpp:71:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value] See ‘/srv/hornik/tmp/CRAN_pretest/CorMID.Rcheck/00install.out’ for details. * used C++ compiler: ‘Debian clang version 19.1.6 (1)’ * 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 ... [0s/0s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [0s/0s] OK * checking loading without being on the library search path ... [0s/0s] 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 ... [3s/3s] 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 ... [0s/0s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... 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 ... [0s/0s] ERROR Running examples in ‘CorMID-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: CorMID > ### Title: CorMID. > ### Aliases: CorMID plot.CorMID print.CorMID > > ### ** Examples > > # make up some fake measurement data for Pyruvic acid 2TMS with 3 biological carbon > # assuming 10% labeling at M3 and 2 fragments > fml <- "C9H20O3Si2" > mid <- c(0.9, 0, 0, 0.1) > r <- unlist(list("M+H" = 0.8, "M+H2O-CH4" = 0.2)) > int <- CorMID::recMID(mid = mid, r = r, fml = fml) > plot(int) > > # full estimation of M and r > out <- CorMID::CorMID(int = int, fml = fml) Error in 1 - rMpH : non-numeric argument to binary operator Calls: -> FitMID -> weight_errors Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [1s/1s] ERROR Running ‘testthat.R’ [1s/1s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(CorMID) > testthat::test_dir(path = "./testthat") ✔ | F W S OK | Context ⠏ | 0 | CalcTheoreticalMDV ✔ | 1 | CalcTheoreticalMDV ⠏ | 0 | CorMID ✖ | 1 0 | CorMID ──────────────────────────────────────────────────────────────────────────────── Error ('test-CorMID.R:6:1'): (code run outside of `test_that()`) Error in `1 - rMpH`: non-numeric argument to binary operator Backtrace: ▆ 1. └─CorMID::CorMID(int = rMID, fml = fml) at test-CorMID.R:6:1 2. └─CorMID:::FitMID(...) 3. └─CorMID:::weight_errors(...) ──────────────────────────────────────────────────────────────────────────────── ⠏ | 0 | CountChemicalElements ✔ | 1 | CountChemicalElements ⠏ | 0 | FitMID ✖ | 1 0 | FitMID ──────────────────────────────────────────────────────────────────────────────── Error ('test-FitMID.R:10:5'): FitMID returns expected result Error in `test_mid[[new_mid_start]]`: attempt to select less than one element in get1index Backtrace: ▆ 1. └─CorMID:::FitMID(md = int, td = td, r = r) at test-FitMID.R:10:5 ──────────────────────────────────────────────────────────────────────────────── ⠏ | 0 | calc_mid_error ✔ | 4 | calc_mid_error ⠏ | 0 | poss_local ✔ | 6 | poss_local ⠏ | 0 | recMID ⠴ | 2 4 | recMID ✔ | 3 4 | recMID ⠏ | 0 | weight_errors ✔ | 4 | weight_errors ══ Results ═════════════════════════════════════════════════════════════════════ ── Skipped tests (3) ─────────────────────────────────────────────────────────── • On CRAN (3): 'test-recMID.R:21:5', 'test-recMID.R:32:5', 'test-recMID.R:44:5' ── Failed tests ──────────────────────────────────────────────────────────────── Error ('test-CorMID.R:6:1'): (code run outside of `test_that()`) Error in `1 - rMpH`: non-numeric argument to binary operator Backtrace: ▆ 1. └─CorMID::CorMID(int = rMID, fml = fml) at test-CorMID.R:6:1 2. └─CorMID:::FitMID(...) 3. └─CorMID:::weight_errors(...) Error ('test-FitMID.R:10:5'): FitMID returns expected result Error in `test_mid[[new_mid_start]]`: attempt to select less than one element in get1index Backtrace: ▆ 1. └─CorMID:::FitMID(md = int, td = td, r = r) at test-FitMID.R:10:5 [ FAIL 2 | WARN 0 | SKIP 3 | PASS 20 ] Deleting unused snapshots: • CorMID/cormid-plot-alt.svg • CorMID/cormid-plot.svg Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [1s/1s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘CorMID.Rmd’ using rmarkdown ** Processing: /srv/hornik/tmp/CRAN_pretest/CorMID.Rcheck/vign_test/CorMID/vignettes/CorMID_files/figure-html/recMID-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 10674 bytes Input file size = 10764 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8398 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8398 Output IDAT size = 8398 bytes (2276 bytes decrease) Output file size = 8476 bytes (2288 bytes = 21.26% decrease) Quitting from lines 124-125 [CorMID2] (CorMID.Rmd) Error: processing vignette 'CorMID.Rmd' failed with diagnostics: non-numeric argument to binary operator --- failed re-building ‘CorMID.Rmd’ SUMMARY: processing the following file failed: ‘CorMID.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [3s/3s] 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: 3 ERRORs, 1 WARNING