• using R version 4.6.0 (2026-04-24)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-16 (Debian 16.1.0-1) 16.1.0     GNU Fortran (Debian 16.1.0-1) 16.1.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8 * current time: 2026-06-13 06:08:16 UTC
• checking for file ‘ProbeDeveloper/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘ProbeDeveloper’ version ‘1.1.1’
• 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 serialization versions ... OK
• checking whether package ‘ProbeDeveloper’ can be installed ... WARNING Found the following significant warnings:   Note: possible error in 'tm_calculate(SubSeqObj, ': unused arguments (salt_corr_method = saltcorr, formamide_value_unit = list(value = fmd, unit = fmdmethod)) See the install log for details. Information on the location(s) of code generating the ‘Note’s can be obtained by re-running with environment variable R_KEEP_PKG_SOURCE set to ‘yes’.
• checking package directory ... OK
• checking for future file timestamps ... 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 ... [24s/31s] OK
• checking whether the package can be loaded with stated dependencies ... [24s/27s] OK
• checking whether the package can be unloaded cleanly ... [23s/30s] OK
• checking whether the namespace can be loaded with stated dependencies ... [23s/27s] OK
• checking whether the namespace can be unloaded cleanly ... [23s/26s] OK
• checking loading without being on the library search path ... [23s/25s] 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 ... [95s/115s] NOTE ProbeMake: possible error in tm_calculate(SubSeqObj, method = TmMethod,   ambiguous = FALSE, complement_seq = NULL, shift = 0, nn_table =   nn_table, tmm_table = tmm_table, imm_table = imm_table, de_table =   de_table, dnac_high = dnac1, dnac_low = dnac2, self_comp = FALSE,   variant = variant, Na = Na, K = K, Tris = Tris, Mg = Mg, dNTPs =   dNTPs, salt_corr_method = saltcorr, dmso_factor = DMSOfactor,   formamide_factor = fmdfactor, DMSO = DMSO, formamide_value_unit =   list(value = fmd, unit = fmdmethod), mismatch = TRUE): unused   arguments (salt_corr_method = saltcorr, formamide_value_unit =   list(value = fmd, unit = fmdmethod))
• 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 ... [4s/5s] OK
• checking data for ASCII and uncompressed saves ... OK
• checking examples ... [27s/33s] OK
• checking PDF version of manual ... [4s/6s] OK
• checking HTML version of manual ... [0s/1s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 WARNING, 1 NOTE