• using R Under development (unstable) (2026-09-23 r90586)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-16 (Debian 16.2.0-3) 16.2.0     GNU Fortran (Debian 16.2.0-3) 16.2.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8 * current time: 2026-09-24 16:04:27 UTC
• checking for file ‘kmeRtone/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘kmeRtone’ version ‘1.0’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [2s/2s] 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 ‘kmeRtone’ can be installed ... OK See the install log for details.
• used C++ compiler: ‘g++-16 (Debian 16.2.0-3) 16.2.0’
• 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 ... [4s/5s] OK
• checking whether the package can be loaded with stated dependencies ... [4s/5s] OK
• checking whether the package can be unloaded cleanly ... [4s/5s] OK
• checking whether the namespace can be loaded with stated dependencies ... [4s/4s] OK
• checking whether the namespace can be unloaded cleanly ... [4s/5s] OK
• checking loading without being on the library search path ... [4s/4s] OK
• checking whether startup messages can be suppressed ... [4s/5s] 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 ... [24s/31s] OK
• checking Rd files ... [1s/1s] 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 line endings in Makefiles ... OK
• checking compilation flags in Makevars ... OK
• checking for GNU extensions in Makefiles ... INFO GNU make is a SystemRequirements.
• 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 sizes of PDF files under ‘inst/doc’ ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking examples ... [4s/5s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [10s/169s] ERROR   Running ‘testthat.R’ [10s/169s] 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/tests.html   > # * https://testthat.r-lib.org/reference/test_package.html#special-files   >   > library(testthat)   > library(kmeRtone)   >   > testthat::test_check("kmeRtone")      Attaching package: 'data.table'      The following object is masked from 'package:base':          %notin%            ------------------------------------------------------------                    Extraction of Case K-mers   ------------------------------------------------------------     % Total % Received % Xferd Average Speed Time Time Time Current                                    Dload Upload Total Spent Left Speed        0 0 0 0 0 0 0 0 00:10 0     2 18.60M 2 382.7k 0 0 33243 0 09:46 00:11 09:35 375.6k    73 18.60M 73 13.60M 0 0 1.05M 0 00:17 00:12 00:05 6.58M   100 18.60M 100 18.60M 0 0 1.42M 0 00:13 00:13 6.58M   100 18.60M 100 18.60M 0 0 1.42M 0 00:13 00:13 6.58M   100 18.60M 100 18.60M 0 0 1.42M 0 00:13 00:13 6.58M     % Total % Received % Xferd Average Speed Time Time Time Current                                    Dload Upload Total Spent Left Speed        0 0 0 0 0 0 0 0 00:11 0     3 11.01M 3 374.8k 0 0 31889 0 06:02 00:12 05:50 368.0k   100 11.01M 100 11.01M 0 0 873.5k 0 00:12 00:12 368.0k   100 11.01M 100 11.01M 0 0 873.5k 0 00:12 00:12 368.0k   100 11.01M 100 11.01M 0 0 873.5k 0 00:12 00:12 368.0k   Extracting 2-mers from chr20............DONE! -- 1.2 mins   Extracting 2-mers from chr21............DONE! -- 29.56 secs   Extracting 2-mers from chr22............   Downloading chr20.fa.gz from UCSC...         Downloading chr21.fa.gz from UCSC...      Saving _problems/test_score-40.R   [ FAIL 1 | WARN 2 | SKIP 0 | PASS 0 ]      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test_score.R:25:1'): (code run outside of `test_that()`) ────────────   Error in `download.file(file, tmpFile, method = method, mode = "wb", quiet = !showProgress)`: cannot open URL 'https://hgdownload.soe.ucsc.edu/goldenPath/hg19/chromosomes/'   Backtrace:        ▆     1. └─kmeRtone::kmeRtone(...) at test_score.R:25:1     2. └─kmeRtone::SCORE(...)     3. └─kmeRtone::extractKmers(...)     4. └─future.apply::future_lapply(...)     5. └─future.apply:::future_xapply(...)     6. └─base::tryCatch(...)     7. └─base (local) tryCatchList(expr, classes, parentenv, handlers)     8. └─base (local) tryCatchOne(...)     9. └─value[[3L]](cond)    10. └─future.apply:::onError(e, futures = fs, debug = debug)      [ FAIL 1 | WARN 2 | SKIP 0 | PASS 0 ]   Error:   ! Test failures.   Execution halted
• checking PDF version of manual ... [5s/7s] OK
• checking HTML version of manual ... [2s/2s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR