* using log directory 'd:/Rcompile/CRANpkg/local/4.5/rmzqc.Rcheck' * using R Under development (unstable) (2025-02-14 r87718 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'rmzqc/DESCRIPTION' ... OK * this is package 'rmzqc' version '0.5.4' * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'rmzqc' can be installed ... OK See 'https://www.r-project.org/nosvn/R.check/r-devel-windows-x86_64/rmzqc-00install.html' for details. * checking installed package size ... OK * checking package directory ... 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] OK * checking whether the package can be loaded with stated dependencies ... [1s] OK * checking whether the package can be unloaded cleanly ... [1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s] OK * checking whether the namespace can be unloaded cleanly ... [1s] OK * checking loading without being on the library search path ... [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 ... [4s] OK * checking Rd files ... [1s] OK * checking Rd metadata ... 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 installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... [6s] OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... [14s] ERROR Running 'testthat.R' [13s] Running the tests in 'tests/testthat.R' failed. Complete output: > library(testthat) > library(rmzqc) > > test_check("rmzqc") Superclass Singleton has cloneable=FALSE, but subclass CV_ has cloneable=TRUE. A subclass cannot be cloneable when its superclass is not cloneable, so cloning will be disabled for CV_. trying URL 'https://api.github.com/repos/HUPO-PSI/psi-ms-CV/releases/latest' Content type 'application/json; charset=utf-8' length 7324 bytes ================================================== downloaded 7324 bytes Downloading obo from 'https://github.com/HUPO-PSI/psi-ms-CV/releases/download/v4.1.191/psi-ms.obo' ... trying URL 'https://github.com/HUPO-PSI/psi-ms-CV/releases/download/v4.1.191/psi-ms.obo' Content type 'application/octet-stream' length 1008314 bytes (984 KB) ================================================== downloaded 984 KB Superclass Singleton has cloneable=FALSE, but subclass CV_ has cloneable=TRUE. A subclass cannot be cloneable when its superclass is not cloneable, so cloning will be disabled for CV_. trying URL 'https://api.github.com/repos/HUPO-PSI/psi-ms-CV/releases/latest' Content type 'application/json; charset=utf-8' length 7324 bytes ================================================== downloaded 7324 bytes Downloading obo from 'https://github.com/HUPO-PSI/psi-ms-CV/releases/download/v4.1.191/psi-ms.obo' ... trying URL 'https://github.com/HUPO-PSI/psi-ms-CV/releases/download/v4.1.191/psi-ms.obo' Content type 'application/octet-stream' length 1008314 bytes (984 KB) ================================================== downloaded 984 KB Downloading obo from 'https://github.com/HUPO-PSI/psi-ms-CV/rele_BROKEN_URL_ases/download/v4.1.147/psi-ms.obo' ... trying URL 'https://github.com/HUPO-PSI/psi-ms-CV/rele_BROKEN_URL_ases/download/v4.1.147/psi-ms.obo' Error in download.file(custom_uri, tmp_filename) : cannot open URL 'https://github.com/HUPO-PSI/psi-ms-CV/rele_BROKEN_URL_ases/download/v4.1.147/psi-ms.obo' Downloading obo from 'https://github.com/HUPO-PSI/psi-ms-CV/rele_BROKEN_URL_ases/download/v4.1.147/psi-ms.obo' ... trying URL 'https://github.com/HUPO-PSI/psi-ms-CV/rele_BROKEN_URL_ases/download/v4.1.147/psi-ms.obo' Error in download.file(custom_uri, tmp_filename) : cannot open URL 'https://github.com/HUPO-PSI/psi-ms-CV/rele_BROKEN_URL_ases/download/v4.1.147/psi-ms.obo' Error in getCVDictionary(source = "custom", custom_uri = "https://github.com/HUPO-PSI/psi-ms-CV/rele_BROKEN_URL_ases/download/v4.1.147/psi-ms.obo", : Download failed. trying URL 'https://api.github.com/repos/HUPO-PSI/psi-ms-CV/releases/latest' Content type 'application/json; charset=utf-8' length 7324 bytes ================================================== downloaded 7324 bytes Superclass Singleton has cloneable=FALSE, but subclass CV_ has cloneable=TRUE. A subclass cannot be cloneable when its superclass is not cloneable, so cloning will be disabled for CV_. Superclass Singleton has cloneable=FALSE, but subclass CV_ has cloneable=TRUE. A subclass cannot be cloneable when its superclass is not cloneable, so cloning will be disabled for CV_. Superclass Singleton has cloneable=FALSE, but subclass CV_ has cloneable=TRUE. A subclass cannot be cloneable when its superclass is not cloneable, so cloning will be disabled for CV_. Superclass Singleton has cloneable=FALSE, but subclass CV_ has cloneable=TRUE. A subclass cannot be cloneable when its superclass is not cloneable, so cloning will be disabled for CV_. Superclass Singleton has cloneable=FALSE, but subclass CV_ has cloneable=TRUE. A subclass cannot be cloneable when its superclass is not cloneable, so cloning will be disabled for CV_. [ FAIL 2 | WARN 14 | SKIP 0 | PASS 87 ] â•â• Failed tests â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â• ── Failure ('test_conversion.R:17:3'): toQCMetric = function(id, value, on_violation = c("error", "warn")) ── `toQCMetric(id = "MS:4000059", value = 13405)` produced messages. ── Failure ('test_conversion.R:18:3'): toQCMetric = function(id, value, on_violation = c("error", "warn")) ── `toQCMetric(id = "MS:4000059", value = "13405")` produced messages. [ FAIL 2 | WARN 14 | SKIP 0 | PASS 87 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [23s] OK * checking PDF version of manual ... [21s] OK * checking HTML version of manual ... [6s] OK * DONE Status: 1 ERROR