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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstatsTMT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstatsTMT_2.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MSstatsTMT.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstatsTMT/DESCRIPTION’ ... OK
* this is package ‘MSstatsTMT’ version ‘2.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 for sufficient/correct file permissions ... OK
* checking whether package ‘MSstatsTMT’ can be installed ... OK
* 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... 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 ... NOTE
.checkRepeatedMeasures: no visible global function definition for ‘.’
.checkSingleSubject: no visible global function definition for ‘.’
.checkTechReplicate: no visible global function definition for ‘.’
.getGroupLabel: no visible binding for global variable ‘Condition’
.getVarComponentTMT : <anonymous>: no visible global function
  definition for ‘is’
.handleSingleContrastTMT: no visible global function definition for
  ‘.mygrad’
.plotProfileTMT: no visible global function definition for ‘.’
.plotProfileTMT: no visible binding for global variable ‘censored’
.savePlotlyPlotHTML: no visible global function definition for ‘zip’
Undefined global functions or variables:
  . .mygrad Condition censored is zip
Consider adding
  importFrom("methods", "is")
  importFrom("utils", "zip")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... 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 ... NOTE
Documented arguments not in \usage in Rd file 'dot-documentFunction.Rd':
  ‘removeProtein_with1Peptide’ ‘use_log_file’ ‘append’ ‘verbose’
  ‘log_file_path’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
dataProcessPlotsTMT 8.425  0.081   8.511
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  INFO  [2024-11-09 08:10:44] ** MSstatsTMT - proteinSummarization function
  INFO  [2024-11-09 08:10:44] ** MSstatsTMT - proteinSummarization function
  INFO  [2024-11-09 08:10:44] ** MSstatsTMT - proteinSummarization function
  INFO  [2024-11-09 08:10:44] ** MSstatsTMT - proteinSummarization function
  INFO  [2024-11-09 08:10:44] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01raw ( 1  of  15 )
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 26 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-groupComparisionTMT.R:6:3'): groupComparision works ──────────
  output$ComparisonResult not equal to MSstatsTMT::test.pairwise$ComparisonResult.
  Column 'SE': Mean relative difference: 0.003179207
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 26 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/MSstatsTMT.Rcheck/00check.log’
for details.