* using log directory 'd:/RCompile/CRANincoming/R-devel/MetaCycle.Rcheck'
* using R Under development (unstable) (2026-01-31 r89365 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.3.0
    GNU Fortran (GCC) 14.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'MetaCycle/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MetaCycle' version '1.2.1'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [50s] NOTE
Maintainer: 'Gang Wu <wggucas@gmail.com>'

Found the following (possibly) invalid URLs:
  URL: http://openwetware.org/wiki/HughesLab:JTK_Cycle
    From: man/meta2d.Rd
          inst/doc/implementation.html
    Status: Error
    Message: Timeout was reached [openwetware.org]:
      Failed to connect to openwetware.org port 80 after 21073 ms: Could not connect to server
* 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 serialization versions ... OK
* checking whether package 'MetaCycle' can be installed ... OK
* checking installed package size ... OK
* 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 ... 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 loading without being on the library search path ... 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 ... [18s] NOTE
OLS: no visible global function definition for 'pt'
OLS: no visible global function definition for 'var'
OLS: no visible global function definition for 'pf'
detrend_linear: no visible global function definition for 'cov'
evaluate: no visible global function definition for 'sd'
fisher.method: no visible global function definition for 'pchisq'
fisher.method: no visible global function definition for 'p.adjust'
getCirCasePVA: no visible global function definition for 'p.adjust'
getCirOmicsAMP : getAMP: no visible global function definition for
  'median'
getCirOmicsAMP : getAMP: no visible global function definition for 'lm'
getCirOmicsPVA : <anonymous>: no visible global function definition for
  'p.adjust'
getCirOmicsPVA: no visible global function definition for 'p.adjust'
get_period: no visible global function definition for 'spec.ar'
meta2d: no visible global function definition for 'read.table'
meta3d: no visible global function definition for 'read.table'
meta3d: no visible global function definition for 'write.table'
outIntegResultF: no visible global function definition for
  'write.table'
outSigResultF: no visible global function definition for 'write.table'
runARS : mainars: no visible global function definition for 'sd'
runARS: no visible global function definition for 'p.adjust'
runJTK : hlm: no visible global function definition for 'median'
runJTK : jtkstat : <anonymous>: no visible global function definition
  for 'pnorm'
runJTK : jtkx: no visible global function definition for 'p.adjust'
runJTK : jtkx: no visible global function definition for 'wilcox.test'
runJTK: no visible global function definition for 'flush.console'
runJTK: no visible global function definition for 'p.adjust'
runLS: no visible global function definition for 'flush.console'
runLS: no visible global function definition for 'p.adjust'
runmeta2dF: no visible global function definition for 'write.table'
Undefined global functions or variables:
  cov flush.console lm median p.adjust pchisq pf pnorm pt read.table sd
  spec.ar var wilcox.test write.table
Consider adding
  importFrom("stats", "cov", "lm", "median", "p.adjust", "pchisq", "pf",
             "pnorm", "pt", "sd", "spec.ar", "var", "wilcox.test")
  importFrom("utils", "flush.console", "read.table", "write.table")
to your NAMESPACE file.
* checking Rd files ... 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 ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... [20s] OK
* checking HTML version of manual ... OK
* DONE
Status: 2 NOTEs