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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:methylclock.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings methylclock_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/methylclock.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘methylclock/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘methylclock’ version ‘1.14.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘methylclock’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘planet’
  All declared Imports should be used.
Unexported object imported by a ':::' call: ‘minfi:::projectCellType’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DNAmAge: no visible binding for global variable ‘coefHorvath’
DNAmAge: no visible binding for global variable ‘coefHannum’
DNAmAge: no visible binding for global variable ‘coefLevine’
DNAmAge: no visible binding for global variable ‘coefSkin’
DNAmAge: no visible binding for global variable ‘coefPedBE’
DNAmAge: no visible binding for global variable ‘coefWu’
DNAmAge: no visible binding for global variable ‘coefTL’
DNAmAge: no visible binding for global variable ‘coefBLUP’
DNAmAge: no visible binding for global variable ‘coefEN’
DNAmGA: no visible binding for global variable ‘coefKnightGA’
DNAmGA: no visible binding for global variable ‘coefBohlin’
DNAmGA: no visible binding for global variable ‘coefMayneGA’
DNAmGA: no visible binding for global variable ‘coefLeeGA’
DNAmGA: no visible binding for global variable ‘coefEPIC’
DNAmGA: no visible global function definition for
  ‘meffil.estimate.cell.counts.from.betas’
DNAmGA: no visible global function definition for ‘install.packages’
DNAmGA: no visible global function definition for ‘data’
DNAmGA: no visible binding for global variable ‘plCellCpGsThird’
checkClocks: no visible binding for global variable ‘MethylationData’
checkClocks: no visible binding for global variable ‘coefHorvath’
checkClocks: no visible binding for global variable ‘coefHannum’
checkClocks: no visible binding for global variable ‘coefLevine’
checkClocks: no visible binding for global variable ‘coefSkin’
checkClocks: no visible binding for global variable ‘coefPedBE’
checkClocks: no visible binding for global variable ‘coefWu’
checkClocks: no visible binding for global variable ‘coefTL’
checkClocks: no visible binding for global variable ‘coefBLUP’
checkClocks: no visible binding for global variable ‘coefEN’
checkClocksGA: no visible binding for global variable ‘coefKnightGA’
checkClocksGA: no visible binding for global variable ‘coefBohlin’
checkClocksGA: no visible binding for global variable ‘coefMayneGA’
checkClocksGA: no visible binding for global variable ‘coefLeeGA’
checkClocksGA: no visible binding for global variable ‘coefEPIC’
cpgs_imputation: no visible binding for global variable ‘cpgs.in’
plotCorClocks: no visible binding for global variable ‘method’
plotCorClocks: no visible binding for global variable ‘clock’
plotCorClocks: no visible binding for global variable ‘age’
plotCorClocks: no visible binding for global variable ‘..rr.label..’
plotCorClocks: no visible binding for global variable ‘..p.label..’
plotDNAmAge: no visible binding for global variable ‘..eq.label..’
plotDNAmAge: no visible binding for global variable ‘..rr.label..’
Undefined global functions or variables:
  ..eq.label.. ..p.label.. ..rr.label.. MethylationData age clock
  coefBLUP coefBohlin coefEN coefEPIC coefHannum coefHorvath
  coefKnightGA coefLeeGA coefLevine coefMayneGA coefPedBE coefSkin
  coefTL coefWu cpgs.in data install.packages
  meffil.estimate.cell.counts.from.betas method plCellCpGsThird
Consider adding
  importFrom("utils", "data", "install.packages")
to your NAMESPACE file.
* 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 ... 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 data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                    user system elapsed
load_DNAm_Clocks_data             44.199  3.691  49.913
commonClockCpgs                   40.819  4.040  48.264
plotDNAmAge                       30.163  3.447  35.903
load_DNAmGA_Clocks_data           28.373  3.039  33.440
checkClocks                       25.463  3.327  31.056
DNAmAge                           25.391  3.053  30.696
checkClocksGA                     14.066  2.171  17.516
DNAmGA                            14.180  1.356  16.892
meffilEstimateCellCountsFromBetas 14.069  0.940  15.466
getCellTypeReference               6.892  3.061  10.165
meffilListCellTypeReferences       6.356  0.576   7.167
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/methylclock.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL methylclock
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘methylclock’ ...
** this is package ‘methylclock’ version ‘1.14.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c NewModel1Clean.cpp -o NewModel1Clean.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c NewModel1Clean_emxAPI.cpp -o NewModel1Clean_emxAPI.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c NewModel1Clean_emxutil.cpp -o NewModel1Clean_emxutil.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c NewModel1Clean_initialize.cpp -o NewModel1Clean_initialize.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c NewModel1Clean_terminate.cpp -o NewModel1Clean_terminate.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c bsxfun.cpp -o bsxfun.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c main.cpp -o main.o
main.cpp:37:14: warning: ‘float argInit_real_T()’ defined but not used [-Wunused-function]
   37 | static float argInit_real_T()
      |              ^~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c repmat.cpp -o repmat.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c rtGetInf.cpp -o rtGetInf.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c rtGetNaN.cpp -o rtGetNaN.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c rt_nonfinite.cpp -o rt_nonfinite.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o methylclock.so NewModel1Clean.o NewModel1Clean_emxAPI.o NewModel1Clean_emxutil.o NewModel1Clean_initialize.o NewModel1Clean_terminate.o RcppExports.o bsxfun.o main.o repmat.o rtGetInf.o rtGetNaN.o rt_nonfinite.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-methylclock/00new/methylclock/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘rtracklayer’ for request: ‘trackName<-’ when loading ‘AnnotationHubData’
Warning message:
replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘ExperimentHubData’ 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘ExperimentHubData’
No methods found in package ‘rtracklayer’ for request: ‘trackName<-’ when loading ‘AnnotationHubData’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘ExperimentHubData’
No methods found in package ‘rtracklayer’ for request: ‘trackName<-’ when loading ‘AnnotationHubData’
** testing if installed package keeps a record of temporary installation path
* DONE (methylclock)