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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:methylclock.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings methylclock_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/methylclock.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘methylclock/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘methylclock’ version ‘1.12.0’
* 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 ‘methylclock’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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
commonClockCpgs                   30.575  1.687  34.737
DNAmAge                           26.069  2.113  30.311
checkClocks                       23.289  2.003  26.982
plotDNAmAge                       19.967  1.138  22.615
load_DNAm_Clocks_data             17.997  0.979  20.609
load_DNAmGA_Clocks_data           16.576  0.963  19.115
DNAmGA                            13.819  0.754  15.528
checkClocksGA                     11.434  0.685  13.094
meffilEstimateCellCountsFromBetas  6.433  0.238   6.982
getCellTypeReference               4.952  1.703   6.822
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/methylclock.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL methylclock
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘methylclock’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c NewModel1Clean.cpp -o NewModel1Clean.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c NewModel1Clean_emxAPI.cpp -o NewModel1Clean_emxAPI.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c NewModel1Clean_emxutil.cpp -o NewModel1Clean_emxutil.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c NewModel1Clean_initialize.cpp -o NewModel1Clean_initialize.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c NewModel1Clean_terminate.cpp -o NewModel1Clean_terminate.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c bsxfun.cpp -o bsxfun.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c main.cpp -o main.o
main.cpp:37:14: warning: unused function 'argInit_real_T' [-Wunused-function]
static float argInit_real_T()
             ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c repmat.cpp -o repmat.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rtGetInf.cpp -o rtGetInf.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rtGetNaN.cpp -o rtGetNaN.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rt_nonfinite.cpp -o rt_nonfinite.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-methylclock/00new/methylclock/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
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’
** 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’
** testing if installed package keeps a record of temporary installation path
* DONE (methylclock)