Dolors Pelegri-Siso
| Snapshot Date: 2024-11-27 13:40 -0500 (Wed, 27 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/methylclock |
| git_branch: devel |
| git_last_commit: 5639edc |
| git_last_commit_date: 2024-10-29 11:01:44 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-28 12:17 -0500 (Thu, 28 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4748 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4459 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4398 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1218/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| methylclock 1.13.0 (landing page) Dolors Pelegri-Siso
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the methylclock package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/methylclock.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: methylclock |
| Version: 1.13.0 |
| Command: /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_1.13.0.tar.gz |
| StartedAt: 2024-11-27 23:40:46 -0500 (Wed, 27 Nov 2024) |
| EndedAt: 2024-11-27 23:52:49 -0500 (Wed, 27 Nov 2024) |
| EllapsedTime: 722.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: methylclock.Rcheck |
| Warnings: 0 |
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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_1.13.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/methylclock.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* 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 ‘1.13.0’
* 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 31.030 1.622 35.299
DNAmAge 26.935 2.257 31.750
checkClocks 21.834 1.685 25.602
plotDNAmAge 21.908 1.221 24.850
load_DNAmGA_Clocks_data 17.104 1.006 19.818
load_DNAm_Clocks_data 16.713 0.966 19.284
DNAmGA 14.975 0.861 17.017
checkClocksGA 11.303 0.654 12.967
getCellTypeReference 5.197 1.683 7.075
meffilEstimateCellCountsFromBetas 6.084 0.231 6.658
* 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-3.21-bioc/meat/methylclock.Rcheck/00check.log’
for details.
methylclock.Rcheck/00install.out
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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/4.5-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/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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/4.5-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)
methylclock.Rcheck/methylclock-Ex.timings
| name | user | system | elapsed | |
| DNAmAge | 26.935 | 2.257 | 31.750 | |
| DNAmGA | 14.975 | 0.861 | 17.017 | |
| checkClocks | 21.834 | 1.685 | 25.602 | |
| checkClocksGA | 11.303 | 0.654 | 12.967 | |
| commonClockCpgs | 31.030 | 1.622 | 35.299 | |
| getCellTypeReference | 5.197 | 1.683 | 7.075 | |
| load_DNAmGA_Clocks_data | 17.104 | 1.006 | 19.818 | |
| load_DNAm_Clocks_data | 16.713 | 0.966 | 19.284 | |
| meffilEstimateCellCountsFromBetas | 6.084 | 0.231 | 6.658 | |
| meffilListCellTypeReferences | 4.084 | 0.137 | 4.400 | |
| plotCorClocks | 0.001 | 0.001 | 0.000 | |
| plotDNAmAge | 21.908 | 1.221 | 24.850 | |
| progress_data | 0.013 | 0.001 | 0.014 | |
| progress_vars | 0.000 | 0.001 | 0.002 | |