Dolors Pelegri-Siso
| Snapshot Date: 2025-08-03 13:25 -0400 (Sun, 03 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/methylclock |
| git_branch: devel |
| git_last_commit: 2eef027 |
| git_last_commit_date: 2025-04-15 12:34:24 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-04 12:12 -0400 (Mon, 04 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4796 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4536 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4578 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4519 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4517 |
| 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 1241/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| methylclock 1.15.0 (landing page) Dolors Pelegri-Siso
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: methylclock |
| Version: 1.15.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:methylclock.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings methylclock_1.15.0.tar.gz |
| StartedAt: 2025-08-01 08:17:44 -0000 (Fri, 01 Aug 2025) |
| EndedAt: 2025-08-01 08:32:31 -0000 (Fri, 01 Aug 2025) |
| EllapsedTime: 887.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: methylclock.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD check --install=check:methylclock.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings methylclock_1.15.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/methylclock.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘methylclock/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘methylclock’ version ‘1.15.0’
* 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: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* 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
commonClockCpgs 39.930 0.744 77.546
plotDNAmAge 38.953 1.709 65.844
load_DNAm_Clocks_data 30.918 1.460 54.474
DNAmAge 29.125 0.922 56.240
checkClocks 27.382 0.754 52.663
load_DNAmGA_Clocks_data 25.795 1.188 49.607
DNAmGA 16.375 0.617 31.497
checkClocksGA 16.286 0.399 31.366
meffilEstimateCellCountsFromBetas 9.890 0.368 15.158
getCellTypeReference 6.128 0.507 9.042
meffilListCellTypeReferences 6.306 0.134 9.650
* 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
‘/home/biocbuild/bbs-3.22-bioc/meat/methylclock.Rcheck/00check.log’
for details.
methylclock.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD INSTALL methylclock
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘methylclock’ ...
** this is package ‘methylclock’ version ‘1.15.0’
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c NewModel1Clean.cpp -o NewModel1Clean.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c NewModel1Clean_emxAPI.cpp -o NewModel1Clean_emxAPI.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c NewModel1Clean_emxutil.cpp -o NewModel1Clean_emxutil.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c NewModel1Clean_initialize.cpp -o NewModel1Clean_initialize.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c NewModel1Clean_terminate.cpp -o NewModel1Clean_terminate.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c bsxfun.cpp -o bsxfun.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/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()
| ^~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c repmat.cpp -o repmat.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c rtGetInf.cpp -o rtGetInf.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c rtGetNaN.cpp -o rtGetNaN.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c rt_nonfinite.cpp -o rt_nonfinite.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.5.0/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/R/R-4.5.0/lib -lR
installing to /home/biocbuild/R/R-4.5.0/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)
methylclock.Rcheck/methylclock-Ex.timings
| name | user | system | elapsed | |
| DNAmAge | 29.125 | 0.922 | 56.240 | |
| DNAmGA | 16.375 | 0.617 | 31.497 | |
| checkClocks | 27.382 | 0.754 | 52.663 | |
| checkClocksGA | 16.286 | 0.399 | 31.366 | |
| commonClockCpgs | 39.930 | 0.744 | 77.546 | |
| getCellTypeReference | 6.128 | 0.507 | 9.042 | |
| load_DNAmGA_Clocks_data | 25.795 | 1.188 | 49.607 | |
| load_DNAm_Clocks_data | 30.918 | 1.460 | 54.474 | |
| meffilEstimateCellCountsFromBetas | 9.890 | 0.368 | 15.158 | |
| meffilListCellTypeReferences | 6.306 | 0.134 | 9.650 | |
| plotCorClocks | 0 | 0 | 0 | |
| plotDNAmAge | 38.953 | 1.709 | 65.844 | |
| progress_data | 0.014 | 0.000 | 0.015 | |
| progress_vars | 0.002 | 0.000 | 0.002 | |