Dolors Pelegri-Siso
| Snapshot Date: 2026-03-20 13:40 -0400 (Fri, 20 Mar 2026) |
| git_url: https://git.bioconductor.org/packages/methylclock |
| git_branch: devel |
| git_last_commit: 33c0153 |
| git_last_commit_date: 2025-10-29 11:10:33 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-21 11:34 -0400 (Sat, 21 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" | 4866 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-20 r89666) -- "Unsuffered Consequences" | 4545 |
| 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 1275/2368 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| methylclock 1.17.0 (landing page) Dolors Pelegri-Siso
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | ERROR | |||||||||
| See other builds for methylclock in R Universe. | ||||||||||||||
|
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: 1.17.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL methylclock |
| StartedAt: 2026-03-20 18:18:37 -0400 (Fri, 20 Mar 2026) |
| EndedAt: 2026-03-20 18:19:08 -0400 (Fri, 20 Mar 2026) |
| EllapsedTime: 31.1 seconds |
| RetCode: 0 |
| Status: OK |
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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/4.6/Resources/library’
* installing *source* package ‘methylclock’ ...
** this is package ‘methylclock’ version ‘1.17.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using SDK: ‘MacOSX26.2.sdk’
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c NewModel1Clean.cpp -o NewModel1Clean.o
NewModel1Clean.cpp:35:14: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
35 | double b_y[isize];
| ^~~~~
NewModel1Clean.cpp:35:14: note: read of non-const variable 'isize' is not allowed in a constant expression
NewModel1Clean.cpp:34:16: note: declared here
34 | unsigned int isize = cpgs*samples;
| ^
NewModel1Clean.cpp:57:12: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
57 | double a[sizeobs];
| ^~~~~~~
NewModel1Clean.cpp:57:12: note: function parameter 'sizeobs' with unknown value cannot be used in a constant expression
NewModel1Clean.cpp:54:65: note: declared here
54 | static void mapminmax_reverse(const double y[], double x[], int sizeobs)
| ^
NewModel1Clean.cpp:271:14: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
271 | double xp1[sizealloc];
| ^~~~~~~~~
NewModel1Clean.cpp:271:14: note: initializer of 'sizealloc' is not a constant expression
NewModel1Clean.cpp:118:13: note: declared here
118 | const int sizealloc = cpgs * samples;
| ^
NewModel1Clean.cpp:272:14: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
272 | double dv1[sizeobs5];
| ^~~~~~~~
NewModel1Clean.cpp:272:14: note: initializer of 'sizeobs5' is not a constant expression
NewModel1Clean.cpp:120:13: note: declared here
120 | const int sizeobs5 = samples*5;
| ^
NewModel1Clean.cpp:273:14: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
273 | double dv2[sizeobs5];
| ^~~~~~~~
NewModel1Clean.cpp:273:14: note: initializer of 'sizeobs5' is not a constant expression
NewModel1Clean.cpp:120:13: note: declared here
120 | const int sizeobs5 = samples*5;
| ^
NewModel1Clean.cpp:276:14: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
276 | double dv3[samples];
| ^~~~~~~
NewModel1Clean.cpp:276:14: note: function parameter 'samples' with unknown value cannot be used in a constant expression
NewModel1Clean.cpp:115:75: note: declared here
115 | void NewModel1Clean( Rcpp::NumericMatrix x1, double b_y1[], int cpgs, int samples)
| ^
6 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c NewModel1Clean_emxAPI.cpp -o NewModel1Clean_emxAPI.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c NewModel1Clean_emxutil.cpp -o NewModel1Clean_emxutil.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c NewModel1Clean_initialize.cpp -o NewModel1Clean_initialize.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c NewModel1Clean_terminate.cpp -o NewModel1Clean_terminate.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bsxfun.cpp -o bsxfun.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c main.cpp -o main.o
main.cpp:58:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
58 | double b_y1[isamples];
| ^~~~~~~~
main.cpp:58:15: note: read of non-const variable 'isamples' is not allowed in a constant expression
main.cpp:57:7: note: declared here
57 | int isamples= data.ncol(); // Samples
| ^
main.cpp:37:14: warning: unused function 'argInit_real_T' [-Wunused-function]
37 | static float argInit_real_T()
| ^~~~~~~~~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c repmat.cpp -o repmat.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rtGetInf.cpp -o rtGetInf.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rtGetNaN.cpp -o rtGetNaN.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rt_nonfinite.cpp -o rt_nonfinite.o
clang++ -arch arm64 -std=gnu++20 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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
installing to /Library/Frameworks/R.framework/Versions/4.6/Resources/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)