Aaron Lun
| Snapshot Date: 2025-11-13 13:40 -0500 (Thu, 13 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/alabaster.base |
| git_branch: devel |
| git_last_commit: 1d97e98 |
| git_last_commit_date: 2025-11-03 02:55:31 -0500 (Mon, 03 Nov 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-14 11:36 -0500 (Fri, 14 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4825 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4547 |
| 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 41/2325 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| alabaster.base 1.11.1 (landing page) Aaron Lun
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
|
To the developers/maintainers of the alabaster.base package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/alabaster.base.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: alabaster.base |
| Version: 1.11.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:alabaster.base.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings alabaster.base_1.11.1.tar.gz |
| StartedAt: 2025-11-13 18:26:09 -0500 (Thu, 13 Nov 2025) |
| EndedAt: 2025-11-13 18:26:56 -0500 (Thu, 13 Nov 2025) |
| EllapsedTime: 47.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: alabaster.base.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:alabaster.base.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings alabaster.base_1.11.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/alabaster.base.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘alabaster.base/DESCRIPTION’ ... OK
* this is package ‘alabaster.base’ version ‘1.11.1’
* 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 ‘alabaster.base’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking C++ specification ... OK
* checking installed package size ... INFO
installed size is 6.0Mb
sub-directories of 1Mb or more:
libs 5.5Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Versioned 'LinkingTo' value for ‘assorthead’ is only usable in R >= 3.0.2
* 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... INFO
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/alabaster.base/libs/alabaster.base.so’:
Found ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
Found ‘___sprintf_chk’, possibly from ‘sprintf’ (C)
Found ‘___stderrp’, possibly from ‘stderr’ (C)
Found ‘___stdoutp’, possibly from ‘stdout’ (C)
Found ‘_abort’, possibly from ‘abort’ (C)
Found ‘_exit’, possibly from ‘exit’ (C)
Found ‘_rand_r’, possibly from ‘rand_r’ (C)
Found ‘_sprintf’, possibly from ‘sprintf’ (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* 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: 1 WARNING, 1 NOTE
See
‘/Users/biocbuild/bbs-3.23-bioc/meat/alabaster.base.Rcheck/00check.log’
for details.
alabaster.base.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL alabaster.base ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’ * installing *source* package ‘alabaster.base’ ... ** this is package ‘alabaster.base’ version ‘1.11.1’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using C++17 using SDK: ‘MacOSX11.3.1.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c check_csv.cpp -o check_csv.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c check_list.cpp -o check_list.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c choose_numeric_missing_placeholder.cpp -o choose_numeric_missing_placeholder.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c is_rfc3339.cpp -o is_rfc3339.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c load_csv.cpp -o load_csv.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c load_list.cpp -o load_list.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c validate.cpp -o validate.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c vls.cpp -o vls.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o alabaster.base.so RcppExports.o check_csv.o check_list.o choose_numeric_missing_placeholder.o is_rfc3339.o load_csv.o load_list.o validate.o vls.o /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rhdf5lib/lib/libhdf5.a -L/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -lz -F/Library/Frameworks/R.framework/.. -framework R ld: warning: ignoring duplicate libraries: '-lz' installing to /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/00LOCK-alabaster.base/00new/alabaster.base/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (alabaster.base)
alabaster.base.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(alabaster.base)
> test_check("alabaster.base")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 741 ]
>
> proc.time()
user system elapsed
18.380 1.548 18.563
alabaster.base.Rcheck/alabaster.base-Ex.timings
| name | user | system | elapsed | |
| Rfc3339 | 0.002 | 0.002 | 0.006 | |
| absolutizePath | 0.000 | 0.001 | 0.001 | |
| acquireFile | 0.175 | 0.019 | 0.205 | |
| altReadObject | 0.049 | 0.006 | 0.067 | |
| altSaveObject | 0.075 | 0.004 | 0.080 | |
| anyMissing | 0 | 0 | 0 | |
| chooseMissingPlaceholderForHdf5 | 0.000 | 0.000 | 0.001 | |
| cloneDirectory | 0.000 | 0.002 | 0.002 | |
| createDedupSession | 0.015 | 0.002 | 0.018 | |
| createRedirection | 0.117 | 0.010 | 0.124 | |
| getSaveEnvironment | 0.005 | 0.002 | 0.008 | |
| listObjects | 0.031 | 0.009 | 0.040 | |
| loadDirectory | 0.190 | 0.016 | 0.161 | |
| moveObject | 0.245 | 0.017 | 0.188 | |
| quickLoadObject | 0.169 | 0.010 | 0.141 | |
| quickReadCsv | 0.014 | 0.002 | 0.018 | |
| readAtomicVector | 0.007 | 0.002 | 0.011 | |
| readBaseFactor | 0.006 | 0.002 | 0.008 | |
| readBaseList | 0.038 | 0.004 | 0.048 | |
| readDataFrame | 0.023 | 0.004 | 0.028 | |
| readDataFrameFactor | 0.062 | 0.005 | 0.075 | |
| readObject | 0.026 | 0.004 | 0.035 | |
| readObjectFile | 0.000 | 0.001 | 0.001 | |
| removeObject | 0.167 | 0.013 | 0.156 | |
| saveAtomicVector | 0.021 | 0.006 | 0.030 | |
| saveBaseFactor | 0.004 | 0.003 | 0.008 | |
| saveBaseList | 0.016 | 0.004 | 0.023 | |
| saveDataFrameFactor | 0.035 | 0.004 | 0.041 | |
| saveFormats | 0 | 0 | 0 | |
| saveObject | 0.021 | 0.003 | 0.029 | |
| stageDataFrame | 0.023 | 0.004 | 0.032 | |
| transformVectorForHdf5 | 0 | 0 | 0 | |
| validateDirectory | 0.030 | 0.006 | 0.036 | |
| validateObject | 0.020 | 0.004 | 0.031 | |
| writeMetadata | 0.060 | 0.005 | 0.057 | |