Jitao David Zhang
| Snapshot Date: 2025-12-11 13:40 -0500 (Thu, 11 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/BioQC |
| git_branch: devel |
| git_last_commit: c2f01e7 |
| git_last_commit_date: 2025-10-29 10:28:57 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-12 11:35 -0500 (Fri, 12 Dec 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" | 4874 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4582 |
| 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 220/2332 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BioQC 1.39.0 (landing page) Jitao David Zhang
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the BioQC package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BioQC.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: BioQC |
| Version: 1.39.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BioQC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BioQC_1.39.0.tar.gz |
| StartedAt: 2025-12-11 18:47:48 -0500 (Thu, 11 Dec 2025) |
| EndedAt: 2025-12-11 18:48:12 -0500 (Thu, 11 Dec 2025) |
| EllapsedTime: 24.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BioQC.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BioQC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BioQC_1.39.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/BioQC.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 ‘BioQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BioQC’ version ‘1.39.0’
* 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 ‘BioQC’ can be installed ... OK
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... 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 ... NOTE
checkRd: (-1) readCurrentSignatures.Rd:13: Lost braces
13 | \item{namespace}{Character, namespace of the gene-set, or code{NULL}, passed
| ^
checkRd: (-1) wmwTest.Rd:282: Lost braces
282 | code{wilcox.test} in the \code{stats} package, and \code{rankSumTestWithCorrelation} in
| ^
* 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 ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... INFO
Note: information on .o files is not available
* 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 NOTE
See
‘/Users/biocbuild/bbs-3.23-bioc/meat/BioQC.Rcheck/00check.log’
for details.
BioQC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BioQC ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’ * installing *source* package ‘BioQC’ ... ** this is package ‘BioQC’ version ‘1.39.0’ ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.1.sdk’ clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `/Library/Frameworks/R.framework/Resources/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gini.c -o gini.o 'CxxFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `/Library/Frameworks/R.framework/Resources/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init.c -o init.o 'CxxFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `/Library/Frameworks/R.framework/Resources/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c read_gmt.cpp -o read_gmt.o 'CxxFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `/Library/Frameworks/R.framework/Resources/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c stat_rank.c -o stat_rank.o 'CxxFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `/Library/Frameworks/R.framework/Resources/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c wmw_test.c -o wmw_test.o 'CxxFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. 'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. 'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. 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 BioQC.so gini.o init.o read_gmt.o stat_rank.o wmw_test.o -F/Library/Frameworks/R.framework/.. -framework R 'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. 'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. installing to /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/00LOCK-BioQC/00new/BioQC/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (BioQC)
BioQC.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(BioQC)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
>
> test_check("BioQC")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 125 ]
>
> proc.time()
user system elapsed
2.546 0.141 2.700
BioQC.Rcheck/BioQC-Ex.timings
| name | user | system | elapsed | |
| GmtList | 0.001 | 0.000 | 0.001 | |
| IndexList | 0.002 | 0.001 | 0.002 | |
| SignedGenesets | 0 | 0 | 0 | |
| SignedIndexList | 0.001 | 0.000 | 0.001 | |
| absLog10p | 0.001 | 0.000 | 0.000 | |
| appendGmtList | 0.001 | 0.001 | 0.002 | |
| as.GmtList | 0 | 0 | 0 | |
| entropy | 0.000 | 0.000 | 0.001 | |
| entropyDiversity | 0.001 | 0.001 | 0.001 | |
| entropySpecificity | 0.001 | 0.000 | 0.002 | |
| filterPmat | 0.001 | 0.001 | 0.000 | |
| getLeadingEdgeIndexFromVector | 0.001 | 0.000 | 0.002 | |
| gini | 0 | 0 | 0 | |
| gmtlist2signedGenesets | 0.004 | 0.000 | 0.004 | |
| matchGenes | 0.021 | 0.000 | 0.021 | |
| offset-set | 0.000 | 0.000 | 0.001 | |
| offset | 0.001 | 0.000 | 0.000 | |
| prettySigNames | 0.019 | 0.000 | 0.029 | |
| readCurrentSignatures | 0.022 | 0.000 | 0.022 | |
| readGmt | 0.029 | 0.001 | 0.030 | |
| readSignedGmt | 0.003 | 0.001 | 0.003 | |
| sampleSpecialization | 0.002 | 0.000 | 0.002 | |
| setNamespace | 0.002 | 0.000 | 0.002 | |
| simplifyMatrix | 0.000 | 0.001 | 0.000 | |
| sub-.GmtList | 0.001 | 0.000 | 0.001 | |
| sub-sub-.GmtList | 0 | 0 | 0 | |
| uniqGenesetsByNamespace | 0.002 | 0.000 | 0.002 | |
| wmwLeadingEdge | 0.003 | 0.001 | 0.003 | |
| wmwTest | 0.065 | 0.004 | 0.070 | |
| wmwTestInR | 0.001 | 0.000 | 0.001 | |