Jitao David Zhang
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/BioQC |
| git_branch: RELEASE_3_16 |
| git_last_commit: c4cfa15 |
| git_last_commit_date: 2022-11-01 11:12:35 -0400 (Tue, 01 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:06:01 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 | ||||
|
To the developers/maintainers of the BioQC package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 199/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BioQC 1.26.0 (landing page) Jitao David Zhang
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: BioQC |
| Version: 1.26.0 |
| 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_1.26.0.tar.gz |
| StartedAt: 2023-04-10 19:05:04 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 19:05:58 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 53.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BioQC.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/BioQC.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BioQC/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BioQC’ version ‘1.26.0’ * 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 * 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 R 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 ... 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 ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE 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 in ‘inst/doc’ ... 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-3.16-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/4.2/Resources/library’ * installing *source* package ‘BioQC’ ... ** using staged installation ** libs clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `/Library/Frameworks/R.framework/Resources/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c gini.c -o gini.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `/Library/Frameworks/R.framework/Resources/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c init.c -o init.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `/Library/Frameworks/R.framework/Resources/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c read_gmt.cpp -o read_gmt.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `/Library/Frameworks/R.framework/Resources/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c stat_rank.c -o stat_rank.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `/Library/Frameworks/R.framework/Resources/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c wmw_test.c -o wmw_test.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o BioQC.so gini.o init.o read_gmt.o stat_rank.o wmw_test.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.2/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 version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)
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
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, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, 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
5.605 0.258 5.981
BioQC.Rcheck/BioQC-Ex.timings
| name | user | system | elapsed | |
| GmtList | 0.002 | 0.001 | 0.003 | |
| IndexList | 0.003 | 0.001 | 0.004 | |
| SignedGenesets | 0.001 | 0.000 | 0.001 | |
| SignedIndexList | 0.003 | 0.001 | 0.003 | |
| absLog10p | 0.000 | 0.000 | 0.001 | |
| appendGmtList | 0.004 | 0.001 | 0.013 | |
| as.GmtList | 0.001 | 0.000 | 0.001 | |
| entropy | 0.001 | 0.000 | 0.005 | |
| entropyDiversity | 0.003 | 0.000 | 0.004 | |
| entropySpecificity | 0.004 | 0.001 | 0.006 | |
| filterPmat | 0.000 | 0.001 | 0.002 | |
| getLeadingEdgeIndexFromVector | 0.003 | 0.001 | 0.004 | |
| gini | 0.000 | 0.000 | 0.001 | |
| gmtlist2signedGenesets | 0.005 | 0.001 | 0.005 | |
| matchGenes | 0.081 | 0.003 | 0.089 | |
| offset-set | 0.001 | 0.000 | 0.008 | |
| offset | 0 | 0 | 0 | |
| prettySigNames | 0.053 | 0.002 | 0.112 | |
| readCurrentSignatures | 0.059 | 0.002 | 0.061 | |
| readGmt | 0.085 | 0.004 | 0.106 | |
| readSignedGmt | 0.007 | 0.001 | 0.008 | |
| sampleSpecialization | 0.005 | 0.001 | 0.006 | |
| setNamespace | 0.008 | 0.001 | 0.015 | |
| simplifyMatrix | 0.000 | 0.000 | 0.001 | |
| sub-.GmtList | 0.002 | 0.001 | 0.002 | |
| sub-sub-.GmtList | 0.001 | 0.000 | 0.001 | |
| uniqGenesetsByNamespace | 0.015 | 0.000 | 0.015 | |
| wmwLeadingEdge | 0.008 | 0.002 | 0.010 | |
| wmwTest | 0.196 | 0.013 | 0.220 | |
| wmwTestInR | 0.005 | 0.001 | 0.009 | |