Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-08-13 17:40 -0400 (Tue, 13 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4758 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4493 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4522 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4471 |
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 217/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BioQC 1.32.0 (landing page) Jitao David Zhang
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 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: 1.32.0 |
Command: E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BioQC.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings BioQC_1.32.0.tar.gz |
StartedAt: 2024-08-11 23:00:29 -0400 (Sun, 11 Aug 2024) |
EndedAt: 2024-08-11 23:02:20 -0400 (Sun, 11 Aug 2024) |
EllapsedTime: 111.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BioQC.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BioQC.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings BioQC_1.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.19-bioc/meat/BioQC.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'BioQC/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'BioQC' version '1.32.0' * 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 whether package 'BioQC' can be installed ... OK * used C compiler: 'gcc.exe (GCC) 13.2.0' * used C++ compiler: 'G__~1.EXE (GCC) 13.2.0' * checking installed package size ... NOTE installed size is 5.4Mb sub-directories of 1Mb or more: extdata 3.9Mb * 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 ... NOTE Note: information on .o files for x64 is not available File 'E:/biocbuild/bbs-3.19-bioc/R/library/BioQC/libs/x64/BioQC.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) 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: 3 NOTEs See 'E:/biocbuild/bbs-3.19-bioc/meat/BioQC.Rcheck/00check.log' for details.
BioQC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL BioQC ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.19-bioc/R/library' * installing *source* package 'BioQC' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' using C++ compiler: 'G__~1.EXE (GCC) 13.2.0' gcc -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG `E:/biocbuild/bbs-3.19-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c gini.c -o gini.o gcc -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG `E:/biocbuild/bbs-3.19-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG `E:/biocbuild/bbs-3.19-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c read_gmt.cpp -o read_gmt.o gcc -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG `E:/biocbuild/bbs-3.19-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c stat_rank.c -o stat_rank.o gcc -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG `E:/biocbuild/bbs-3.19-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c wmw_test.c -o wmw_test.o wmw_test.c: In function 'wmw_test_list': wmw_test.c:118: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 118 | #pragma omp parallel for | wmw_test.c: In function 'wmw_test': wmw_test.c:168: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 168 | #pragma omp parallel for | wmw_test.c: In function 'signed_wmw_test_list': wmw_test.c:201: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 201 | #pragma omp parallel for | wmw_test.c: In function 'signed_wmw_test': wmw_test.c:270: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 270 | #pragma omp parallel for | g++ -std=gnu++17 -shared -s -static-libgcc -o BioQC.dll tmp.def gini.o init.o read_gmt.o stat_rank.o wmw_test.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR installing to E:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-BioQC/00new/BioQC/libs/x64 ** 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 ** 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 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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, 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 9.29 0.53 10.18
BioQC.Rcheck/BioQC-Ex.timings
name | user | system | elapsed | |
GmtList | 0 | 0 | 0 | |
IndexList | 0 | 0 | 0 | |
SignedGenesets | 0 | 0 | 0 | |
SignedIndexList | 0.01 | 0.00 | 0.01 | |
absLog10p | 0 | 0 | 0 | |
appendGmtList | 0.02 | 0.00 | 0.02 | |
as.GmtList | 0 | 0 | 0 | |
entropy | 0 | 0 | 0 | |
entropyDiversity | 0 | 0 | 0 | |
entropySpecificity | 0.02 | 0.00 | 0.01 | |
filterPmat | 0 | 0 | 0 | |
getLeadingEdgeIndexFromVector | 0 | 0 | 0 | |
gini | 0 | 0 | 0 | |
gmtlist2signedGenesets | 0 | 0 | 0 | |
matchGenes | 0.11 | 0.00 | 0.11 | |
offset-set | 0 | 0 | 0 | |
offset | 0 | 0 | 0 | |
prettySigNames | 0.11 | 0.00 | 0.11 | |
readCurrentSignatures | 0.09 | 0.00 | 0.09 | |
readGmt | 0.11 | 0.02 | 0.13 | |
readSignedGmt | 0.02 | 0.00 | 0.01 | |
sampleSpecialization | 0 | 0 | 0 | |
setNamespace | 0 | 0 | 0 | |
simplifyMatrix | 0 | 0 | 0 | |
sub-.GmtList | 0.01 | 0.00 | 0.01 | |
sub-sub-.GmtList | 0 | 0 | 0 | |
uniqGenesetsByNamespace | 0 | 0 | 0 | |
wmwLeadingEdge | 0.02 | 0.00 | 0.02 | |
wmwTest | 0.27 | 0.02 | 0.30 | |
wmwTestInR | 0 | 0 | 0 | |