Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-11-02 11:41:11 -0400 (Thu, 02 Nov 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
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 1755/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
J. Toedling
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the Ringo package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Ringo.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: Ringo |
Version: 1.66.0 |
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:Ringo.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings Ringo_1.66.0.tar.gz |
StartedAt: 2023-11-02 13:44:58 -0000 (Thu, 02 Nov 2023) |
EndedAt: 2023-11-02 13:48:26 -0000 (Thu, 02 Nov 2023) |
EllapsedTime: 208.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: Ringo.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:Ringo.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings Ringo_1.66.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/Ringo.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Ringo/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Ringo’ version ‘1.66.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'Biobase', 'RColorBrewer', 'limma', 'Matrix', 'grid', 'lattice' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 ‘Ringo’ can be installed ... WARNING Found the following significant warnings: Warning: Package 'Ringo' is deprecated and will be removed from Bioconductor See ‘/home/biocbuild/bbs-3.18-bioc/meat/Ringo.Rcheck/00install.out’ for details. * used C compiler: ‘gcc (GCC) 10.3.1’ * used C++ compiler: ‘g++ (GCC) 10.3.1’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘limma’ A package should be listed in only one of these fields. * 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 loading without being on the library search path ... OK * checking startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE 'library' or 'require' call to ‘grid’ which was already attached by Depends. Please remove these calls from your code. 'library' or 'require' calls in package code: ‘mclust’ ‘rtracklayer’ ‘topGO’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Namespace in Imports field not imported from: ‘limma’ All declared Imports should be used. Packages in Depends field not imported from: ‘Biobase’ ‘Matrix’ ‘RColorBrewer’ ‘grid’ ‘lattice’ ‘limma’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘clusters’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .onAttach: no visible global function definition for ‘addVigs2WinMenu’ asExprSet: no visible global function definition for ‘featureNames<-’ asExprSet: no visible global function definition for ‘featureData<-’ autocor: no visible global function definition for ‘featureNames’ autocor: no visible global function definition for ‘exprs’ autocor : <anonymous>: no visible global function definition for ‘matchpt’ autocor: no visible global function definition for ‘cor’ chersToBED: no visible global function definition for ‘write.table’ chipAlongChrom: no visible global function definition for ‘featureNames’ chipAlongChrom: no visible global function definition for ‘exprs’ chipAlongChrom: no visible global function definition for ‘brewer.pal’ chipAlongChrom: no visible global function definition for ‘pushViewport’ chipAlongChrom: no visible global function definition for ‘viewport’ chipAlongChrom: no visible global function definition for ‘grid.layout’ chipAlongChrom: no visible global function definition for ‘dataViewport’ chipAlongChrom: no visible global function definition for ‘grid.yaxis’ chipAlongChrom: no visible global function definition for ‘gpar’ chipAlongChrom: no visible global function definition for ‘grid.text’ chipAlongChrom: no visible global function definition for ‘unit’ chipAlongChrom: no visible global function definition for ‘draw.key’ chipAlongChrom: no visible global function definition for ‘sampleNames’ chipAlongChrom: no visible global function definition for ‘strwidth’ chipAlongChrom: no visible global function definition for ‘strheight’ chipAlongChrom: no visible global function definition for ‘popViewport’ chipAlongChrom: no visible global function definition for ‘grid.lines’ chipAlongChrom: no visible global function definition for ‘grid.segments’ chipAlongChrom: no visible global function definition for ‘arrow’ chipAlongChrom1: no visible global function definition for ‘featureNames’ chipAlongChrom1: no visible global function definition for ‘exprs’ chipAlongChrom1: no visible global function definition for ‘colors’ chipAlongChrom1: no visible global function definition for ‘brewer.pal’ chipAlongChrom1: no visible global function definition for ‘axis’ chipAlongChrom1: no visible global function definition for ‘mtext’ chipAlongChrom1: no visible global function definition for ‘abline’ chipAlongChrom1: no visible global function definition for ‘lines’ chipAlongChrom1: no visible global function definition for ‘points’ chipAlongChrom1: no visible global function definition for ‘rug’ chipAlongChrom1: no visible global function definition for ‘sampleNames’ chipAlongChrom1: no visible global function definition for ‘legend’ compute.gc: no visible global function definition for ‘listLen’ computeRunningMedians: no visible global function definition for ‘varLabels’ computeRunningMedians: no visible global function definition for ‘pData’ computeRunningMedians: no visible global function definition for ‘sampleNames’ computeRunningMedians: no visible global function definition for ‘exprs’ computeRunningMedians: no visible global function definition for ‘featureNames’ computeRunningMedians: no visible global function definition for ‘phenoData’ computeRunningMedians: no visible global function definition for ‘featureNames<-’ computeRunningMedians: no visible global function definition for ‘featureData<-’ computeRunningMedians: no visible global function definition for ‘featureData’ computeRunningMedians: no visible global function definition for ‘sampleNames<-’ computeSlidingT: no visible global function definition for ‘exprs’ computeSlidingT: no visible global function definition for ‘featureNames’ computeSlidingT: no visible global function definition for ‘sampleNames’ computeSlidingT: no visible binding for global variable ‘median’ computeSlidingT: no visible global function definition for ‘median’ computeSlidingT: no visible global function definition for ‘featureNames<-’ computeSlidingT: no visible global function definition for ‘featureData<-’ computeSlidingT: no visible global function definition for ‘featureData’ computeSlidingT: no visible global function definition for ‘sampleNames<-’ corPlot: no visible global function definition for ‘exprs’ corPlot: no visible global function definition for ‘relevel’ corPlot: no visible global function definition for ‘pairs’ corPlot : <anonymous>: no visible global function definition for ‘par’ corPlot : <anonymous>: no visible global function definition for ‘abline’ exportCCData: no visible global function definition for ‘exprs’ exportCCData: no visible global function definition for ‘exprs<-’ exportCCData: no visible global function definition for ‘package.version’ exportCCData: no visible global function definition for ‘write.table’ exportCherList: no visible global function definition for ‘IRanges’ exportCherList: no visible global function definition for ‘GenomicData’ exportCherList: no visible global function definition for ‘export’ findChersOnSmoothed: no visible global function definition for ‘pData’ findChersOnSmoothed: no visible global function definition for ‘sampleNames’ findChersOnSmoothed: no visible global function definition for ‘featureNames’ findChersOnSmoothed : <anonymous>: no visible global function definition for ‘exprs’ ftr2xys: no visible global function definition for ‘read.delim’ ftr2xys: no visible global function definition for ‘write.table’ image.RGList: no visible global function definition for ‘colorRampPalette’ image.RGList: no visible global function definition for ‘brewer.pal’ image.RGList: no visible global function definition for ‘quantile’ image.RGList: no visible global function definition for ‘points’ merge.RGList: no visible global function definition for ‘makeUnique’ newVP: no visible global function definition for ‘pushViewport’ newVP: no visible global function definition for ‘viewport’ newVP: no visible global function definition for ‘grid.layout’ newVP: no visible global function definition for ‘grid.text’ newVP: no visible global function definition for ‘gpar’ newVP: no visible global function definition for ‘popViewport’ nimblegenScale : tukey.biweight: no visible global function definition for ‘median’ normalizeBetweenArraysVSN: no visible global function definition for ‘exprs’ oneChannelVSN: no visible global function definition for ‘predict’ pair2xys: no visible global function definition for ‘read.delim’ pair2xys: no visible global function definition for ‘write.table’ panel.cor: no visible global function definition for ‘par’ panel.cor: no visible global function definition for ‘cor’ panel.cor: no visible global function definition for ‘strwidth’ panel.cor: no visible global function definition for ‘text’ panel.scatter: no visible global function definition for ‘points’ panel.scatter: no visible global function definition for ‘abline’ plot.cher: no visible global function definition for ‘sampleNames’ plot.cher: no visible global function definition for ‘rug’ plot.cher: no visible global function definition for ‘legend’ plotAlongChromLegend : formatRow: no visible global function definition for ‘convertWidth’ plotAlongChromLegend : formatRow: no visible global function definition for ‘stringWidth’ plotAlongChromLegend : formatRow: no visible global function definition for ‘grid.rect’ plotAlongChromLegend : formatRow: no visible global function definition for ‘unit’ plotAlongChromLegend : formatRow: no visible binding for global variable ‘gpar’ plotAlongChromLegend : formatRow: no visible global function definition for ‘grid.text’ plotAlongChromLegend : formatRow: no visible global function definition for ‘gpar’ plotAlongChromLegend: no visible global function definition for ‘pushViewport’ plotAlongChromLegend: no visible global function definition for ‘viewport’ plotAlongChromLegend: no visible global function definition for ‘popViewport’ plotBM: no visible global function definition for ‘arrows’ plotBM: no visible global function definition for ‘axis’ plotFeatures: no visible global function definition for ‘pushViewport’ plotFeatures: no visible global function definition for ‘dataViewport’ plotFeatures: no visible global function definition for ‘grid.segments’ plotFeatures: no visible global function definition for ‘gpar’ plotFeatures: no visible global function definition for ‘listLen’ plotFeatures: no visible global function definition for ‘grid.rect’ plotFeatures: no visible global function definition for ‘convertWidth’ plotFeatures: no visible global function definition for ‘stringWidth’ plotFeatures: no visible global function definition for ‘grid.text’ plotFeatures: no visible global function definition for ‘popViewport’ plotOneChIPSample: no visible global function definition for ‘unit’ plotOneChIPSample: no visible global function definition for ‘quantile’ plotOneChIPSample: no visible global function definition for ‘pushViewport’ plotOneChIPSample: no visible global function definition for ‘dataViewport’ plotOneChIPSample: no visible global function definition for ‘grid.yaxis’ plotOneChIPSample: no visible global function definition for ‘gpar’ plotOneChIPSample: no visible global function definition for ‘grid.text’ plotOneChIPSample: no visible global function definition for ‘grid.lines’ plotOneChIPSample: no visible global function definition for ‘grid.polyline’ plotOneChIPSample: no visible global function definition for ‘grid.points’ plotOneChIPSample: no visible global function definition for ‘popViewport’ posToProbeAnno: no visible global function definition for ‘read.delim’ preprocess: no visible global function definition for ‘normalizeWithinArrays’ preprocess: no visible global function definition for ‘normalizeBetweenArrays’ quantilesOverPositions: no visible global function definition for ‘exprs’ quantilesOverPositions : <anonymous>: no visible global function definition for ‘approx’ quantilesOverPositions: no visible global function definition for ‘sampleNames’ quantilesOverPositions : <anonymous>: no visible binding for global variable ‘quantile’ quantilesOverPositions: no visible global function definition for ‘density’ quantilesOverPositions: no visible global function definition for ‘approx’ readNgIntensitiesTxt: no visible global function definition for ‘read.table’ readNgIntensitiesTxt: no visible global function definition for ‘removeExt’ readNimblegen: no visible global function definition for ‘readTargets’ readNimblegen: no visible global function definition for ‘readSpotTypes’ readNimblegen: no visible global function definition for ‘controlStatus’ sigGOTable: no visible global function definition for ‘mappedkeys’ sigGOTable: no visible binding for global variable ‘annFUN.gene2GO’ sigGOTable: no visible binding for global variable ‘annFUN.org’ sigGOTable: no visible global function definition for ‘runTest’ sigGOTable: no visible global function definition for ‘GenTable’ sigGOTable: no visible global function definition for ‘usedGO’ sigGOTable: no visible binding for global variable ‘p.value’ splitAndSimplify: no visible global function definition for ‘listLen’ takeMeanOverGroups: no visible global function definition for ‘pData’ takeMeanOverGroups: no visible global function definition for ‘exprs’ takeMeanOverGroups: no visible global function definition for ‘featureNames<-’ takeMeanOverGroups: no visible global function definition for ‘featureNames’ twoGaussiansNull: no visible binding for global variable ‘p.adjust.methods’ twoGaussiansNull: no visible global function definition for ‘Mclust’ twoGaussiansNull: no visible global function definition for ‘na.omit’ twoGaussiansNull: no visible global function definition for ‘pnorm’ upperBoundNull: no visible global function definition for ‘na.omit’ upperBoundNull: no visible global function definition for ‘quantile’ cbind2,ExpressionSet-ExpressionSet: no visible global function definition for ‘featureNames’ cbind2,ExpressionSet-ExpressionSet: no visible global function definition for ‘exprs’ cbind2,ExpressionSet-ExpressionSet: no visible global function definition for ‘sampleNames’ plot,cher-ExpressionSet: no visible global function definition for ‘sampleNames’ plot,qop-ANY: no visible global function definition for ‘axis’ plot,qop-ANY: no visible global function definition for ‘rainbow’ plot,qop-ANY: no visible global function definition for ‘lines’ plot,qop-ANY: no visible global function definition for ‘legend’ Undefined global functions or variables: GenTable GenomicData IRanges Mclust abline addVigs2WinMenu annFUN.gene2GO annFUN.org approx arrow arrows axis brewer.pal colorRampPalette colors controlStatus convertWidth cor dataViewport density draw.key export exprs exprs<- featureData featureData<- featureNames featureNames<- gpar grid.layout grid.lines grid.points grid.polyline grid.rect grid.segments grid.text grid.yaxis legend lines listLen makeUnique mappedkeys matchpt median mtext na.omit normalizeBetweenArrays normalizeWithinArrays p.adjust.methods p.value pData package.version pairs par phenoData pnorm points popViewport predict pushViewport quantile rainbow read.delim read.table readSpotTypes readTargets relevel removeExt rug runTest sampleNames sampleNames<- strheight stringWidth strwidth text unit usedGO varLabels viewport write.table Consider adding importFrom("grDevices", "colorRampPalette", "colors", "rainbow") importFrom("graphics", "abline", "arrows", "axis", "legend", "lines", "mtext", "pairs", "par", "points", "rug", "strheight", "strwidth", "text") importFrom("stats", "approx", "cor", "density", "median", "na.omit", "p.adjust.methods", "pnorm", "predict", "quantile", "relevel") importFrom("utils", "read.delim", "read.table", "write.table") to your NAMESPACE file. * 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 for GNU extensions in Makefiles ... OK * checking include directives 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 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 WARNING, 5 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/Ringo.Rcheck/00check.log’ for details.
Ringo.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL Ringo ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’ * installing *source* package ‘Ringo’ ... ** using staged installation ** libs using C compiler: ‘gcc (GCC) 10.3.1’ using C++ compiler: ‘g++ (GCC) 10.3.1’ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c mmeansd.cpp -o mmeansd.o mmeansd.cpp: In function ‘SEXPREC* moving_mean_sd(SEXP, SEXP, SEXP)’: mmeansd.cpp:29:24: warning: variable ‘is’ set but not used [-Wunused-but-set-variable] 29 | int * x, nval, hs, is, i; | ^~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c mmedian.cpp -o mmedian.o gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c region_overlap.c -o region_overlap.o gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c ringo_init.c -o ringo_init.o g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o Ringo.so mmeansd.o mmedian.o region_overlap.o ringo_init.o -L/home/biocbuild/R/R-4.3.1/lib -lR installing to /home/biocbuild/R/R-4.3.1/site-library/00LOCK-Ringo/00new/Ringo/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for ‘ls’ from package ‘base’ in package ‘Ringo’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: Package 'Ringo' is deprecated and will be removed from Bioconductor version 3.19 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning: Package 'Ringo' is deprecated and will be removed from Bioconductor version 3.19 ** testing if installed package keeps a record of temporary installation path * DONE (Ringo)
Ringo.Rcheck/Ringo-Ex.timings
name | user | system | elapsed | |
arrayImage | 0.073 | 0.004 | 0.080 | |
asExprSet | 0.136 | 0.020 | 0.156 | |
autocorr | 0.118 | 0.004 | 0.124 | |
cherByThreshold | 0.009 | 0.000 | 0.008 | |
cherClass | 0.235 | 0.000 | 0.236 | |
chipAlongChrom | 0.106 | 0.000 | 0.106 | |
chipAlongChromOld | 0.047 | 0.000 | 0.048 | |
computeRunningMedians | 0.206 | 0.008 | 0.215 | |
compute_gc | 0.001 | 0.000 | 0.002 | |
compute_sliding_t | 0.050 | 0.000 | 0.051 | |
corrPlot | 0.014 | 0.000 | 0.018 | |
exportCherList | 0 | 0 | 0 | |
features2Probes | 0.793 | 0.052 | 0.847 | |
findChersOnSmoothed | 0.081 | 0.004 | 0.084 | |
ftr2xys | 0 | 0 | 0 | |
newCER | 0.001 | 0.000 | 0.001 | |
nonzero | 0.015 | 0.000 | 0.015 | |
plotAutocorr | 0 | 0 | 0 | |
plotBM | 0.021 | 0.004 | 0.025 | |
posToProbeAnnoEnvironment | 0.022 | 0.004 | 0.027 | |
preprocess | 0.172 | 0.004 | 0.176 | |
probeAnnoClass | 0.017 | 0.000 | 0.016 | |
qopS4 | 0.001 | 0.000 | 0.000 | |
quantilesOverPositions | 0.820 | 0.004 | 0.825 | |
readNimblegen | 0.049 | 0.004 | 0.054 | |
regionoverlap | 0.005 | 0.000 | 0.005 | |
relateCERs | 0 | 0 | 0 | |
sigGOTable | 0 | 0 | 0 | |
sliding_meansd | 0.002 | 0.000 | 0.002 | |
sliding_quantile | 0.019 | 0.000 | 0.019 | |
twoGaussiansNull | 0.131 | 0.008 | 0.152 | |
upperBoundNull | 0.050 | 0.000 | 0.051 | |
validProbeAnno | 0.011 | 0.004 | 0.015 | |