Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:47 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the PAA package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PAA.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1332/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
PAA 1.26.0 (landing page) Michael Turewicz
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: PAA |
Version: 1.26.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:PAA.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings PAA_1.26.0.tar.gz |
StartedAt: 2021-10-14 10:54:51 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 10:58:35 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 224.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: PAA.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:PAA.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings PAA_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/PAA.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘PAA/DESCRIPTION’ ... OK * this is package ‘PAA’ version ‘1.26.0’ * 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 ‘PAA’ can be installed ... OK * checking installed package size ... NOTE installed size is 5.3Mb sub-directories of 1Mb or more: extdata 2.3Mb libs 1.6Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Authors@R field gives more than one person with maintainer role: Michael Turewicz <michael.turewicz@rub.de> [aut, cre] Martin Eisenacher <martin.eisenacher@rub.de> [ctb, cre] * 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 ... NOTE batchFilter: no visible global function definition for ‘t.test’ batchFilter: no visible global function definition for ‘points’ batchFilter: no visible global function definition for ‘abline’ batchFilter: no visible global function definition for ‘write.table’ batchFilter: no visible global function definition for ‘tiff’ batchFilter: no visible global function definition for ‘dev.off’ batchFilter.anova: no visible global function definition for ‘combn’ batchFilter.anova: no visible global function definition for ‘oneway.test’ batchFilter.anova: no visible global function definition for ‘points’ batchFilter.anova: no visible global function definition for ‘abline’ batchFilter.anova: no visible global function definition for ‘write.table’ batchFilter.anova: no visible global function definition for ‘tiff’ batchFilter.anova: no visible global function definition for ‘dev.off’ classify.svm.ensemble: no visible global function definition for ‘predict’ classify.svm.ensemble: no visible global function definition for ‘tiff’ classify.svm.ensemble: no visible global function definition for ‘dev.off’ diffAnalysis: no visible global function definition for ‘t.test’ diffAnalysis: no visible global function definition for ‘median’ diffAnalysis: no visible global function definition for ‘sd’ diffAnalysis: no visible global function definition for ‘p.adjust’ diffAnalysis: no visible global function definition for ‘write.table’ final.classify.rf: no visible global function definition for ‘predict’ final.classify.rf: no visible global function definition for ‘tiff’ final.classify.rf: no visible global function definition for ‘dev.off’ final.classify.svm: no visible global function definition for ‘predict’ final.classify.svm: no visible global function definition for ‘tiff’ final.classify.svm: no visible global function definition for ‘dev.off’ normalizeRLM: no visible global function definition for ‘rnorm’ normalizeRLM: no visible global function definition for ‘tiff’ normalizeRLM: no visible global function definition for ‘boxplot’ normalizeRLM: no visible global function definition for ‘dev.off’ plotArray: no visible global function definition for ‘par’ plotArrayPng: no visible global function definition for ‘png’ plotArrayPng: no visible global function definition for ‘dev.off’ plotArrayTiff: no visible global function definition for ‘tiff’ plotArrayTiff: no visible global function definition for ‘dev.off’ plotFeatures: no visible global function definition for ‘tiff’ plotFeatures: no visible global function definition for ‘par’ plotFeatures: no visible global function definition for ‘axis’ plotFeatures: no visible global function definition for ‘box’ plotFeatures: no visible global function definition for ‘points’ plotFeatures: no visible global function definition for ‘legend’ plotFeatures: no visible global function definition for ‘dev.off’ plotFeaturesHeatmap: no visible global function definition for ‘na.exclude’ plotFeaturesHeatmap : my.dist: no visible global function definition for ‘as.dist’ plotFeaturesHeatmap : my.dist: no visible global function definition for ‘cor’ plotFeaturesHeatmap : my.hclust: no visible global function definition for ‘hclust’ plotFeaturesHeatmap: no visible global function definition for ‘tiff’ plotFeaturesHeatmap: no visible global function definition for ‘heatmap’ plotFeaturesHeatmap: no visible global function definition for ‘dev.off’ plotFeaturesHeatmap.2: no visible global function definition for ‘na.exclude’ plotFeaturesHeatmap.2 : my.dist: no visible global function definition for ‘as.dist’ plotFeaturesHeatmap.2 : my.dist: no visible global function definition for ‘cor’ plotFeaturesHeatmap.2: no visible global function definition for ‘png’ plotFeaturesHeatmap.2 : <anonymous>: no visible global function definition for ‘as.dist’ plotFeaturesHeatmap.2 : <anonymous>: no visible global function definition for ‘cor’ plotFeaturesHeatmap.2: no visible global function definition for ‘par’ plotFeaturesHeatmap.2: no visible global function definition for ‘legend’ plotFeaturesHeatmap.2: no visible global function definition for ‘dev.off’ plotMAPlots: no visible binding for global variable ‘median’ plotMAPlots: no visible global function definition for ‘tiff’ plotMAPlots: no visible global function definition for ‘par’ plotMAPlots: no visible global function definition for ‘abline’ plotMAPlots: no visible global function definition for ‘lines’ plotMAPlots: no visible global function definition for ‘lowess’ plotMAPlots: no visible global function definition for ‘dev.off’ plotNormMethods: no visible global function definition for ‘par’ plotNormMethods: no visible global function definition for ‘boxplot’ plotNormMethods: no visible global function definition for ‘dev.off’ plotNormMethods: no visible global function definition for ‘tiff’ printFeatures: no visible global function definition for ‘write.table’ pvaluePlot: no visible global function definition for ‘t.test’ pvaluePlot: no visible global function definition for ‘p.adjust’ pvaluePlot: no visible global function definition for ‘abline’ pvaluePlot: no visible global function definition for ‘legend’ pvaluePlot: no visible global function definition for ‘tiff’ pvaluePlot: no visible global function definition for ‘dev.off’ rj.rfe: no visible global function definition for ‘write.table’ rj.rfe: no visible global function definition for ‘read.table’ selectFeatures.ensemble: no visible global function definition for ‘write.table’ selectFeatures.frequency.cv: no visible global function definition for ‘write.table’ selectFeatures.frequency.cv: no visible global function definition for ‘read.table’ selectFeatures.frequency.cv: no visible global function definition for ‘tiff’ selectFeatures.frequency.cv: no visible global function definition for ‘title’ selectFeatures.frequency.cv: no visible global function definition for ‘dev.off’ selectFeatures.frequency.cv: no visible global function definition for ‘na.omit’ svm.rfe: no visible global function definition for ‘predict’ tTest: no visible global function definition for ‘t.test’ tTestFS: no visible global function definition for ‘t.test’ volcanoPlot: no visible global function definition for ‘t.test’ volcanoPlot: no visible global function definition for ‘tiff’ volcanoPlot: no visible global function definition for ‘dev.off’ volcanoPlot: no visible global function definition for ‘points’ volcanoPlot: no visible global function definition for ‘abline’ Undefined global functions or variables: abline as.dist axis box boxplot combn cor dev.off hclust heatmap legend lines lowess median na.exclude na.omit oneway.test p.adjust par png points predict read.table rnorm sd t.test tiff title write.table Consider adding importFrom("grDevices", "dev.off", "png", "tiff") importFrom("graphics", "abline", "axis", "box", "boxplot", "legend", "lines", "par", "points", "title") importFrom("stats", "as.dist", "cor", "hclust", "heatmap", "lowess", "median", "na.exclude", "na.omit", "oneway.test", "p.adjust", "predict", "rnorm", "sd", "t.test") importFrom("utils", "combn", "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 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed batchFilter.anova 6.091 0.087 9.903 preselect 3.729 0.268 6.062 diffAnalysis 3.599 0.396 7.447 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.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: 4 NOTEs See ‘/home/biocbuild/bbs-3.13-bioc/meat/PAA.Rcheck/00check.log’ for details.
PAA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL PAA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘PAA’ ... ** using staged installation ** libs gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c PAA_init.c -o PAA_init.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c joinMCountResults.cpp -o joinMCountResults.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c mCount.cpp -o mCount.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c mMsMatrix.cpp -o mMsMatrix.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c sampling.cpp -o sampling.o g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o PAA.so PAA_init.o RcppExports.o joinMCountResults.o mCount.o mMsMatrix.o sampling.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-PAA/00new/PAA/libs ** R ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ‘PAA_vignette.Rnw’ ** 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 (PAA)
PAA.Rcheck/tests/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (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. > BiocGenerics:::testPackage("PAA") Found2batches Adjusting for1covariate(s) or covariate level(s) Standardizing Data across genes Fitting L/S model and finding priors Finding parametric adjustments Adjusting the Data batchFilter - number of features to discard: 0 Read /home/biocbuild/bbs-3.13-bioc/R/library/PAA/extdata/dummy_GSM734833_PA41992_-_AD1.gpr Read /home/biocbuild/bbs-3.13-bioc/R/library/PAA/extdata/dummy_GSM734834_PA41994_-_AD2.gpr Read /home/biocbuild/bbs-3.13-bioc/R/library/PAA/extdata/dummy_GSM734835_PA42006_-AD3.gpr Read /home/biocbuild/bbs-3.13-bioc/R/library/PAA/extdata/dummy_GSM734836_PA42005_-_AD4.gpr Read /home/biocbuild/bbs-3.13-bioc/R/library/PAA/extdata/dummy_GSM734837_PA41957_-_AD5.gpr Read /home/biocbuild/bbs-3.13-bioc/R/library/PAA/extdata/dummy_GSM735203_PA42023_-_CO13.gpr Read /home/biocbuild/bbs-3.13-bioc/R/library/PAA/extdata/dummy_GSM735204_PA42025_-_CO14.gpr Read /home/biocbuild/bbs-3.13-bioc/R/library/PAA/extdata/dummy_GSM735205_PA42026_-_CO15.gpr Read /home/biocbuild/bbs-3.13-bioc/R/library/PAA/extdata/dummy_GSM735206_PA42028_-_CO16.gpr Read /home/biocbuild/bbs-3.13-bioc/R/library/PAA/extdata/dummy_GSM735207_PA42029_-_CO17.gpr No aggregation performed. RUNIT TEST PROTOCOL -- Thu Oct 14 10:58:21 2021 *********************************************** Number of test functions: 6 Number of errors: 0 Number of failures: 0 1 Test Suite : PAA RUnit Tests - 6 test functions, 0 errors, 0 failures Number of test functions: 6 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 13.284 0.689 24.944
PAA.Rcheck/PAA-Ex.timings
name | user | system | elapsed | |
batchAdjust | 3.099 | 0.039 | 4.420 | |
batchFilter | 1.158 | 0.096 | 2.468 | |
batchFilter.anova | 6.091 | 0.087 | 9.903 | |
diffAnalysis | 3.599 | 0.396 | 7.447 | |
loadGPR | 0.301 | 0.057 | 0.773 | |
mMsMatrix | 0.000 | 0.000 | 0.001 | |
normalizeArrays | 0.382 | 0.036 | 0.859 | |
plotArray | 1.313 | 0.065 | 1.704 | |
plotFeatures | 0.779 | 0.047 | 1.643 | |
plotFeaturesHeatmap.2 | 0.702 | 0.039 | 1.479 | |
plotFeaturesHeatmap | 0.506 | 0.031 | 1.410 | |
plotMAPlots | 2.024 | 0.020 | 4.954 | |
plotNormMethods | 0.996 | 0.004 | 1.740 | |
preselect | 3.729 | 0.268 | 6.062 | |
printFeatures | 0.479 | 0.032 | 0.703 | |
pvaluePlot | 1.128 | 0.012 | 1.140 | |
selectFeatures | 1.453 | 0.016 | 1.470 | |
shuffleData | 0.291 | 0.016 | 0.307 | |
volcanoPlot | 1.856 | 0.008 | 1.880 | |