Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:28:02 -0400 (Thu, 06 May 2021).
To the developers/maintainers of the iSEEu package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 915/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
iSEEu 1.2.0 (landing page) Kevin Rue-Albrecht
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: iSEEu |
Version: 1.2.0 |
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:iSEEu.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings iSEEu_1.2.0.tar.gz |
StartedAt: 2021-05-06 02:45:31 -0400 (Thu, 06 May 2021) |
EndedAt: 2021-05-06 02:53:08 -0400 (Thu, 06 May 2021) |
EllapsedTime: 457.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: iSEEu.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:iSEEu.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings iSEEu_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/iSEEu.Rcheck’ * using R version 4.0.5 (2021-03-31) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘iSEEu/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘iSEEu’ version ‘1.2.0’ * 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 ‘iSEEu’ 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 files in ‘vignettes’ ... OK * checking examples ... WARNING Found the following significant warnings: Warning: '.setOrganism' is deprecated. Warning: '.setIdentifierType' is deprecated. Warning: 'GeneSetTable' is deprecated. Warning: '.getAcceptablePValueFields' is deprecated. Warning: '.setAcceptablePValueFields' is deprecated. Warning: '.getAcceptablePValueFields' is deprecated. Warning: '.setAcceptablePValueFields' is deprecated. Warning: '.setIdentifierType' is deprecated. Warning: '.getIdentifierType' is deprecated. Warning: '.setOrganism' is deprecated. Warning: '.getOrganism' is deprecated. Warning: '.getGeneSetCommands' is deprecated. Warning: '.getOrganism' is deprecated. Warning: '.getOrganism' is deprecated. Warning: '.getGeneSetCommands' is deprecated. Warning: '.getIdentifierType' is deprecated. Warning: '.getOrganism' is deprecated. Warning: '.getOrganism' is deprecated. Warning: '.setGeneSetCommands' is deprecated. Warning: '.getGeneSetCommands' is deprecated. Warning: '.getGeneSetCommands' is deprecated. Deprecated functions may be defunct as soon as of the next release of R. See ?Deprecated. Examples with CPU (user + system) or elapsed time > 5s user system elapsed AggregatedDotPlot 25.016 0.640 28.338 modeReducedDim 21.212 0.228 22.312 FeatureSetTable-class 19.200 0.316 21.079 GeneSetTable-class 17.472 0.212 18.886 DynamicMarkerTable-class 16.572 0.212 17.565 ReducedDimensionHexPlot-class 16.404 0.220 17.419 DynamicReducedDimensionPlot-class 15.252 0.188 16.226 modeGating 12.864 0.224 13.867 * 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 WARNING See ‘/home/biocbuild/bbs-3.12-bioc/meat/iSEEu.Rcheck/00check.log’ for details.
iSEEu.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL iSEEu ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’ * installing *source* package ‘iSEEu’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (iSEEu)
iSEEu.Rcheck/tests/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw" 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. > library(testthat) > library(iSEEu) Loading required package: iSEE Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB 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, 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 Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Loading required package: SingleCellExperiment > > test_check("iSEEu") snapshotDate(): 2020-10-27 see ?scRNAseq and browseVignettes('scRNAseq') for documentation loading from cache see ?scRNAseq and browseVignettes('scRNAseq') for documentation loading from cache see ?scRNAseq and browseVignettes('scRNAseq') for documentation loading from cache Loading required package: ggplot2 [ FAIL 0 | WARN 4 | SKIP 0 | PASS 253 ] > > proc.time() user system elapsed 84.688 2.172 92.527
iSEEu.Rcheck/iSEEu-Ex.timings
name | user | system | elapsed | |
AggregatedDotPlot | 25.016 | 0.640 | 28.338 | |
DynamicMarkerTable-class | 16.572 | 0.212 | 17.565 | |
DynamicReducedDimensionPlot-class | 15.252 | 0.188 | 16.226 | |
FeatureSetTable-class | 19.200 | 0.316 | 21.079 | |
GeneSetTable-class | 17.472 | 0.212 | 18.886 | |
LogFCLogFCPlot-class | 0.044 | 0.000 | 0.047 | |
MAPlot-class | 0.036 | 0.000 | 0.032 | |
ReducedDimensionHexPlot-class | 16.404 | 0.220 | 17.419 | |
VolcanoPlot-class | 0.052 | 0.000 | 0.051 | |
createGeneSetCommands | 0 | 0 | 0 | |
global-FeatureSetCommands | 0.000 | 0.000 | 0.001 | |
global-TableExtraFields | 0.000 | 0.000 | 0.001 | |
globals-PValuePattern | 0 | 0 | 0 | |
modeEmpty | 0.628 | 0.000 | 0.692 | |
modeGating | 12.864 | 0.224 | 13.867 | |
modeReducedDim | 21.212 | 0.228 | 22.312 | |
utils-de | 0.000 | 0.000 | 0.002 | |
utils-geneset | 0.008 | 0.000 | 0.006 | |