Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-05-16 11:04:41 -0400 (Mon, 16 May 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.2.0 (2022-04-22) -- "Vigorous Calisthenics" | 4379 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" | 4153 |
merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.0 (2022-04-22) -- "Vigorous Calisthenics" | 4220 |
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 benchdamic package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/benchdamic.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 140/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
benchdamic 1.2.0 (landing page) Matteo Calgaro
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
Package: benchdamic |
Version: 1.2.0 |
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings benchdamic_1.2.0.tar.gz |
StartedAt: 2022-05-15 18:30:52 -0400 (Sun, 15 May 2022) |
EndedAt: 2022-05-15 18:39:15 -0400 (Sun, 15 May 2022) |
EllapsedTime: 502.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: benchdamic.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings benchdamic_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/benchdamic.Rcheck’ * using R version 4.2.0 (2022-04-22) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘benchdamic/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘benchdamic’ 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 ‘benchdamic’ 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed createConcordance 7.596 0.080 7.676 plotConcordance 5.742 0.084 5.827 * 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: OK
benchdamic.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL benchdamic ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’ * installing *source* package ‘benchdamic’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’ ** testing if installed package can be loaded from final location No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’ ** testing if installed package keeps a record of temporary installation path * DONE (benchdamic)
benchdamic.Rcheck/tests/testthat.Rout
R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics" Copyright (C) 2022 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(benchdamic) Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi' > > test_check("benchdamic") it= 0, nll=95.14, log10(eps+1)=Inf, stillActive=88 it= 1, nll=95.09, log10(eps+1)=0.04, stillActive=54 it= 2, nll=93.07, log10(eps+1)=0.05, stillActive=45 it= 3, nll=91.44, log10(eps+1)=0.06, stillActive=33 it= 4, nll=89.63, log10(eps+1)=0.08, stillActive=29 it= 5, nll=89.95, log10(eps+1)=0.06, stillActive=24 it= 6, nll=91.74, log10(eps+1)=0.05, stillActive=11 it= 7, nll=91.72, log10(eps+1)=0.06, stillActive=8 it= 8, nll=91.60, log10(eps+1)=0.06, stillActive=6 it= 9, nll=91.20, log10(eps+1)=0.08, stillActive=5 it=10, nll=91.30, log10(eps+1)=0.04, stillActive=4 it=11, nll=91.44, log10(eps+1)=0.06, stillActive=3 it=12, nll=91.34, log10(eps+1)=0.02, stillActive=3 it=13, nll=91.51, log10(eps+1)=0.02, stillActive=2 it=14, nll=91.30, log10(eps+1)=0.05, stillActive=2 it=15, nll=90.93, log10(eps+1)=0.09, stillActive=2 it=16, nll=91.56, log10(eps+1)=0.00, stillActive=0 |------------(25%)----------(50%)----------(75%)----------| Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| | | | 0% | |======== | 11% | |================ | 22% | |======================= | 33% | |=============================== | 44% | |======================================= | 56% | |=============================================== | 67% | |====================================================== | 78% | |============================================================== | 89% | |======================================================================| 100% | | | 0% | |======================================================================| 100% + Running now: norm_edgeR Parameters: method=TMM * Running now: DA_limma Parameters: pseudo_count=FALSE, design=~1 + HMP_BODY_SUBSITE, coef=2, norm=TMM, weights=FALSE + Running now: norm_edgeR Parameters: method=TMM * Running now: DA_limma Parameters: pseudo_count=FALSE, design=~1 + HMP_BODY_SUBSITE, coef=2, norm=TMM, weights=FALSE + Running now: norm_edgeR Parameters: method=TMM * Running now: DA_limma Parameters: pseudo_count=FALSE, design=~1 + HMP_BODY_SUBSITE, coef=2, norm=TMM, weights=FALSE + Running now: norm_edgeR Parameters: method=TMM * Running now: DA_limma Parameters: pseudo_count=FALSE, design=~1 + HMP_BODY_SUBSITE, coef=2, norm=TMM, weights=FALSE + Running now: norm_edgeR Parameters: method=TMM * Running now: DA_limma Parameters: pseudo_count=FALSE, design=~1 + HMP_BODY_SUBSITE, coef=2, norm=TMM, weights=FALSE + Running now: norm_edgeR Parameters: method=TMM * Running now: DA_limma Parameters: pseudo_count=FALSE, design=~1 + HMP_BODY_SUBSITE, coef=2, norm=TMM, weights=FALSE + Running now: norm_edgeR Parameters: method=TMM + Running now: norm_CSS Parameters: method=median * Running now: DA_limma Parameters: pseudo_count=FALSE, design=~1 + HMP_BODY_SUBSITE, coef=2, norm=CSSmedian, weights=FALSE * Running now: DA_limma Parameters: pseudo_count=FALSE, design=~1 + HMP_BODY_SUBSITE, coef=2, norm=TMM, weights=FALSE + Running now: norm_edgeR Parameters: method=TMM + Running now: norm_CSS Parameters: method=median * Running now: DA_limma Parameters: pseudo_count=FALSE, design=~1 + HMP_BODY_SUBSITE, coef=2, norm=CSSmedian, weights=FALSE * Running now: DA_limma Parameters: pseudo_count=FALSE, design=~1 + HMP_BODY_SUBSITE, coef=2, norm=TMM, weights=FALSE + Running now: norm_edgeR Parameters: method=TMM + Running now: norm_CSS Parameters: method=median * Running now: DA_limma Parameters: pseudo_count=FALSE, design=~1 + HMP_BODY_SUBSITE, coef=2, norm=CSSmedian, weights=FALSE * Running now: DA_limma Parameters: pseudo_count=FALSE, design=~1 + HMP_BODY_SUBSITE, coef=2, norm=TMM, weights=FALSE + Running now: norm_edgeR Parameters: method=TMM + Running now: norm_DESeq2 Parameters: method=poscounts + Running now: norm_CSS Parameters: method=default + Running now: norm_TSS Parameters: method=TSS [ FAIL 0 | WARN 6 | SKIP 0 | PASS 127 ] [ FAIL 0 | WARN 6 | SKIP 0 | PASS 127 ] > > proc.time() user system elapsed 48.922 2.153 51.032
benchdamic.Rcheck/benchdamic-Ex.timings
name | user | system | elapsed | |
DA_ALDEx2 | 3.141 | 0.308 | 3.450 | |
DA_DESeq2 | 3.180 | 0.148 | 3.329 | |
DA_MAST | 0.650 | 0.052 | 0.702 | |
DA_Seurat | 1.072 | 0.024 | 1.096 | |
DA_corncob | 3.236 | 0.156 | 3.397 | |
DA_edgeR | 0.182 | 0.012 | 0.194 | |
DA_limma | 0.085 | 0.008 | 0.093 | |
DA_metagenomeSeq | 0.252 | 0.004 | 0.255 | |
RMSE | 0.001 | 0.000 | 0.001 | |
addKnowledge | 0.128 | 0.004 | 0.132 | |
areaCAT | 4.909 | 0.064 | 4.973 | |
checkNormalization | 0 | 0 | 0 | |
createColors | 0.002 | 0.003 | 0.006 | |
createConcordance | 7.596 | 0.080 | 7.676 | |
createEnrichment | 0.191 | 0.008 | 0.199 | |
createMocks | 0.002 | 0.002 | 0.004 | |
createPositives | 0.740 | 0.009 | 0.749 | |
createSplits | 0.037 | 0.000 | 0.037 | |
createTIEC | 1.675 | 0.024 | 1.699 | |
enrichmentTest | 0.087 | 0.000 | 0.087 | |
extractDA | 0.199 | 0.000 | 0.199 | |
extractStatistics | 0.171 | 0.004 | 0.175 | |
fitDM | 0.033 | 0.000 | 0.033 | |
fitHURDLE | 0.400 | 0.022 | 0.421 | |
fitModels | 1.406 | 0.062 | 1.468 | |
fitNB | 0.045 | 0.000 | 0.045 | |
fitZIG | 0.059 | 0.000 | 0.059 | |
fitZINB | 0.426 | 0.012 | 0.438 | |
getDA | 0.085 | 0.004 | 0.089 | |
getPositives | 0.087 | 0.000 | 0.087 | |
getStatistics | 0.066 | 0.009 | 0.076 | |
iterative_ordering | 0.011 | 0.001 | 0.012 | |
meanDifferences | 0.002 | 0.000 | 0.002 | |
norm_CSS | 0.086 | 0.000 | 0.086 | |
norm_DESeq2 | 0.527 | 0.001 | 0.528 | |
norm_TSS | 0.031 | 0.002 | 0.033 | |
norm_edgeR | 0.066 | 0.000 | 0.066 | |
plotConcordance | 5.742 | 0.084 | 5.827 | |
plotContingency | 0.886 | 0.004 | 0.890 | |
plotEnrichment | 0.952 | 0.000 | 0.952 | |
plotFPR | 1.207 | 0.008 | 1.216 | |
plotKS | 1.205 | 0.012 | 1.218 | |
plotMD | 2.671 | 0.016 | 2.687 | |
plotMutualFindings | 1.098 | 0.008 | 1.106 | |
plotPositives | 0.668 | 0.004 | 0.672 | |
plotQQ | 1.496 | 0.016 | 1.513 | |
plotRMSE | 1.588 | 0.008 | 1.596 | |
prepareObserved | 0.001 | 0.000 | 0.002 | |
runDA | 0.52 | 0.02 | 0.54 | |
runMocks | 0.902 | 0.004 | 0.906 | |
runNormalizations | 0.504 | 0.008 | 0.512 | |
runSplits | 3.222 | 0.036 | 3.258 | |
setNormalizations | 0.001 | 0.000 | 0.001 | |
set_ALDEx2 | 0.005 | 0.000 | 0.006 | |
set_DESeq2 | 0.003 | 0.004 | 0.006 | |
set_MAST | 0.006 | 0.000 | 0.005 | |
set_Seurat | 0.006 | 0.000 | 0.006 | |
set_corncob | 0.000 | 0.006 | 0.006 | |
set_edgeR | 0.010 | 0.001 | 0.011 | |
set_limma | 0.008 | 0.000 | 0.008 | |
set_metagenomeSeq | 0.006 | 0.000 | 0.005 | |
weights_ZINB | 0.390 | 0.012 | 0.402 | |