Matteo Calgaro
| Snapshot Date: 2022-06-23 13:55:15 -0400 (Thu, 23 Jun 2022) |
| git_url: https://git.bioconductor.org/packages/benchdamic |
| git_branch: RELEASE_3_15 |
| git_last_commit: a0ce080 |
| git_last_commit_date: 2022-04-26 12:19:21 -0400 (Tue, 26 Apr 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-06-24 12:07:05 -0400 (Fri, 24 Jun 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" | 4380 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" | 4156 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.0 (2022-04-22) -- "Vigorous Calisthenics" | 4221 |
| 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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings benchdamic_1.2.0.tar.gz |
| StartedAt: 2022-06-23 23:48:57 -0400 (Thu, 23 Jun 2022) |
| EndedAt: 2022-06-24 00:06:03 -0400 (Fri, 24 Jun 2022) |
| EllapsedTime: 1026.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: benchdamic.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings benchdamic_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/benchdamic.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-apple-darwin17.0 (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 18.174 0.132 18.730
plotConcordance 12.166 0.085 12.494
areaCAT 10.744 0.143 11.029
DA_DESeq2 6.907 0.278 7.238
runSplits 7.111 0.072 7.370
DA_ALDEx2 5.977 0.743 6.973
plotMD 5.679 0.037 6.039
* 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: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL benchdamic ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/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-apple-darwin17.0 (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=95.21, log10(eps+1)=Inf, stillActive=88
it= 1, nll=95.00, log10(eps+1)=0.04, stillActive=55
it= 2, nll=92.99, log10(eps+1)=0.05, stillActive=45
it= 3, nll=91.27, log10(eps+1)=0.06, stillActive=36
it= 4, nll=89.73, log10(eps+1)=0.07, stillActive=32
it= 5, nll=89.24, log10(eps+1)=0.07, stillActive=27
it= 6, nll=89.44, log10(eps+1)=0.06, stillActive=13
it= 7, nll=89.12, log10(eps+1)=0.08, stillActive=10
it= 8, nll=90.03, log10(eps+1)=0.07, stillActive=5
it= 9, nll=89.94, log10(eps+1)=0.02, stillActive=4
it=10, nll=89.89, log10(eps+1)=0.03, stillActive=3
it=11, nll=89.63, log10(eps+1)=0.07, stillActive=3
it=12, nll=89.60, log10(eps+1)=0.10, stillActive=2
it=13, nll=89.74, log10(eps+1)=0.09, stillActive=1
it=14, nll=90.05, log10(eps+1)=0.00, stillActive=0
|------------(25%)----------(50%)----------(75%)----------|
Performing log-normalization
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
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+ 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
97.285 3.586 111.648
benchdamic.Rcheck/benchdamic-Ex.timings
| name | user | system | elapsed | |
| DA_ALDEx2 | 5.977 | 0.743 | 6.973 | |
| DA_DESeq2 | 6.907 | 0.278 | 7.238 | |
| DA_MAST | 1.294 | 0.013 | 1.309 | |
| DA_Seurat | 1.205 | 0.019 | 1.236 | |
| DA_corncob | 4.048 | 0.100 | 4.245 | |
| DA_edgeR | 0.342 | 0.007 | 0.353 | |
| DA_limma | 0.152 | 0.004 | 0.156 | |
| DA_metagenomeSeq | 0.462 | 0.006 | 0.469 | |
| RMSE | 0.001 | 0.000 | 0.002 | |
| addKnowledge | 0.235 | 0.008 | 0.244 | |
| areaCAT | 10.744 | 0.143 | 11.029 | |
| checkNormalization | 0.000 | 0.000 | 0.001 | |
| createColors | 0.009 | 0.000 | 0.009 | |
| createConcordance | 18.174 | 0.132 | 18.730 | |
| createEnrichment | 0.425 | 0.006 | 0.447 | |
| createMocks | 0.006 | 0.002 | 0.007 | |
| createPositives | 1.640 | 0.020 | 1.754 | |
| createSplits | 0.111 | 0.003 | 0.124 | |
| createTIEC | 3.484 | 0.038 | 3.642 | |
| enrichmentTest | 0.167 | 0.004 | 0.173 | |
| extractDA | 0.390 | 0.005 | 0.400 | |
| extractStatistics | 0.384 | 0.006 | 0.394 | |
| fitDM | 0.071 | 0.001 | 0.072 | |
| fitHURDLE | 0.746 | 0.005 | 0.755 | |
| fitModels | 2.774 | 0.018 | 2.811 | |
| fitNB | 0.089 | 0.000 | 0.090 | |
| fitZIG | 0.106 | 0.000 | 0.107 | |
| fitZINB | 0.978 | 0.003 | 0.990 | |
| getDA | 0.160 | 0.006 | 0.168 | |
| getPositives | 0.159 | 0.003 | 0.163 | |
| getStatistics | 0.140 | 0.005 | 0.145 | |
| iterative_ordering | 0.021 | 0.001 | 0.021 | |
| meanDifferences | 0.003 | 0.000 | 0.004 | |
| norm_CSS | 0.138 | 0.001 | 0.141 | |
| norm_DESeq2 | 1.049 | 0.006 | 1.063 | |
| norm_TSS | 0.072 | 0.000 | 0.073 | |
| norm_edgeR | 0.075 | 0.001 | 0.076 | |
| plotConcordance | 12.166 | 0.085 | 12.494 | |
| plotContingency | 2.024 | 0.014 | 2.098 | |
| plotEnrichment | 1.908 | 0.011 | 1.946 | |
| plotFPR | 2.945 | 0.019 | 2.977 | |
| plotKS | 3.173 | 0.032 | 3.433 | |
| plotMD | 5.679 | 0.037 | 6.039 | |
| plotMutualFindings | 2.007 | 0.014 | 2.131 | |
| plotPositives | 1.450 | 0.009 | 1.536 | |
| plotQQ | 3.217 | 0.023 | 3.602 | |
| plotRMSE | 4.042 | 0.021 | 4.337 | |
| prepareObserved | 0.003 | 0.000 | 0.003 | |
| runDA | 1.291 | 0.011 | 1.399 | |
| runMocks | 1.792 | 0.036 | 1.930 | |
| runNormalizations | 1.187 | 0.004 | 1.257 | |
| runSplits | 7.111 | 0.072 | 7.370 | |
| setNormalizations | 0.001 | 0.001 | 0.001 | |
| set_ALDEx2 | 0.013 | 0.000 | 0.013 | |
| set_DESeq2 | 0.017 | 0.000 | 0.017 | |
| set_MAST | 0.014 | 0.001 | 0.014 | |
| set_Seurat | 0.015 | 0.000 | 0.016 | |
| set_corncob | 0.014 | 0.000 | 0.014 | |
| set_edgeR | 0.031 | 0.001 | 0.032 | |
| set_limma | 0.015 | 0.001 | 0.016 | |
| set_metagenomeSeq | 0.013 | 0.000 | 0.014 | |
| weights_ZINB | 0.976 | 0.003 | 0.983 | |