Matteo Calgaro
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/benchdamic |
| git_branch: RELEASE_3_14 |
| git_last_commit: 5175773 |
| git_last_commit_date: 2021-10-26 13:13:35 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:07:40 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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 139/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| benchdamic 1.0.0 (landing page) Matteo Calgaro
| nebbiolo2 | Linux (Ubuntu 20.04.4 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: benchdamic |
| Version: 1.0.0 |
| 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_1.0.0.tar.gz |
| StartedAt: 2022-04-12 10:41:50 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 10:55:01 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 790.9 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_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/benchdamic.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.0.0’
* 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 15.425 0.132 15.587
areaCAT 10.447 0.165 10.977
plotConcordance 10.481 0.069 10.737
DA_DESeq2 10.094 0.259 10.375
runSplits 5.986 0.047 6.045
DA_ALDEx2 5.108 0.641 5.761
* 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/4.1/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 4.1.3 (2022-03-10) -- "One Push-Up"
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=95.24, log10(eps+1)=Inf, stillActive=88
it= 1, nll=95.01, log10(eps+1)=0.04, stillActive=56
it= 2, nll=93.01, log10(eps+1)=0.05, stillActive=48
it= 3, nll=91.18, log10(eps+1)=0.06, stillActive=39
it= 4, nll=89.97, log10(eps+1)=0.06, stillActive=34
it= 5, nll=90.17, log10(eps+1)=0.06, stillActive=26
it= 6, nll=91.51, log10(eps+1)=0.06, stillActive=14
it= 7, nll=90.90, log10(eps+1)=0.07, stillActive=11
it= 8, nll=90.63, log10(eps+1)=0.09, stillActive=10
it= 9, nll=92.39, log10(eps+1)=0.07, stillActive=4
it=10, nll=92.35, log10(eps+1)=0.03, stillActive=4
it=11, nll=92.62, log10(eps+1)=0.06, stillActive=3
it=12, nll=92.54, log10(eps+1)=0.07, stillActive=3
it=13, nll=92.56, log10(eps+1)=0.01, stillActive=3
it=14, nll=92.94, log10(eps+1)=0.01, stillActive=1
it=15, nll=92.96, log10(eps+1)=0.01, stillActive=1
it=16, nll=92.96, log10(eps+1)=0.02, stillActive=1
it=17, nll=93.02, log10(eps+1)=0.00, stillActive=0
|------------(25%)----------(50%)----------(75%)----------|
Performing log-normalization
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
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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
84.085 3.191 87.492
benchdamic.Rcheck/benchdamic-Ex.timings
| name | user | system | elapsed | |
| DA_ALDEx2 | 5.108 | 0.641 | 5.761 | |
| DA_DESeq2 | 10.094 | 0.259 | 10.375 | |
| DA_MAST | 1.447 | 0.018 | 1.466 | |
| DA_Seurat | 1.045 | 0.025 | 1.074 | |
| DA_corncob | 2.291 | 0.102 | 2.549 | |
| DA_edgeR | 0.350 | 0.009 | 0.361 | |
| DA_limma | 0.219 | 0.006 | 0.226 | |
| DA_metagenomeSeq | 0.355 | 0.006 | 0.364 | |
| RMSE | 0.001 | 0.000 | 0.002 | |
| addKnowledge | 0.220 | 0.006 | 0.226 | |
| areaCAT | 10.447 | 0.165 | 10.977 | |
| checkNormalization | 0.000 | 0.001 | 0.000 | |
| createColors | 0.006 | 0.000 | 0.006 | |
| createConcordance | 15.425 | 0.132 | 15.587 | |
| createEnrichment | 0.341 | 0.007 | 0.348 | |
| createMocks | 0.005 | 0.004 | 0.009 | |
| createPositives | 1.267 | 0.015 | 1.286 | |
| createSplits | 0.078 | 0.003 | 0.082 | |
| createTIEC | 2.688 | 0.031 | 2.728 | |
| enrichmentTest | 0.140 | 0.004 | 0.144 | |
| extractDA | 0.336 | 0.005 | 0.342 | |
| extractStatistics | 0.404 | 0.014 | 0.418 | |
| fitDM | 0.058 | 0.002 | 0.060 | |
| fitHURDLE | 0.798 | 0.002 | 0.803 | |
| fitModels | 2.752 | 0.023 | 2.781 | |
| fitNB | 0.065 | 0.001 | 0.066 | |
| fitZIG | 0.101 | 0.001 | 0.103 | |
| fitZINB | 0.615 | 0.006 | 0.621 | |
| getDA | 0.111 | 0.012 | 0.124 | |
| getPositives | 0.104 | 0.003 | 0.107 | |
| getStatistics | 0.097 | 0.005 | 0.103 | |
| iterative_ordering | 0.017 | 0.002 | 0.018 | |
| meanDifferences | 0.003 | 0.001 | 0.004 | |
| norm_CSS | 0.133 | 0.002 | 0.135 | |
| norm_DESeq2 | 1.428 | 0.008 | 1.440 | |
| norm_TSS | 0.063 | 0.002 | 0.064 | |
| norm_edgeR | 0.059 | 0.001 | 0.060 | |
| plotConcordance | 10.481 | 0.069 | 10.737 | |
| plotContingency | 1.577 | 0.011 | 1.592 | |
| plotEnrichment | 1.497 | 0.012 | 1.555 | |
| plotFPR | 2.460 | 0.019 | 2.720 | |
| plotKS | 2.257 | 0.021 | 2.282 | |
| plotMD | 4.417 | 0.032 | 4.463 | |
| plotMutualFindings | 1.473 | 0.010 | 1.486 | |
| plotPositives | 1.206 | 0.010 | 1.216 | |
| plotQQ | 2.493 | 0.023 | 2.949 | |
| plotRMSE | 3.375 | 0.016 | 3.548 | |
| prepareObserved | 0.002 | 0.000 | 0.001 | |
| runDA | 1.698 | 0.004 | 1.704 | |
| runMocks | 1.311 | 0.013 | 1.326 | |
| runNormalizations | 1.647 | 0.004 | 1.652 | |
| runSplits | 5.986 | 0.047 | 6.045 | |
| setNormalizations | 0.000 | 0.000 | 0.001 | |
| set_ALDEx2 | 0.012 | 0.000 | 0.013 | |
| set_DESeq2 | 0.017 | 0.000 | 0.017 | |
| set_MAST | 0.012 | 0.001 | 0.013 | |
| set_Seurat | 0.012 | 0.001 | 0.012 | |
| set_corncob | 0.014 | 0.001 | 0.015 | |
| set_edgeR | 0.025 | 0.001 | 0.026 | |
| set_limma | 0.015 | 0.000 | 0.015 | |
| set_metagenomeSeq | 0.011 | 0.001 | 0.012 | |
| weights_ZINB | 0.594 | 0.004 | 0.598 | |