Matteo Calgaro
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/benchdamic |
| git_branch: master |
| git_last_commit: 7854ed4 |
| git_last_commit_date: 2021-10-26 13:13:35 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:00 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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? 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 137/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| benchdamic 1.1.0 (landing page) Matteo Calgaro
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | 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: 1.1.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:benchdamic.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings benchdamic_1.1.0.tar.gz |
| StartedAt: 2022-03-17 18:30:52 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:38:05 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 432.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: benchdamic.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:benchdamic.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings benchdamic_1.1.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/benchdamic.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'benchdamic/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'benchdamic' version '1.1.0'
* 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 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 5.82 0.03 5.84
* 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
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL benchdamic
###
##############################################################################
##############################################################################
* installing to library 'D:/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
converting help for package 'benchdamic'
finding HTML links ... done
DA_ALDEx2 html
DA_DESeq2 html
DA_MAST html
DA_Seurat html
DA_corncob html
DA_edgeR html
DA_limma html
DA_metagenomeSeq html
RMSE html
addKnowledge html
areaCAT html
checkNormalization html
createColors html
createConcordance html
createEnrichment html
createMocks html
createPositives html
createSplits html
createTIEC html
enrichmentTest html
extractDA html
extractStatistics html
fitDM html
finding level-2 HTML links ... done
fitHURDLE html
fitModels html
fitNB html
fitZIG html
fitZINB html
getDA html
getPositives html
getStatistics html
iterative_ordering html
meanDifferences html
microbial_metabolism html
norm_CSS html
norm_DESeq2 html
norm_TSS html
norm_edgeR html
plotConcordance html
plotConcordanceDendrogram html
plotConcordanceHeatmap html
plotContingency html
plotEnrichment html
plotFPR html
plotKS html
plotMD html
plotMutualFindings html
plotPositives html
plotQQ html
plotRMSE html
prepareObserved html
ps_plaque_16S html
ps_stool_16S html
runDA html
runMocks html
runNormalizations html
runSplits html
setNormalizations html
set_ALDEx2 html
set_DESeq2 html
set_MAST html
set_Seurat html
set_corncob html
set_edgeR html
set_limma html
set_metagenomeSeq html
weights_ZINB html
** 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)
Making 'packages.html' ... done
benchdamic.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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=95.84, log10(eps+1)=0.03, stillActive=45
it= 2, nll=93.78, log10(eps+1)=0.05, stillActive=43
it= 3, nll=92.34, log10(eps+1)=0.05, stillActive=35
it= 4, nll=90.81, log10(eps+1)=0.07, stillActive=31
it= 5, nll=89.86, log10(eps+1)=0.07, stillActive=28
it= 6, nll=91.65, log10(eps+1)=0.08, stillActive=12
it= 7, nll=92.44, log10(eps+1)=0.06, stillActive=4
it= 8, nll=92.38, log10(eps+1)=0.04, stillActive=4
it= 9, nll=92.50, log10(eps+1)=0.07, stillActive=3
it=10, nll=92.76, log10(eps+1)=0.04, stillActive=2
it=11, nll=92.88, log10(eps+1)=0.00, stillActive=1
it=12, nll=92.90, log10(eps+1)=0.01, stillActive=1
it=13, nll=92.88, log10(eps+1)=0.02, stillActive=1
it=14, nll=92.79, log10(eps+1)=0.06, stillActive=1
it=15, nll=92.66, log10(eps+1)=0.08, stillActive=1
it=16, nll=92.63, log10(eps+1)=0.02, stillActive=1
it=17, nll=92.80, 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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
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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 5 | SKIP 0 | PASS 127 ]
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 127 ]
>
> proc.time()
user system elapsed
42.60 3.23 45.82
benchdamic.Rcheck/benchdamic-Ex.timings
| name | user | system | elapsed | |
| DA_ALDEx2 | 2.38 | 1.28 | 3.66 | |
| DA_DESeq2 | 4.39 | 0.03 | 4.45 | |
| DA_MAST | 0.53 | 0.01 | 0.54 | |
| DA_Seurat | 0.56 | 0.05 | 0.61 | |
| DA_corncob | 1.16 | 0.05 | 1.21 | |
| DA_edgeR | 0.17 | 0.00 | 0.17 | |
| DA_limma | 0.06 | 0.00 | 0.06 | |
| DA_metagenomeSeq | 0.19 | 0.00 | 0.19 | |
| RMSE | 0 | 0 | 0 | |
| addKnowledge | 0.11 | 0.00 | 0.11 | |
| areaCAT | 4.15 | 0.01 | 4.17 | |
| checkNormalization | 0 | 0 | 0 | |
| createColors | 0 | 0 | 0 | |
| createConcordance | 5.82 | 0.03 | 5.84 | |
| createEnrichment | 0.14 | 0.00 | 0.14 | |
| createMocks | 0 | 0 | 0 | |
| createPositives | 0.59 | 0.02 | 0.61 | |
| createSplits | 0.05 | 0.00 | 0.05 | |
| createTIEC | 1.26 | 0.02 | 1.28 | |
| enrichmentTest | 0.06 | 0.00 | 0.06 | |
| extractDA | 0.13 | 0.00 | 0.13 | |
| extractStatistics | 0.16 | 0.01 | 0.17 | |
| fitDM | 0.03 | 0.00 | 0.03 | |
| fitHURDLE | 0.29 | 0.00 | 0.30 | |
| fitModels | 1.11 | 0.00 | 1.11 | |
| fitNB | 0.05 | 0.00 | 0.05 | |
| fitZIG | 0.06 | 0.00 | 0.06 | |
| fitZINB | 0.44 | 0.00 | 0.44 | |
| getDA | 0.04 | 0.02 | 0.06 | |
| getPositives | 0.05 | 0.01 | 0.06 | |
| getStatistics | 0.05 | 0.00 | 0.05 | |
| iterative_ordering | 0.01 | 0.00 | 0.01 | |
| meanDifferences | 0 | 0 | 0 | |
| norm_CSS | 0.05 | 0.00 | 0.05 | |
| norm_DESeq2 | 0.58 | 0.00 | 0.58 | |
| norm_TSS | 0.01 | 0.00 | 0.01 | |
| norm_edgeR | 0.03 | 0.00 | 0.03 | |
| plotConcordance | 4.68 | 0.00 | 4.75 | |
| plotContingency | 0.75 | 0.00 | 0.83 | |
| plotEnrichment | 0.76 | 0.00 | 0.77 | |
| plotFPR | 1.28 | 0.03 | 1.33 | |
| plotKS | 1.22 | 0.00 | 1.22 | |
| plotMD | 2.08 | 0.02 | 2.09 | |
| plotMutualFindings | 0.81 | 0.03 | 0.88 | |
| plotPositives | 0.53 | 0.00 | 0.53 | |
| plotQQ | 1.18 | 0.00 | 1.18 | |
| plotRMSE | 1.96 | 0.00 | 1.96 | |
| prepareObserved | 0 | 0 | 0 | |
| runDA | 0.57 | 0.00 | 0.57 | |
| runMocks | 0.7 | 0.0 | 0.7 | |
| runNormalizations | 0.58 | 0.00 | 0.58 | |
| runSplits | 2.86 | 0.00 | 2.86 | |
| setNormalizations | 0 | 0 | 0 | |
| set_ALDEx2 | 0.02 | 0.00 | 0.02 | |
| set_DESeq2 | 0.03 | 0.00 | 0.03 | |
| set_MAST | 0.02 | 0.00 | 0.02 | |
| set_Seurat | 0 | 0 | 0 | |
| set_corncob | 0.01 | 0.00 | 0.01 | |
| set_edgeR | 0.02 | 0.00 | 0.02 | |
| set_limma | 0 | 0 | 0 | |
| set_metagenomeSeq | 0.01 | 0.00 | 0.01 | |
| weights_ZINB | 0.33 | 0.00 | 0.33 | |