Charlotte Soneson
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/compcodeR |
| git_branch: master |
| git_last_commit: 730c4d0 |
| git_last_commit_date: 2022-01-24 06:27:05 -0400 (Mon, 24 Jan 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:14 -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 compcodeR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/compcodeR.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 379/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| compcodeR 1.31.1 (landing page) Charlotte Soneson
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: compcodeR |
| Version: 1.31.1 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:compcodeR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings compcodeR_1.31.1.tar.gz |
| StartedAt: 2022-03-17 18:47:32 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:50:36 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 184.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: compcodeR.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:compcodeR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings compcodeR_1.31.1.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/compcodeR.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 'compcodeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'compcodeR' version '1.31.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'rpanel'
* 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 'compcodeR' 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
NBPSeq.createRmd 39.90 2.16 42.08
DESeq2.createRmd 12.34 0.77 13.16
EBSeq.createRmd 9.11 0.09 9.24
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Complete output:
> if (requireNamespace("testthat", quietly = TRUE)) {
+
+ library(testthat)
+ library(compcodeR)
+
+ test_check("compcodeR")
+
+ }
Loading required package: sm
Package 'sm', version 2.2-5.7: type help(sm) for summary information
* 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 ERROR, 1 NOTE
See
'D:/biocbuild/bbs-3.15-bioc/meat/compcodeR.Rcheck/00check.log'
for details.
compcodeR.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL compcodeR
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'compcodeR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'compcodeR'
finding HTML links ... done
DESeq2.createRmd html
DESeq2.length.createRmd html
DSS.createRmd html
EBSeq.createRmd html
NBPSeq.createRmd html
NB_to_PLN html
NOISeq.prenorm.createRmd html
TCC.createRmd html
add_replicates html
baySeq.createRmd html
checkDataObject html
checkParamMatrix html
checkParamVector html
checkSpecies html
checkTableConsistency html
check_compData html
check_compData_results html
check_phyloCompData html
compData-class html
compData html
compcodeR-package html
computeFactorLengths html
convertListTocompData html
convertListTophyloCompData html
convertcompDataToList html
convertphyloCompDataToList html
edgeR.GLM.createRmd html
edgeR.exact.createRmd html
extract_results_phylolm html
generateCodeHTMLs html
generateLengths html
generateLengthsPhylo html
generateSyntheticData html
getNegativeBinomialDispersion html
getNegativeBinomialMean html
getNegativeBinomialParameters html
getTree html
get_model_factor html
get_poisson_log_normal_parameters html
lengthNorm.limma.createRmd html
listcreateRmd html
logcpm.limma.createRmd html
nEffNaive html
nEffRatio html
phyloCompData-class html
phyloCompData html
phyloCompDataFromCompData html
phylolm.createRmd html
phylolm_analysis html
runComparison html
runComparisonGUI html
runDiffExp html
scale_variance_process html
show-compData-method html
show-phyloCompData-method html
show_compData html
simulateData html
simulateDataPhylo html
simulatePhyloPoissonLogNormal html
sqrtcpm.limma.createRmd html
summarizeSyntheticDataSet html
ttest.createRmd html
voom.limma.createRmd html
voom.ttest.createRmd html
writeNormalization html
** 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 (compcodeR)
Making 'packages.html' ... done
compcodeR.Rcheck/tests/testthat.Rout.fail
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.
> if (requireNamespace("testthat", quietly = TRUE)) {
+
+ library(testthat)
+ library(compcodeR)
+
+ test_check("compcodeR")
+
+ }
Loading required package: sm
Package 'sm', version 2.2-5.7: type help(sm) for summary information
compcodeR.Rcheck/compcodeR-Ex.timings
| name | user | system | elapsed | |
| DESeq2.createRmd | 12.34 | 0.77 | 13.16 | |
| DESeq2.length.createRmd | 0.48 | 0.06 | 0.55 | |
| DSS.createRmd | 4.01 | 0.21 | 4.24 | |
| EBSeq.createRmd | 9.11 | 0.09 | 9.24 | |
| NBPSeq.createRmd | 39.90 | 2.16 | 42.08 | |
| NOISeq.prenorm.createRmd | 2.42 | 0.34 | 2.81 | |
| TCC.createRmd | 2.21 | 0.11 | 2.34 | |
| baySeq.createRmd | 2.45 | 0.09 | 2.58 | |
| checkDataObject | 0.19 | 0.02 | 0.20 | |
| checkTableConsistency | 1.05 | 0.09 | 1.19 | |
| check_compData | 0.17 | 0.00 | 0.17 | |
| check_compData_results | 0.40 | 0.05 | 0.47 | |
| check_phyloCompData | 0.58 | 0.06 | 0.66 | |
| compData | 0 | 0 | 0 | |
| convertListTocompData | 0 | 0 | 0 | |
| convertListTophyloCompData | 0.02 | 0.00 | 0.01 | |
| convertcompDataToList | 2.70 | 0.16 | 2.86 | |
| convertphyloCompDataToList | 0.23 | 0.00 | 0.24 | |
| edgeR.GLM.createRmd | 2.02 | 0.06 | 2.11 | |
| edgeR.exact.createRmd | 0.58 | 0.09 | 0.67 | |
| generateCodeHTMLs | 0.51 | 0.05 | 0.64 | |
| generateSyntheticData | 0.39 | 0.02 | 0.42 | |
| lengthNorm.limma.createRmd | 0.35 | 0.01 | 0.36 | |
| listcreateRmd | 0 | 0 | 0 | |
| logcpm.limma.createRmd | 0.47 | 0.08 | 0.55 | |
| nEffRatio | 0.29 | 0.00 | 0.29 | |
| phyloCompData | 0 | 0 | 0 | |
| phylolm.createRmd | 0.46 | 0.00 | 0.46 | |
| runComparison | 1.01 | 0.06 | 1.09 | |
| runComparisonGUI | 0 | 0 | 0 | |
| runDiffExp | 0.55 | 0.02 | 0.56 | |
| show-compData-method | 2.67 | 0.08 | 2.77 | |
| show-phyloCompData-method | 0.44 | 0.00 | 0.44 | |
| sqrtcpm.limma.createRmd | 0.51 | 0.03 | 0.54 | |
| summarizeSyntheticDataSet | 0.27 | 0.00 | 0.27 | |
| ttest.createRmd | 0.45 | 0.08 | 0.59 | |
| voom.limma.createRmd | 0.51 | 0.03 | 0.58 | |
| voom.ttest.createRmd | 0.41 | 0.07 | 0.50 | |