| Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-03-18 11:07:34 -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 gCrisprTools package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gCrisprTools.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 707/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| gCrisprTools 2.1.3 (landing page) Russell Bainer
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
| Package: gCrisprTools |
| Version: 2.1.3 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:gCrisprTools.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings gCrisprTools_2.1.3.tar.gz |
| StartedAt: 2022-03-17 19:08:47 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:13:50 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 302.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: gCrisprTools.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:gCrisprTools.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings gCrisprTools_2.1.3.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/gCrisprTools.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 'gCrisprTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'gCrisprTools' version '2.1.3'
* 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 'gCrisprTools' can be installed ... OK
* checking installed package size ... NOTE
installed size is 8.9Mb
sub-directories of 1Mb or more:
data 2.6Mb
* 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 ... NOTE
ct.seas: no visible global function definition for 'ct.compileSparrow'
Undefined global functions or variables:
ct.compileSparrow
* 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 data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'gCrisprTools-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ct.seas
> ### Title: Geneset Enrichment within a CRISPR screen using 'sparrow'
> ### Aliases: ct.seas
>
> ### ** Examples
>
> data('resultsDF')
> gdb <- sparrow::getMSigGeneSetDb(collection = 'h', species = 'human', id.type = 'entrez')
> ct.seas(list('longer' = resultsDF, 'shorter' = resultsDF[1:10000,]), gdb)
GeneSetDb feature_ids coded as geneIDs.
Depending on the composition of your library, you might consider switching to a target-level analysis; see ?ct.GREATdb() for details.
Removed genes absent from the provided GeneSetDb.
Warning in fn(gsd, x, design, contrast, logFC = logFC, use.treat = use.treat, :
logical column to identify enriched genes not found: selectedsetting `significant` column manually
Warning in ora(logFC, gsd, selected = selected, groups = groups, feature.bias = feature.bias, :
Only 0 / 1features found in 'dat'
Warning in sparrow::seas(x = ipt, gsd = gdb, methods = c("ora", "fgsea"), :
The following GSEA methods failed and are removed from the downstream result: ora,fgsea
Error in names(results) <- sub("\\.all$", "", names(results)) :
attempt to set an attribute on NULL
Calls: ct.seas -> lapply -> FUN -> <Anonymous>
Warning in sparrow::seas(x = ipt, gsd = gdb, methods = c("ora", "fgsea"), :
An error in `seas` stopped it from finishing ...
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'unit.tests.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: 1 ERROR, 2 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/gCrisprTools.Rcheck/00check.log'
for details.
gCrisprTools.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL gCrisprTools
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'gCrisprTools' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'gCrisprTools'
finding HTML links ... done
aln html
ann html
appendDateAndExt html
ct.CAT html
ct.DirectionalTests html
ct.GCbias html
ct.GREATdb html
ct.PRC html
ct.ROC html
ct.RRAaPvals html
ct.RRAalpha html
ct.RRAalphaBatch html
ct.alignmentChart html
ct.alphaBeta html
ct.applyAlpha html
ct.buildSE html
ct.compareContrasts html
ct.contrastBarchart html
ct.drawColorLegend html
ct.drawFlat html
ct.ecdf html
ct.expandAnnotation html
ct.exprsColor html
ct.filterReads html
ct.gRNARankByReplicate html
ct.generateResults html
ct.guideCDF html
ct.inputCheck html
ct.keyCheck html
ct.makeContrastReport html
ct.makeQCReport html
ct.makeReport html
ct.makeRhoNull html
ct.normalizeBySlope html
ct.normalizeFQ html
ct.normalizeGuides html
ct.normalizeMedians html
ct.normalizeNTC html
ct.normalizeSpline html
ct.numcores html
ct.parseGeneSymbol html
ct.prepareAnnotation html
ct.preprocessFit html
ct.rankSimple html
ct.rawCountDensities html
ct.regularizeContrasts html
ct.resultCheck html
ct.scatter html
ct.seas html
ct.seasPrep html
ct.signalSummary html
ct.simpleResult html
ct.softLog html
ct.stackGuides html
ct.targetSetEnrichment html
ct.topTargets html
ct.upSet html
ct.viewControls html
ct.viewGuides html
dir.writable html
es html
essential.genes html
fit html
gCrisprTools-package html
initOutDir html
renderReport html
resultsDF 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 (gCrisprTools)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'RUVcorr' is missing or broken
done
gCrisprTools.Rcheck/tests/unit.tests.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.
> #require("BiocGenerics", quietly = TRUE)
> BiocGenerics:::testPackage("gCrisprTools")
RUNIT TEST PROTOCOL -- Thu Mar 17 19:13:40 2022
***********************************************
Number of test functions: 0
Number of errors: 0
Number of failures: 0
1 Test Suite :
gCrisprTools RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
5.20 0.40 5.59
gCrisprTools.Rcheck/gCrisprTools-Ex.timings
| name | user | system | elapsed | |
| aln | 0.02 | 0.00 | 0.01 | |
| ann | 0.06 | 0.00 | 0.06 | |
| ct.CAT | 1.46 | 0.12 | 1.58 | |
| ct.DirectionalTests | 0.37 | 0.13 | 0.50 | |
| ct.GCbias | 6.42 | 0.42 | 6.89 | |
| ct.GREATdb | 21.86 | 3.39 | 25.23 | |
| ct.PRC | 1.61 | 0.25 | 1.86 | |
| ct.ROC | 0.88 | 0.00 | 0.88 | |
| ct.RRAaPvals | 0.36 | 0.09 | 0.45 | |
| ct.RRAalpha | 0.17 | 0.00 | 0.17 | |
| ct.alignmentChart | 0.02 | 0.00 | 0.02 | |
| ct.alphaBeta | 0 | 0 | 0 | |
| ct.applyAlpha | 0.01 | 0.00 | 0.01 | |
| ct.buildSE | 0.27 | 0.02 | 0.28 | |
| ct.compareContrasts | 7.43 | 1.76 | 9.21 | |
| ct.contrastBarchart | 4.13 | 0.03 | 4.15 | |
| ct.expandAnnotation | 0.03 | 0.02 | 0.05 | |
| ct.filterReads | 0.17 | 0.06 | 0.24 | |
| ct.gRNARankByReplicate | 0.36 | 0.06 | 0.42 | |
| ct.generateResults | 0.33 | 0.05 | 0.37 | |
| ct.guideCDF | 10.62 | 12.08 | 22.71 | |
| ct.keyCheck | 0.11 | 0.02 | 0.12 | |
| ct.makeContrastReport | 7.07 | 6.10 | 13.92 | |
| ct.makeQCReport | 2.64 | 2.52 | 5.72 | |
| ct.makeReport | 12.42 | 21.97 | 35.44 | |
| ct.makeRhoNull | 0 | 0 | 0 | |
| ct.normalizeBySlope | 1.09 | 0.08 | 1.17 | |
| ct.normalizeFQ | 0.81 | 0.01 | 0.82 | |
| ct.normalizeGuides | 2.94 | 0.50 | 3.44 | |
| ct.normalizeMedians | 0.70 | 0.21 | 0.91 | |
| ct.normalizeNTC | 0.70 | 0.06 | 0.76 | |
| ct.normalizeSpline | 0.91 | 0.08 | 0.99 | |
| ct.parseGeneSymbol | 0 | 0 | 0 | |
| ct.prepareAnnotation | 0.41 | 0.04 | 0.45 | |
| ct.preprocessFit | 1.17 | 0.02 | 1.19 | |
| ct.rankSimple | 2.61 | 0.00 | 2.61 | |
| ct.rawCountDensities | 0.09 | 0.01 | 0.11 | |
| ct.regularizeContrasts | 0.06 | 0.00 | 0.06 | |
| ct.resultCheck | 0.05 | 0.00 | 0.05 | |
| ct.scatter | 0.36 | 0.00 | 0.36 | |