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This page was generated on 2022-03-18 11:07:34 -0400 (Fri, 18 Mar 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" 4334
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4097
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" 4083
merida1macOS 10.14.6 Mojavex86_64R 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

CHECK results for gCrisprTools on riesling1


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.

raw results

Package 707/2090HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gCrisprTools 2.1.3  (landing page)
Russell Bainer
Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022)
git_url: https://git.bioconductor.org/packages/gCrisprTools
git_branch: master
git_last_commit: efe750a
git_last_commit_date: 2022-03-07 14:18:11 -0400 (Mon, 07 Mar 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    ERROR  
riesling1Windows Server 2019 Standard / x64  OK    OK    ERROR    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

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

Command output

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* 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.


Installation output

gCrisprTools.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL gCrisprTools
###
##############################################################################
##############################################################################


* 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

Tests output

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 

Example timings

gCrisprTools.Rcheck/gCrisprTools-Ex.timings

nameusersystemelapsed
aln0.020.000.01
ann0.060.000.06
ct.CAT1.460.121.58
ct.DirectionalTests0.370.130.50
ct.GCbias6.420.426.89
ct.GREATdb21.86 3.3925.23
ct.PRC1.610.251.86
ct.ROC0.880.000.88
ct.RRAaPvals0.360.090.45
ct.RRAalpha0.170.000.17
ct.alignmentChart0.020.000.02
ct.alphaBeta000
ct.applyAlpha0.010.000.01
ct.buildSE0.270.020.28
ct.compareContrasts7.431.769.21
ct.contrastBarchart4.130.034.15
ct.expandAnnotation0.030.020.05
ct.filterReads0.170.060.24
ct.gRNARankByReplicate0.360.060.42
ct.generateResults0.330.050.37
ct.guideCDF10.6212.0822.71
ct.keyCheck0.110.020.12
ct.makeContrastReport 7.07 6.1013.92
ct.makeQCReport2.642.525.72
ct.makeReport12.4221.9735.44
ct.makeRhoNull000
ct.normalizeBySlope1.090.081.17
ct.normalizeFQ0.810.010.82
ct.normalizeGuides2.940.503.44
ct.normalizeMedians0.700.210.91
ct.normalizeNTC0.700.060.76
ct.normalizeSpline0.910.080.99
ct.parseGeneSymbol000
ct.prepareAnnotation0.410.040.45
ct.preprocessFit1.170.021.19
ct.rankSimple2.610.002.61
ct.rawCountDensities0.090.010.11
ct.regularizeContrasts0.060.000.06
ct.resultCheck0.050.000.05
ct.scatter0.360.000.36