Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-24 09:03 -0400 (Wed, 24 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4747 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4489 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4518 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4467 |
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 |
Package 1524/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Samuel Zimmerman
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the pathVar package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pathVar.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: pathVar |
Version: 1.34.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:pathVar.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings pathVar_1.34.0.tar.gz |
StartedAt: 2024-07-22 03:28:38 -0400 (Mon, 22 Jul 2024) |
EndedAt: 2024-07-22 03:31:47 -0400 (Mon, 22 Jul 2024) |
EllapsedTime: 189.4 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: pathVar.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:pathVar.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings pathVar_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/pathVar.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘pathVar/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘pathVar’ version ‘1.34.0’ * 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 ‘pathVar’ 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 code 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 loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... 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 diagnosticsVarPlots: no visible binding for global variable ‘avg’ diagnosticsVarPlots: no visible binding for global variable ‘standDev’ diagnosticsVarPlots: no visible binding for global variable ‘medAbsDev’ diagnosticsVarPlots: no visible binding for global variable ‘cv’ diagnosticsVarPlotsTwoSample: no visible binding for global variable ‘avg’ diagnosticsVarPlotsTwoSample: no visible binding for global variable ‘standDev’ diagnosticsVarPlotsTwoSample: no visible binding for global variable ‘medAbsDev’ diagnosticsVarPlotsTwoSample: no visible binding for global variable ‘cv’ pathVarOneSample: no visible binding for global variable ‘APval’ pathVarOneSample: no visible binding for global variable ‘PercOfGenesInPway’ pathVarTwoSamplesCont: no visible binding for global variable ‘APval’ pathVarTwoSamplesCont: no visible binding for global variable ‘PercOfGenesInPway’ pathVarTwoSamplesDisc: no visible binding for global variable ‘APval’ pathVarTwoSamplesDisc: no visible binding for global variable ‘PercOfGenesInPway’ plotAllTwoSampleDistributionCounts: no visible binding for global variable ‘Cluster’ plotAllTwoSampleDistributionCounts: no visible binding for global variable ‘Number_of_genes’ plotOneSample: no visible binding for global variable ‘Cluster’ plotOneSample: no visible binding for global variable ‘Number_of_genes’ plotTwoSamplesCont: no visible binding for global variable ‘PwayName’ plotTwoSamplesCont: no visible binding for global variable ‘NumOfGenesFromDataSetInPathway’ plotTwoSamplesCont: no visible binding for global variable ‘value’ plotTwoSamplesCont: no visible binding for global variable ‘..density..’ plotTwoSamplesCont: no visible binding for global variable ‘group’ plotTwoSamplesDisc: no visible binding for global variable ‘Cluster’ plotTwoSamplesDisc: no visible binding for global variable ‘Number_of_genes’ sigOneSample: no visible binding for global variable ‘APval’ sigOneSample: no visible binding for global variable ‘PwayName’ sigTwoSamplesCont: no visible binding for global variable ‘APval’ sigTwoSamplesCont: no visible binding for global variable ‘PwayName’ sigTwoSamplesDisc: no visible binding for global variable ‘APval’ sigTwoSamplesDisc: no visible binding for global variable ‘PwayName’ Undefined global functions or variables: ..density.. APval Cluster NumOfGenesFromDataSetInPathway Number_of_genes PercOfGenesInPway PwayName avg cv group medAbsDev standDev value * 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 ... ERROR Running examples in ‘pathVar-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: plotPway > ### Title: Checks if an object is from the one sample or two samples cases > ### and then plots reference distribution and the chosen pathway. > ### Aliases: plotPway > ### Keywords: methods > > ### ** Examples > > # we run the 2 samples analysis on the first 10 pathways from kegg > pways.kegg.10pways <- lapply(pways.kegg, function(x) x[1:10]) > results_2samples=pathVarTwoSamplesCont(bock,pways.kegg.10pways,groups=as.factor(c(rep(1,10),rep(2,10)))) > sigPways <- sigPway(results_2samples,0.05) > plotPway(results_2samples,"Glycolysis / Gluconeogenesis",sigPways) Error: The melt generic in data.table has been passed a data.frame, but data.table::melt currently only has a method for data.tables. Please confirm your input is a data.table, with setDT(df) or as.data.table(df). If you intend to use a method from reshape2, try installing that package first, but do note that reshape2 is superseded and is no longer actively developed. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: ... --- re-building ‘pathVar.Rnw’ using Sweave Loading required package: ggplot2 Loading required package: gridExtra Warning in fun(libname, pkgname) : Package 'pathVar' is deprecated and will be removed from Bioconductor version 3.20 `geom_smooth()` using formula = 'y ~ x' `geom_smooth()` using formula = 'y ~ x' `geom_smooth()` using formula = 'y ~ x' `geom_smooth()` using formula = 'y ~ x' `geom_smooth()` using formula = 'y ~ x' `geom_smooth()` using formula = 'y ~ x' Error: processing vignette 'pathVar.Rnw' failed with diagnostics: chunk 19 (label = dens_1) Error : The melt generic in data.table has been passed a data.frame, but data.table::melt currently only has a method for data.tables. Please confirm your input is a data.table, with setDT(df) or as.data.table(df). If you intend to use a method from reshape2, try installing that package first, but do note that reshape2 is superseded and is no longer actively developed. --- failed re-building ‘pathVar.Rnw’ SUMMARY: processing the following file failed: ‘pathVar.Rnw’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 1 NOTE See ‘/home/biocbuild/bbs-3.19-bioc/meat/pathVar.Rcheck/00check.log’ for details.
pathVar.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL pathVar ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘pathVar’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning in fun(libname, pkgname) : Package 'pathVar' is deprecated and will be removed from Bioconductor version 3.20 ** testing if installed package can be loaded from final location Warning in fun(libname, pkgname) : Package 'pathVar' is deprecated and will be removed from Bioconductor version 3.20 ** testing if installed package keeps a record of temporary installation path * DONE (pathVar)
pathVar.Rcheck/pathVar-Ex.timings
name | user | system | elapsed | |
bock | 0.014 | 0.000 | 0.015 | |
diagnosticsVarPlots | 33.439 | 0.551 | 35.446 | |
diagnosticsVarPlotsTwoSample | 18.236 | 0.284 | 19.683 | |
geneDistributionSet-class | 0.007 | 0.000 | 0.007 | |
geneDistributionSet2-class | 0.004 | 0.000 | 0.003 | |
geneDistributionSet3-class | 0.003 | 0.000 | 0.004 | |
geneSet-class | 0.003 | 0.000 | 0.002 | |
getGenes | 2.424 | 0.072 | 2.496 | |
makeDBList | 0 | 0 | 0 | |
pathVar-package | 2.306 | 0.019 | 2.326 | |
pathVarOneSample | 2.268 | 0.016 | 2.285 | |
pathVarTwoSamplesCont | 3.656 | 0.012 | 4.076 | |
pathVarTwoSamplesDisc | 1.239 | 0.000 | 1.500 | |
plotAllTwoSampleDistributionCounts | 4.710 | 0.012 | 4.886 | |