| Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:08:02 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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 | ||||
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To the developers/maintainers of the genArise package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/genArise.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 714/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| genArise 1.70.0 (landing page) IFC Development Team
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: genArise |
| Version: 1.70.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:genArise.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings genArise_1.70.0.tar.gz |
| StartedAt: 2022-04-12 13:31:38 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 13:32:45 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 66.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: genArise.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:genArise.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings genArise_1.70.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/genArise.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘genArise/DESCRIPTION’ ... OK * this is package ‘genArise’ version ‘1.70.0’ * 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 ‘genArise’ can be installed ... WARNING Found the following significant warnings: Note: possible error in 'pdf(paste(name, ".pdf", ': unused argument (horiz = FALSE) Note: possible error in 'pdf(paste(name, "OriginalCy3vsCy5.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "OriginalRvsI.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "OriginalMvsA.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "CorrectedCy3vsCy5.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "CorrectedRvsI.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "CorrectedMvsA.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "NormalCy3vsCy5.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "NormalRvsI.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "NormalMvsA.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "FilterCy3vsCy5.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "FilterRvsI.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "FilterMvsA.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "NoDuplicatesCy3vsCy5.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "NoDuplicatesRvsI.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "NoDuplicatesMvsA.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(name, horiz = F, ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "R&G.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "BgCy5.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "BgCy3.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "Swap.pdf", ': unused argument (horiz = F) See ‘/Users/biocbuild/bbs-3.14-bioc/meat/genArise.Rcheck/00install.out’ for details. Information on the location(s) of code generating the ‘Note’s can be obtained by re-running with environment variable R_KEEP_PKG_SOURCE set to ‘yes’. * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘methods’ A package should be listed in only one of these fields. * 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 ... NOTE Packages in Depends field not imported from: ‘locfit’ ‘tkrplot’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE genMerge: warning in assign(gene.association.file$V1[i], list(GO = gene.association.file$V2[i]), env = GMRGgenomehash): partial argument match of 'env' to 'envir' genMerge: warning in assign(des.file$V1[i], list(Description = des.file$V2[i]), env = descriptionHash): partial argument match of 'env' to 'envir' genMerge: warning in ls(env = GMRGgenomehash): partial argument match of 'env' to 'envir' genMerge: warning in get(population.file$V1[i], env = GMRGgenomehash): partial argument match of 'env' to 'envir' genMerge: warning in assign(unique.list$values[i], list(count = unique.list$lengths[i], frequence = unique.list$lengths[i]/total.no.detected.genes), env = output.hash): partial argument match of 'env' to 'envir' genMerge: warning in get(study.genes.file$V1[i], env = GMRGgenomehash): partial argument match of 'env' to 'envir' genMerge: warning in get(updownGMRGs[k], env = id.hash): partial argument match of 'env' to 'envir' genMerge: warning in assign(updownGMRGs[k], unique.list, env = id.hash): partial argument match of 'env' to 'envir' genMerge: warning in assign(updownGMRGs[k], study.genes.file$V1[i], env = id.hash): partial argument match of 'env' to 'envir' genMerge: warning in get(output2$uniqueUpDownGMRGIDs[i], env = output.hash): partial argument match of 'env' to 'envir' genMerge: warning in get(output2$uniqueUpDownGMRGIDs[k], env = descriptionHash): partial argument match of 'env' to 'envir' genMerge: warning in get(output2$uniqueUpDownGMRGIDs[k], env = id.hash): partial argument match of 'env' to 'envir' Zscore.points : <anonymous>: no visible global function definition for ‘tkrreplot’ Zscore.points : <anonymous>: possible error in pdf(paste(name, ".pdf", sep = ""), horiz = FALSE, height = 8, width = 8, title = name): unused argument (horiz = FALSE) Zscore.points: no visible global function definition for ‘tkrplot’ analysis.window : bg.question: no visible binding for '<<-' assignment to ‘op.counter’ analysis.window : bg.question: no visible binding for global variable ‘op.counter’ analysis.window : normalized.gui: no visible binding for '<<-' assignment to ‘op.counter’ analysis.window : normalized.gui: no visible binding for global variable ‘op.counter’ analysis.window : normalized.gui: no visible global function definition for ‘tkrreplot’ analysis.window : filter.gui: no visible binding for '<<-' assignment to ‘op.counter’ analysis.window : filter.gui: no visible binding for global variable ‘op.counter’ analysis.window : filter.gui: no visible global function definition for ‘tkrreplot’ analysis.window : remove.duplicates.gui: no visible binding for '<<-' assignment to ‘op.counter’ analysis.window : remove.duplicates.gui: no visible binding for global variable ‘op.counter’ analysis.window : remove.duplicates.gui: no visible global function definition for ‘tkrreplot’ analysis.window : <anonymous>: no visible global function definition for ‘tkrreplot’ analysis.window : cys.plot: no visible global function definition for ‘tkrreplot’ analysis.window : <anonymous>: possible error in pdf(paste(name, "OriginalCy3vsCy5.pdf", sep = "_"), horiz = F, height = 8, width = 8, title = paste(name, "OriginalCy3vsCy5.pdf", sep = "_")): unused argument (horiz = F) analysis.window : <anonymous>: possible error in pdf(paste(name, "OriginalRvsI.pdf", sep = "_"), horiz = F, height = 8, width = 8, title = paste(name, "OriginalRvsI.pdf", sep = "_")): unused argument (horiz = F) analysis.window : <anonymous>: possible error in pdf(paste(name, "OriginalMvsA.pdf", sep = "_"), horiz = F, height = 8, width = 8, title = paste(name, "OriginalMvsA.pdf", sep = "_")): unused argument (horiz = F) analysis.window : <anonymous>: possible error in pdf(paste(name, "CorrectedCy3vsCy5.pdf", sep = "_"), horiz = F, height = 8, width = 8, title = paste(name, "CorrectedCy3vsCy5.pdf", sep = "_")): unused argument (horiz = F) analysis.window : <anonymous>: possible error in pdf(paste(name, "CorrectedRvsI.pdf", sep = "_"), horiz = F, height = 8, width = 8, title = paste(name, "CorrectedRvsI.pdf", sep = "_")): unused argument (horiz = F) analysis.window : <anonymous>: possible error in pdf(paste(name, "CorrectedMvsA.pdf", sep = "_"), horiz = F, height = 8, width = 8, title = paste(name, "CorrectedMvsA.pdf", sep = "_")): unused argument (horiz = F) analysis.window : <anonymous>: possible error in pdf(paste(name, "NormalCy3vsCy5.pdf", sep = "_"), horiz = F, height = 8, width = 8, title = paste(name, "NormalCy3vsCy5.pdf", sep = "_")): unused argument (horiz = F) analysis.window : <anonymous>: possible error in pdf(paste(name, "NormalRvsI.pdf", sep = "_"), horiz = F, height = 8, width = 8, title = paste(name, "NormalRvsI.pdf", sep = "_")): unused argument (horiz = F) analysis.window : <anonymous>: possible error in pdf(paste(name, "NormalMvsA.pdf", sep = "_"), horiz = F, height = 8, width = 8, title = paste(name, "NormalMvsA.pdf", sep = "_")): unused argument (horiz = F) analysis.window : <anonymous>: possible error in pdf(paste(name, "FilterCy3vsCy5.pdf", sep = "_"), horiz = F, height = 8, width = 8, title = paste(name, "FilterCy3vsCy5.pdf", sep = "_")): unused argument (horiz = F) analysis.window : <anonymous>: possible error in pdf(paste(name, "FilterRvsI.pdf", sep = "_"), horiz = F, height = 8, width = 8, title = paste(name, "FilterRvsI.pdf", sep = "_")): unused argument (horiz = F) analysis.window : <anonymous>: possible error in pdf(paste(name, "FilterMvsA.pdf", sep = "_"), horiz = F, height = 8, width = 8, title = paste(name, "FilterMvsA.pdf", sep = "_")): unused argument (horiz = F) analysis.window : <anonymous>: possible error in pdf(paste(name, "NoDuplicatesCy3vsCy5.pdf", sep = "_"), horiz = F, height = 8, width = 8, title = paste(name, "NoDuplicatesCy3vsCy5.pdf", sep = "_")): unused argument (horiz = F) analysis.window : <anonymous>: possible error in pdf(paste(name, "NoDuplicatesRvsI.pdf", sep = "_"), horiz = F, height = 8, width = 8, title = paste(name, "NoDuplicatesRvsI.pdf", sep = "_")): unused argument (horiz = F) analysis.window : <anonymous>: possible error in pdf(paste(name, "NoDuplicatesMvsA.pdf", sep = "_"), horiz = F, height = 8, width = 8, title = paste(name, "NoDuplicatesMvsA.pdf", sep = "_")): unused argument (horiz = F) analysis.window: no visible global function definition for ‘tkrplot’ analysis.window: no visible binding for '<<-' assignment to ‘op.counter’ analysis.window: no visible binding for global variable ‘op.counter’ annotations: no visible global function definition for ‘print.xtable’ genArise.init: no visible binding for '<<-' assignment to ‘op.counter’ genArise.init : nuevo.project: no visible global function definition for ‘select.experiments’ global.norm: no visible global function definition for ‘locfit’ global.norm: no visible global function definition for ‘rbox’ grid.norm: no visible global function definition for ‘locfit’ grid.norm: no visible global function definition for ‘rbox’ old.project : selected.zscore: no visible global function definition for ‘tkrreplot’ old.project : save.pdf: possible error in pdf(name, horiz = F, height = 8, width = 8, title = paste(name, sep = "_")): unused argument (horiz = F) old.project : imageLimma.plot: no visible global function definition for ‘tkrreplot’ old.project : otra.funcion: no visible global function definition for ‘tkrreplot’ old.project: no visible global function definition for ‘tkrplot’ old.project : <anonymous>: no visible global function definition for ‘tkrreplot’ old.project : <anonymous>: possible error in pdf(paste(name, ".pdf", sep = ""), horiz = FALSE, height = 8, width = 8, title = name): unused argument (horiz = FALSE) principal : save.as.pdf: possible error in pdf(paste(name, "R&G.pdf", sep = "_"), horiz = F, height = 8, width = 8, title = paste(name, "R&G.pdf", sep = "_")): unused argument (horiz = F) principal : save.as.pdf: possible error in pdf(paste(name, "BgCy5.pdf", sep = "_"), horiz = F, height = 8, width = 8, title = paste(name, "BgCy5.pdf", sep = "_")): unused argument (horiz = F) principal : save.as.pdf: possible error in pdf(paste(name, "BgCy3.pdf", sep = "_"), horiz = F, height = 8, width = 8, title = paste(name, "BgCy3.pdf", sep = "_")): unused argument (horiz = F) principal : save.as.pdf: possible error in pdf(paste(name, "Swap.pdf", sep = "_"), horiz = F, height = 8, width = 8, title = paste(name, "Swap.pdf", sep = "_")): unused argument (horiz = F) principal: no visible global function definition for ‘tkrplot’ principal : <anonymous>: no visible global function definition for ‘tkrreplot’ Undefined global functions or variables: locfit op.counter print.xtable rbox select.experiments tkrplot tkrreplot * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... 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 WARNING, 3 NOTEs See ‘/Users/biocbuild/bbs-3.14-bioc/meat/genArise.Rcheck/00check.log’ for details.
genArise.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL genArise ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘genArise’ ... ** using staged installation ** R ** data ** byte-compile and prepare package for lazy loading Note: possible error in 'pdf(paste(name, ".pdf", ': unused argument (horiz = FALSE) Note: possible error in 'pdf(paste(name, ".pdf", ': unused argument (horiz = FALSE) Note: possible error in 'pdf(paste(name, "OriginalCy3vsCy5.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "OriginalRvsI.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "OriginalMvsA.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "CorrectedCy3vsCy5.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "CorrectedRvsI.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "CorrectedMvsA.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "NormalCy3vsCy5.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "NormalRvsI.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "NormalMvsA.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "FilterCy3vsCy5.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "FilterRvsI.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "FilterMvsA.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "NoDuplicatesCy3vsCy5.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "NoDuplicatesRvsI.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "NoDuplicatesMvsA.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "OriginalCy3vsCy5.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "OriginalRvsI.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "OriginalMvsA.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "CorrectedCy3vsCy5.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "CorrectedRvsI.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "CorrectedMvsA.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "NormalCy3vsCy5.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "NormalRvsI.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "NormalMvsA.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "FilterCy3vsCy5.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "FilterRvsI.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "FilterMvsA.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "NoDuplicatesCy3vsCy5.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "NoDuplicatesRvsI.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "NoDuplicatesMvsA.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(name, horiz = F, ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, ".pdf", ': unused argument (horiz = FALSE) Note: possible error in 'pdf(paste(name, "R&G.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "BgCy5.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "BgCy3.pdf", ': unused argument (horiz = F) Note: possible error in 'pdf(paste(name, "Swap.pdf", ': unused argument (horiz = F) ** help *** installing help indices ** 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 (genArise)
genArise.Rcheck/genArise-Ex.timings
| name | user | system | elapsed | |
| Simon | 0.050 | 0.009 | 0.060 | |
| WT.dataset | 0.069 | 0.017 | 0.086 | |
| Zscore | 0.515 | 0.128 | 0.630 | |
| Zscore.plot | 0.104 | 0.008 | 0.112 | |
| a.arise | 0.005 | 0.002 | 0.007 | |
| alter.unique | 0.141 | 0.016 | 0.156 | |
| bg.correct | 0.005 | 0.002 | 0.007 | |
| cys.plot | 0.094 | 0.005 | 0.099 | |
| filter.spot | 0.102 | 0.116 | 0.216 | |
| global.norm | 0.028 | 0.004 | 0.031 | |
| grid.norm | 0.075 | 0.007 | 0.082 | |
| i.arise | 0.013 | 0.024 | 0.036 | |
| imageLimma | 0.024 | 0.005 | 0.028 | |
| m.arise | 0.005 | 0.003 | 0.007 | |
| ma.plot | 0.024 | 0.003 | 0.026 | |
| meanUnique | 0.192 | 0.093 | 0.280 | |
| r.arise | 0.005 | 0.002 | 0.007 | |
| ri.plot | 0.032 | 0.004 | 0.036 | |
| spotUnique | 0.161 | 0.075 | 0.235 | |
| trim | 0.000 | 0.000 | 0.001 | |
| write.dataSet | 0.023 | 0.005 | 0.028 | |
| write.spot | 0.023 | 0.004 | 0.027 | |
| write.zscore | 0.034 | 0.004 | 0.039 | |