Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:41 -0400 (Fri, 15 Oct 2021).
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? 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 705/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
genArise 1.68.0 (landing page) IFC Development Team
| nebbiolo1 | Linux (Ubuntu 20.04.2 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: 1.68.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:genArise.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings genArise_1.68.0.tar.gz |
StartedAt: 2021-10-14 09:55:42 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 09:56:13 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 31.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: genArise.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:genArise.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings genArise_1.68.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/genArise.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘genArise/DESCRIPTION’ ... OK * this is package ‘genArise’ version ‘1.68.0’ * 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 ‘/home/biocbuild/bbs-3.13-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 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 ‘/home/biocbuild/bbs-3.13-bioc/meat/genArise.Rcheck/00check.log’ for details.
genArise.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL genArise ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/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 | 0.032 | 0.004 | 0.036 | |
WT.dataset | 0.056 | 0.009 | 0.063 | |
Zscore | 0.279 | 0.025 | 0.295 | |
Zscore.plot | 0.092 | 0.011 | 0.103 | |
a.arise | 0.004 | 0.000 | 0.004 | |
alter.unique | 0.065 | 0.007 | 0.071 | |
bg.correct | 0.003 | 0.001 | 0.003 | |
cys.plot | 0.067 | 0.004 | 0.070 | |
filter.spot | 0.045 | 0.085 | 0.128 | |
global.norm | 0.017 | 0.000 | 0.017 | |
grid.norm | 0.028 | 0.011 | 0.038 | |
i.arise | 0.007 | 0.016 | 0.023 | |
imageLimma | 0.017 | 0.000 | 0.018 | |
m.arise | 0.003 | 0.000 | 0.004 | |
ma.plot | 0.020 | 0.000 | 0.021 | |
meanUnique | 0.106 | 0.029 | 0.128 | |
r.arise | 0.003 | 0.000 | 0.003 | |
ri.plot | 0.024 | 0.000 | 0.025 | |
spotUnique | 0.074 | 0.048 | 0.122 | |
trim | 0.000 | 0.000 | 0.001 | |
write.dataSet | 0.015 | 0.000 | 0.015 | |
write.spot | 0.023 | 0.001 | 0.023 | |
write.zscore | 0.021 | 0.008 | 0.029 | |