| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 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 788/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| genArise 1.82.0 (landing page) IFC Development Team
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
|
To the developers/maintainers of the genArise package: - 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 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: genArise |
| Version: 1.82.0 |
| 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_1.82.0.tar.gz |
| StartedAt: 2024-12-20 20:11:37 -0500 (Fri, 20 Dec 2024) |
| EndedAt: 2024-12-20 20:12:21 -0500 (Fri, 20 Dec 2024) |
| EllapsedTime: 43.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: genArise.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### 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_1.82.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/genArise.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genArise/DESCRIPTION’ ... OK
* this is package ‘genArise’ version ‘1.82.0’
* 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-3.20-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 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 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 ... 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-3.20-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/4.4-arm64/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 | 0.030 | 0.007 | 0.038 | |
| WT.dataset | 0.059 | 0.011 | 0.070 | |
| Zscore | 0.261 | 0.048 | 0.309 | |
| Zscore.plot | 0.139 | 0.007 | 0.145 | |
| a.arise | 0.004 | 0.002 | 0.006 | |
| alter.unique | 0.067 | 0.007 | 0.073 | |
| bg.correct | 0.003 | 0.002 | 0.006 | |
| cys.plot | 0.096 | 0.004 | 0.102 | |
| filter.spot | 0.065 | 0.062 | 0.127 | |
| global.norm | 0.022 | 0.003 | 0.024 | |
| grid.norm | 0.045 | 0.005 | 0.050 | |
| i.arise | 0.007 | 0.013 | 0.020 | |
| imageLimma | 0.022 | 0.004 | 0.026 | |
| m.arise | 0.004 | 0.002 | 0.007 | |
| ma.plot | 0.024 | 0.004 | 0.028 | |
| meanUnique | 0.113 | 0.041 | 0.154 | |
| r.arise | 0.004 | 0.002 | 0.005 | |
| ri.plot | 0.031 | 0.003 | 0.034 | |
| spotUnique | 0.087 | 0.035 | 0.121 | |
| trim | 0.001 | 0.000 | 0.001 | |
| write.dataSet | 0.014 | 0.003 | 0.017 | |
| write.spot | 0.019 | 0.003 | 0.021 | |
| write.zscore | 0.024 | 0.004 | 0.027 | |