Back to Multiple platform build/check report for BioC 3.20: simplified long |
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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 1482/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
OTUbase 1.56.0 (landing page) Daniel Beck
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | 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 OTUbase package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OTUbase.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: OTUbase |
Version: 1.56.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OTUbase.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OTUbase_1.56.0.tar.gz |
StartedAt: 2024-12-21 04:04:00 -0500 (Sat, 21 Dec 2024) |
EndedAt: 2024-12-21 04:07:57 -0500 (Sat, 21 Dec 2024) |
EllapsedTime: 237.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: OTUbase.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OTUbase.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OTUbase_1.56.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/OTUbase.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 ‘OTUbase/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OTUbase’ version ‘1.56.0’ * 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 ‘OTUbase’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Package in Depends field not imported from: ‘vegan’ 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 .onAttach: warning in packageDescription("OTUbase", field = "Version"): partial argument match of 'field' to 'fields' .readADF: warning in read.table(file.path(dirPath, ADF), sep = "\t", head = T): partial argument match of 'head' to 'header' .readRDP: warning in read.table(file.path(dirPath, ADF), head = F, sep = "\t", stringsAsFactors = F): partial argument match of 'head' to 'header' .readrdpfix: warning in read.table(file.path(dirPath, rdpfile), head = F, stringsAsFactors = F, sep = "\t"): partial argument match of 'head' to 'header' readTAXset: warning in read.table(file.path(dirPath, namefile), head = F, stringsAsFactors = F, sep = "\t"): partial argument match of 'head' to 'header' o_diversity: no visible global function definition for ‘diversity’ o_estimateR : <anonymous>: no visible global function definition for ‘estimateR’ clusterSamples,.OTUset: no visible global function definition for ‘vegdist’ clusterSamples,.TAXset: no visible global function definition for ‘vegdist’ Undefined global functions or variables: diversity estimateR vegdist * checking Rd files ... NOTE checkRd: (-1) abundance.Rd:24: Lost braces in \itemize; meant \describe ? checkRd: (-1) abundance.Rd:25: Lost braces in \itemize; meant \describe ? checkRd: (-1) abundance.Rd:26: Lost braces in \itemize; meant \describe ? checkRd: (-1) abundance.Rd:27: Lost braces in \itemize; meant \describe ? checkRd: (-1) abundance.Rd:28: Lost braces in \itemize; meant \describe ? checkRd: (-1) clusterSamples.Rd:27: Lost braces in \itemize; meant \describe ? checkRd: (-1) clusterSamples.Rd:28: Lost braces in \itemize; meant \describe ? checkRd: (-1) clusterSamples.Rd:29: Lost braces in \itemize; meant \describe ? checkRd: (-1) clusterSamples.Rd:30: Lost braces in \itemize; meant \describe ? checkRd: (-1) clusterSamples.Rd:31: Lost braces in \itemize; meant \describe ? checkRd: (-1) other_functions.Rd:36: Lost braces in \itemize; meant \describe ? checkRd: (-1) other_functions.Rd:38: Lost braces in \itemize; meant \describe ? checkRd: (-1) other_functions.Rd:40: Lost braces in \itemize; meant \describe ? checkRd: (-1) other_functions.Rd:42: Lost braces in \itemize; meant \describe ? checkRd: (-1) other_functions.Rd:44: Lost braces in \itemize; meant \describe ? checkRd: (-1) other_functions.Rd:46: Lost braces in \itemize; meant \describe ? checkRd: (-1) other_functions.Rd:48: Lost braces in \itemize; meant \describe ? checkRd: (-1) other_functions.Rd:50: Lost braces in \itemize; meant \describe ? checkRd: (-1) other_functions.Rd:52: Lost braces in \itemize; meant \describe ? checkRd: (-1) other_functions.Rd:54: Lost braces in \itemize; meant \describe ? * 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 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: 4 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/OTUbase.Rcheck/00check.log’ for details.
OTUbase.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL OTUbase ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘OTUbase’ ... ** using staged installation ** R ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (OTUbase)
OTUbase.Rcheck/OTUbase-Ex.timings
name | user | system | elapsed | |
OTUset-class | 0.274 | 0.034 | 0.308 | |
TAXset-class | 0.287 | 0.011 | 0.299 | |
abundance | 0.148 | 0.020 | 0.170 | |
accessors | 0.077 | 0.011 | 0.089 | |
assignmentData | 0.059 | 0.002 | 0.061 | |
clusterSamples | 0.083 | 0.003 | 0.086 | |
other_functions | 0.068 | 0.003 | 0.070 | |
other_generics | 0.061 | 0.004 | 0.071 | |
readOTUset | 0.061 | 0.002 | 0.063 | |
readTAXset | 0.057 | 0.004 | 0.061 | |
sampleData | 0.064 | 0.002 | 0.067 | |
subOTUset | 0.082 | 0.002 | 0.084 | |
subTAXset | 0.064 | 0.003 | 0.067 | |