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This page was generated on 2024-12-02 12:04 -0500 (Mon, 02 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4739
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4482
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4510
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4462
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 1482/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OTUbase 1.56.0  (landing page)
Daniel Beck
Snapshot Date: 2024-11-28 13:00 -0500 (Thu, 28 Nov 2024)
git_url: https://git.bioconductor.org/packages/OTUbase
git_branch: RELEASE_3_20
git_last_commit: 36f950e
git_last_commit_date: 2024-10-29 09:34:46 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for OTUbase on nebbiolo2

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.

raw results


Summary

Package: OTUbase
Version: 1.56.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:OTUbase.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings OTUbase_1.56.0.tar.gz
StartedAt: 2024-11-29 04:04:05 -0500 (Fri, 29 Nov 2024)
EndedAt: 2024-11-29 04:13:34 -0500 (Fri, 29 Nov 2024)
EllapsedTime: 569.5 seconds
RetCode: 0
Status:   OK  
CheckDir: OTUbase.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:OTUbase.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings OTUbase_1.56.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/OTUbase.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/OTUbase.Rcheck/00check.log’
for details.


Installation output

OTUbase.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL OTUbase
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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)

Tests output


Example timings

OTUbase.Rcheck/OTUbase-Ex.timings

nameusersystemelapsed
OTUset-class0.2830.0600.344
TAXset-class0.2820.0460.329
abundance0.1620.0110.173
accessors0.0820.0040.087
assignmentData0.0910.0000.092
clusterSamples0.0870.0010.088
other_functions0.0710.0010.072
other_generics0.0660.0000.066
readOTUset0.0690.0010.069
readTAXset0.0680.0020.070
sampleData0.0690.0000.070
subOTUset0.0980.0010.099
subTAXset0.0990.0030.101