Back to Multiple platform build/check report for BioC 3.13
ABCDEFGHIJKLMN[O]PQRSTUVWXYZ

This page was generated on 2021-10-15 15:06:15 -0400 (Fri, 15 Oct 2021).

CHECK results for OTUbase on tokay2

To the developers/maintainers of the OTUbase package:
- Please 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 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.

raw results

Package 1328/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OTUbase 1.42.0  (landing page)
Daniel Beck
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/OTUbase
git_branch: RELEASE_3_13
git_last_commit: d423dfc
git_last_commit_date: 2021-05-19 11:46:21 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: OTUbase
Version: 1.42.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OTUbase.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings OTUbase_1.42.0.tar.gz
StartedAt: 2021-10-15 03:02:47 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 03:06:45 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 238.0 seconds
RetCode: 0
Status:   OK  
CheckDir: OTUbase.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OTUbase.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings OTUbase_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/OTUbase.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'OTUbase/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'OTUbase' version '1.42.0'
* 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 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
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 ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/OTUbase.Rcheck/00check.log'
for details.



Installation output

OTUbase.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/OTUbase_1.42.0.tar.gz && rm -rf OTUbase.buildbin-libdir && mkdir OTUbase.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=OTUbase.buildbin-libdir OTUbase_1.42.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL OTUbase_1.42.0.zip && rm OTUbase_1.42.0.tar.gz OTUbase_1.42.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 87949  100 87949    0     0   553k      0 --:--:-- --:--:-- --:--:--  557k

install for i386

* installing *source* package 'OTUbase' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'OTUbase'
    finding HTML links ... done
    OTUbase-package                         html  
    OTUset-class                            html  
    TAXset-class                            html  
    abundance                               html  
    accessors                               html  
    finding level-2 HTML links ... done

    assignmentData                          html  
    clusterSamples                          html  
    other_functions                         html  
    other_generics                          html  
    readOTUset                              html  
    readTAXset                              html  
    sampleData                              html  
    subOTUset                               html  
    subTAXset                               html  
** 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

install for x64

* installing *source* package 'OTUbase' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'OTUbase' as OTUbase_1.42.0.zip
* DONE (OTUbase)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'OTUbase' successfully unpacked and MD5 sums checked

Tests output


Example timings

OTUbase.Rcheck/examples_i386/OTUbase-Ex.timings

nameusersystemelapsed
OTUset-class0.870.020.89
TAXset-class0.300.170.47
abundance0.280.100.50
accessors0.110.060.18
assignmentData0.080.030.11
clusterSamples0.110.060.17
other_functions0.040.080.11
other_generics0.070.000.10
readOTUset0.070.030.09
readTAXset0.090.040.14
sampleData0.110.000.11
subOTUset0.120.020.14
subTAXset0.070.070.14

OTUbase.Rcheck/examples_x64/OTUbase-Ex.timings

nameusersystemelapsed
OTUset-class0.550.000.55
TAXset-class0.450.050.50
abundance0.220.000.21
accessors0.080.050.13
assignmentData0.060.010.08
clusterSamples0.120.000.12
other_functions0.10.00.1
other_generics0.080.000.07
readOTUset0.070.000.08
readTAXset0.080.000.08
sampleData0.080.000.08
subOTUset0.110.000.11
subTAXset0.110.000.11