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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Rtpca.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings Rtpca_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/Rtpca.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Rtpca/DESCRIPTION' ... OK
* this is package 'Rtpca' version '1.5.0'
* package encoding: UTF-8
* 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 'Rtpca' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
Namespace in Imports field not imported from: 'tibble'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.getRandomProteinPairs: no visible binding for global variable 'pair'
Undefined global functions or variables:
  pair
* 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 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 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: 2 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/Rtpca.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL Rtpca
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'Rtpca' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Rtpca'
    finding HTML links ... done
    CommonFeatures-tpcaResult-method        html  
    ComplexAnnotation-tpcaResult-method     html  
    ComplexBackgroundDistributionList-tpcaResult-method
                                            html  
    ComplexRocTable-tpcaResult-method       html  
    ContrastCondName-tpcaResult-method      html  
    ContrastDistMat-tpcaResult-method       html  
    ContrastList-tpcaResult-method          html  
    CtrlCondName-tpcaResult-method          html  
    DistMat-tpcaResult-method               html  
    DistMethod-tpcaResult-method            html  
    ObjList-tpcaResult-method               html  
    PPiAnnotation-tpcaResult-method         html  
    PPiRocTable-tpcaResult-method           html  
    PPiRocTableAnno-tpcaResult-method       html  
    SetCommonFeatures-tpcaResult-method     html  
    SetComplexAnnotation-tpcaResult-method
                                            html  
    SetComplexBackgroundDistributionList-tpcaResult-method
                                            html  
    SetComplexRocTable-tpcaResult-method    html  
    SetContrastCondName-tpcaResult-method   html  
    SetContrastDistMat-tpcaResult-method    html  
    SetCtrlCondName-tpcaResult-method       html  
    SetDiffTpcaResultTable-tpcaResult-method
                                            html  
    SetDistMat-tpcaResult-method            html  
    SetDistMethod-tpcaResult-method         html  
    SetPPiRocTable-tpcaResult-method        html  
    SetPPiRocTableAnno-tpcaResult-method    html  
    SetSummaryMethod-tpcaResult-method      html  
    SetTpcaResultTable-tpcaResult-method    html  
    SummaryMethod-tpcaResult-method         html  
    createDistMat                           html  
    diffTpcaResultTable-tpcaResult-method   html  
    ori_et_al_complex_ppis                  html  
    ori_et_al_complexes_df                  html  
    plotComplexRoc                          html  
    plotDiffTpcaVolcano                     html  
    plotPPiProfiles                         html  
    plotPPiRoc                              html  
    plotTpcaVolcano                         html  
    runDiffTPCA                             html  
    runTPCA                                 html  
    string_ppi_df                           html  
    tpcaResult-class                        html  
    tpcaResultTable-tpcaResult-method       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
* DONE (Rtpca)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'vissE' is missing or broken
 done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(Rtpca)
Loading required package: dplyr

Attaching package: 'dplyr'

The following object is masked from 'package:testthat':

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: tidyr

Attaching package: 'tidyr'

The following object is masked from 'package:testthat':

    matches

> 
> test_check("Rtpca")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 38 ]
> 
> proc.time()
   user  system elapsed 
   3.64    0.25    3.87