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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DrugVsDisease.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DrugVsDisease_2.48.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/DrugVsDisease.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DrugVsDisease/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DrugVsDisease’ version ‘2.48.0’
* 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'
 NOTE
Depends: includes the non-default packages:
  'affy', 'limma', 'biomaRt', 'ArrayExpress', 'GEOquery',
  'DrugVsDiseasedata', 'cMap2data', 'qvalue'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘DrugVsDisease’ 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 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
'library' or 'require' calls to packages already attached by Depends:
  ‘ArrayExpress’ ‘DrugVsDiseasedata’ ‘GEOquery’ ‘affy’ ‘biomaRt’
  ‘limma’ ‘qvalue’
  Please remove these calls from your code.
Namespaces in Imports field not imported from:
  ‘BiocGenerics’ ‘RUnit’ ‘annotate’ ‘hgu133a.db’ ‘hgu133a2.db’
  ‘hgu133plus2.db’ ‘xtable’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘ArrayExpress’ ‘DrugVsDiseasedata’ ‘GEOquery’ ‘affy’ ‘biomaRt’
  ‘cMap2data’ ‘limma’ ‘qvalue’
  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
.averagecluster: no visible binding for global variable ‘drugClusters’
.averagecluster: no visible binding for global variable
  ‘diseaseClusters’
.calculateES: no visible binding for global variable ‘drugRL’
.calculateES: no visible binding for global variable ‘diseaseRL’
.calculateES : <anonymous>: no visible global function definition for
  ‘qvalue’
.convertEnsembl: no visible binding for global variable
  ‘annotationlist’
.convertEnsembl: no visible global function definition for ‘useMart’
.convertEnsembl: no visible global function definition for ‘getBM’
.datafromAE: no visible global function definition for ‘ArrayExpress’
.datafromAE: no visible global function definition for ‘annotation’
.datafromAE: no visible global function definition for ‘pData’
.datafromGEO: no visible global function definition for ‘getGEO’
.datafromGEO: no visible global function definition for ‘GDS2eSet’
.datafromGEO: no visible global function definition for ‘pData’
.datafromGEO: no visible global function definition for ‘annotation’
.datafromGEO: no visible binding for global variable ‘GEOfactorvalues’
.datafromGEO: no visible global function definition for ‘exprs’
.findCluster: no visible binding for global variable ‘drugClusters’
.findCluster: no visible binding for global variable ‘diseaseClusters’
.findSignifCompounds: no visible global function definition for
  ‘qvalue’
.fitlms: no visible global function definition for ‘lmFit’
.multcontrast: no visible global function definition for
  ‘contrasts.fit’
.multcontrast: no visible global function definition for ‘eBayes’
.normalisedata: no visible global function definition for ‘rma’
.normalisedata: no visible global function definition for ‘mas5’
.readlocalAE: no visible global function definition for ‘ReadAffy’
.readlocalCEL: no visible global function definition for ‘ReadAffy’
.singlecontrast: no visible global function definition for ‘lmFit’
.singlecontrast: no visible global function definition for
  ‘contrasts.fit’
.singlecontrast: no visible global function definition for ‘eBayes’
.treatmentonlyfit: no visible global function definition for ‘lmFit’
.writecytoscape: no visible binding for global variable ‘drugClusters’
.writecytoscape: no visible binding for global variable ‘cytodrug’
.writecytoscape: no visible binding for global variable ‘druglabels’
.writecytoscape: no visible binding for global variable
  ‘diseaseClusters’
.writecytoscape: no visible binding for global variable ‘cytodisease’
.writecytoscape: no visible binding for global variable ‘diseaselabels’
generateprofiles: no visible binding for global variable ‘genelist’
generateprofiles: no visible global function definition for ‘exprs’
Undefined global functions or variables:
  ArrayExpress GDS2eSet GEOfactorvalues ReadAffy annotation
  annotationlist contrasts.fit cytodisease cytodrug diseaseClusters
  diseaseRL diseaselabels drugClusters drugRL druglabels eBayes exprs
  genelist getBM getGEO lmFit mas5 pData qvalue rma useMart
* 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 LazyData ... 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
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
classifyprofile   7.339  1.684   9.030
selectrankedlists 4.757  1.714   6.477
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  1 Test Suite : 
  DrugVsDisease RUnit Tests - 2 test functions, 0 errors, 1 failure
  FAILURE in test_.KS.drug.disease: Error in checkTrue(sum(diag(DrugVsDisease:::.KS.drug.disease(d, d))) ==  : 
    Test not TRUE
  
  
  Test files with failing tests
  
     test_.KS.drug.disease.R 
       test_.KS.drug.disease 
  
  
  Error in BiocGenerics:::testPackage("DrugVsDisease") : 
    unit tests failed for package DrugVsDisease
  Execution halted
* 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 ERROR, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/DrugVsDisease.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DrugVsDisease
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘DrugVsDisease’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (DrugVsDisease)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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.

> require("DrugVsDisease")||stop("unable to load DrugVsDisease")
Loading required package: DrugVsDisease
Loading required package: affy
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: limma

Attaching package: 'limma'

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

    plotMA

Loading required package: biomaRt
Loading required package: ArrayExpress
Loading required package: GEOquery
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: DrugVsDiseasedata
Loading required package: cMap2data

Attaching package: 'cMap2data'

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

    genelist

Loading required package: qvalue
[1] TRUE
> library(BiocGenerics)
> library(RUnit)
> BiocGenerics:::testPackage("DrugVsDisease")
Timing stopped at: 0.03 0.003 0.033
Error in checkTrue(sum(diag(DrugVsDisease:::.KS.drug.disease(d, d))) ==  : 
  Test not TRUE



RUNIT TEST PROTOCOL -- Sat Nov  9 01:22:42 2024 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 1 

 
1 Test Suite : 
DrugVsDisease RUnit Tests - 2 test functions, 0 errors, 1 failure
FAILURE in test_.KS.drug.disease: Error in checkTrue(sum(diag(DrugVsDisease:::.KS.drug.disease(d, d))) ==  : 
  Test not TRUE


Test files with failing tests

   test_.KS.drug.disease.R 
     test_.KS.drug.disease 


Error in BiocGenerics:::testPackage("DrugVsDisease") : 
  unit tests failed for package DrugVsDisease
Execution halted