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### Running command:
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###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:AMARETTO.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings AMARETTO_1.18.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/AMARETTO.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘AMARETTO/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AMARETTO’ version ‘1.18.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘AMARETTO’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data      1.5Mb
    extdata   3.8Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
  Apache License (== 2.0) + file LICENSE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘knitr’
A package should be listed in only one of these fields.
'LinkingTo' field is unused: package has no 'src' directory
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
AMARETTO_HTMLreport: no visible binding for global variable ‘ModuleNr’
AMARETTO_HTMLreport: no visible binding for global variable ‘Weights’
AMARETTO_HTMLreport: no visible binding for global variable
  ‘RegulatorIDs’
AMARETTO_HTMLreport: no visible binding for global variable ‘TargetIDs’
AMARETTO_HTMLreport: no visible binding for global variable ‘moduleNr’
AMARETTO_HTMLreport: no visible binding for global variable ‘Testset’
AMARETTO_HTMLreport: no visible binding for global variable ‘padj’
AMARETTO_HTMLreport: no visible binding for global variable
  ‘n_Overlapping’
AMARETTO_HTMLreport: no visible binding for global variable
  ‘NumberGenes’
AMARETTO_HTMLreport: no visible binding for global variable
  ‘overlap_perc’
AMARETTO_HTMLreport: no visible binding for global variable ‘Geneset’
AMARETTO_HTMLreport: no visible binding for global variable
  ‘Description’
AMARETTO_HTMLreport: no visible binding for global variable
  ‘Geneset_length’
AMARETTO_HTMLreport: no visible binding for global variable
  ‘Overlapping_genes’
AMARETTO_HTMLreport: no visible binding for global variable ‘p_value’
AMARETTO_HTMLreport: no visible binding for global variable ‘p.value’
AMARETTO_HTMLreport: no visible binding for global variable ‘q.value’
AMARETTO_HTMLreport: no visible binding for global variable ‘Genes’
AMARETTO_HTMLreport: no visible binding for global variable ‘value’
AMARETTO_HTMLreport: no visible binding for global variable ‘Type’
AMARETTO_HTMLreport: no visible binding for global variable ‘Color’
AMARETTO_HTMLreport: no visible binding for global variable ‘Modules’
AMARETTO_HTMLreport: no visible binding for global variable
  ‘dt_gensesetsall’
GeneSetDescription: no visible binding for global variable
  ‘MsigdbMapping’
GeneSetDescription : <anonymous>: no visible binding for global
  variable ‘MsigdbMapping’
GmtFromModules: no visible binding for global variable ‘value’
GmtFromModules: no visible binding for global variable ‘variable’
GmtFromModules: no visible binding for global variable ‘GeneNames’
HyperGTestGeneEnrichment: no visible binding for global variable ‘i’
HyperGTestGeneEnrichment: no visible binding for global variable ‘j’
read_gct: no visible binding for global variable ‘Description’
Undefined global functions or variables:
  Color Description GeneNames Genes Geneset Geneset_length ModuleNr
  Modules MsigdbMapping NumberGenes Overlapping_genes RegulatorIDs
  TargetIDs Testset Type Weights dt_gensesetsall i j moduleNr
  n_Overlapping overlap_perc p.value p_value padj q.value value
  variable
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'get_firehoseData':
get_firehoseData
  Code: function(TargetDirectory = "./", TCGA_acronym_uppercase =
                 "LUAD", dataType = "stddata", dataFileTag =
                 "mRNAseq_Preprocess.Level_3", FFPE = FALSE, fileType =
                 "tar.gz", gdacURL =
                 "https://gdac.broadinstitute.org/runs/", untarUngzip =
                 TRUE, printDisease_abbr = FALSE)
  Docs: function(TargetDirectory = "./", TCGA_acronym_uppercase =
                 "LUAD", dataType = "stddata", dataFileTag =
                 "mRNAseq_Preprocess.Level_3", FFPE = FALSE, fileType =
                 "tar.gz", gdacURL =
                 "http://gdac.broadinstitute.org/runs/", untarUngzip =
                 TRUE, printDisease_abbr = FALSE)
  Mismatches in argument default values:
    Name: 'gdacURL' Code: "https://gdac.broadinstitute.org/runs/" Docs: "http://gdac.broadinstitute.org/runs/"

* 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 ... NOTE
  Note: found 152 marked UTF-8 strings
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ...

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### Running command:
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###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL AMARETTO
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* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘AMARETTO’ ...
** 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 (AMARETTO)