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### Running command:
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###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AMARETTO.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings AMARETTO_1.8.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/AMARETTO.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 'AMARETTO/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'AMARETTO' version '1.8.0'
* 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 'AMARETTO' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.4Mb
  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
* 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 ... 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 ... 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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                  user system elapsed
AMARETTO_Download                18.20   2.03   25.48
AMARETTO_VisualizeModule          3.35   0.06   13.68
AMARETTO_CreateModuleData         1.28   0.51   12.91
AMARETTO_ExportResults            1.44   0.25   13.40
plot_run_history                  1.39   0.06   12.88
AMARETTO_CreateRegulatorPrograms  1.25   0.07   12.92
AMARETTO_Run                      1.01   0.08   11.69
AMARETTO_EvaluateTestSet          0.98   0.03   12.83
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                  user system elapsed
AMARETTO_Download                19.09   1.76   25.87
AMARETTO_VisualizeModule          4.36   0.03   15.06
plot_run_history                  1.70   0.06   13.22
AMARETTO_ExportResults            1.48   0.17   13.30
AMARETTO_CreateRegulatorPrograms  1.28   0.05   11.75
AMARETTO_EvaluateTestSet          1.18   0.02   11.86
AMARETTO_Run                      1.02   0.07   12.34
AMARETTO_CreateModuleData         0.98   0.05   12.06
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/AMARETTO.Rcheck/00check.log'
for details.