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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:octad.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings octad_1.10.0.tar.gz
###
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/octad.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'octad/DESCRIPTION' ... OK
* this is package 'octad' version '1.10.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Depends: includes the non-default packages:
  'magrittr', 'dplyr', 'ggplot2', 'edgeR', 'RUVSeq', 'DESeq2', 'limma',
  'rhdf5', 'foreach', 'Rfast', 'octad.db', 'httr', 'qpdf',
  'ExperimentHub', 'AnnotationHub', 'Biobase', 'S4Vectors'
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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'octad' 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
Packages in Depends field not imported from:
  'httr' 'qpdf'
  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
diffExp: no visible binding for global variable 'case'
diffExp: no visible binding for global variable 'control'
runsRGES: no visible binding for global variable 'RGES'
topLineEval: no visible binding for global variable 'sRGES'
topLineEval: no visible binding for global variable 'medauc'
Undefined global functions or variables:
  RGES case control medauc sRGES
* 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 ... ERROR
Running examples in 'octad-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: computeRefTissue
> ### Title: Compute correlating reference control samples.
> ### Aliases: computeRefTissue
> ### Keywords: computeRefTissue
> 
> ### ** Examples
> 
> #select data
> #load data.frame with samples included in the OCTAD database
> phenoDF=get_ExperimentHub_data('EH7274') 
see ?octad.db and browseVignettes('octad.db') for documentation
loading from cache
> HCC_primary=subset(phenoDF,cancer=='Liver Hepatocellular Carcinoma'&
+ sample.type == 'primary'&data.source == 'TCGA')
> #select cases
> case_id=HCC_primary$sample.id
> #computing reference tissue, by default using small autoEncoder,
> #but can use custom expression set,
> #by default output=TRUE and outputFolder option is empty,
> #which creates control corMatrix.csv to working directory
> control_id=computeRefTissue(case_id,outputFolder='',output=TRUE,
+ expSet = "octad",control_size = 50)
see ?octad.db and browseVignettes('octad.db') for documentation
loading from cache
Error in dir.create(outputFolder) : zero-length 'path' argument
Calls: computeRefTissue -> dir.create
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
computeCellLine 66.7   4.62   80.65
* 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
  'E:/biocbuild/bbs-3.21-bioc/meat/octad.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL octad
###
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* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'octad' ...
** this is package 'octad' version '1.10.0'
** using staged installation
** R
** data
** 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 (octad)