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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NeuCA.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings NeuCA_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/NeuCA.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'NeuCA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'NeuCA' version '1.0.0'
* 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 'NeuCA' 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
* 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 ... NOTE
Package in Depends field not imported from: 'e1071'
  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
HNN_assign: no visible global function definition for 'txtProgressBar'
HNN_assign: no visible global function definition for
  'setTxtProgressBar'
HNN_assign: no visible global function definition for 'predict'
NeuCA: no visible global function definition for 'is'
NeuCA: no visible global function definition for 'assay'
NeuCA: no visible global function definition for 'predict'
SCHwrapper: no visible binding for global variable 'sd'
SampleNorm: no visible binding for global variable 'sd'
assignCT: no visible global function definition for 'na.omit'
cor.det: no visible global function definition for 'cor'
train_SCH: no visible global function definition for 'na.omit'
train_SCH: no visible global function definition for 'dist'
train_SCH: no visible global function definition for 'hclust'
Undefined global functions or variables:
  assay cor dist hclust is na.omit predict sd setTxtProgressBar
  txtProgressBar
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "cor", "dist", "hclust", "na.omit", "predict",
             "sd")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ...
** running examples for arch 'i386' ... ERROR
Running examples in 'NeuCA-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: NeuCA
> ### Title: A NEUral-network based Cell Annotation (NeuCA) tool for cell
> ###   type annotation using single-cell RNA-seq data.
> ### Aliases: NeuCA
> 
> ### ** Examples
> 
> #1. Load in example scRNA-seq data
> #Baron_scRNA is the training scRNA-seq dataset
> #Seg_scRNA is the testing scRNA-seq dataset
> data("Baron_scRNA")
> data("Seg_scRNA")
> 
> #2. Create SingleCellExperiment object as the input for NeuCA (if data are not already in SingleCellExperiment format)
> Baron_anno = data.frame(Baron_true_cell_label, row.names = colnames(Baron_counts))
> Baron_sce = SingleCellExperiment(
+     assays = list(normcounts = as.matrix(Baron_counts)),
+     colData = Baron_anno
+     )
> # use gene names as feature symbols
> rowData(Baron_sce)$feature_symbol <- rownames(Baron_sce)
> # remove features with duplicated names
> Baron_sce <- Baron_sce[!duplicated(rownames(Baron_sce)), ]
> 
> #similarly for Seg data
> Seg_anno = data.frame(Seg_true_cell_label, row.names = colnames(Seg_counts))
> Seg_sce <- SingleCellExperiment(
+     assays = list(normcounts = as.matrix(Seg_counts)),
+     colData = Seg_anno
+ )
> # use gene names as feature symbols
> rowData(Seg_sce)$feature_symbol <- rownames(Seg_sce)
> # remove features with duplicated names
> Seg_sce <- Seg_sce[!duplicated(rownames(Seg_sce)), ]
> 
> 
> #3. NeuCA training and cell type prediction
> predicted.label = NeuCA(train = Baron_sce, test = Seg_sce, model.size = "big", verbose = FALSE)
Working on scRNA-seq data cell label training and testing:
Based on correlation values, direct neural network IS adopted
Neural network: big
Error: Installation of Python not found, Python bindings not loaded.
Use reticulate::install_miniconda() if you'd like to install a Miniconda Python environment.
Execution halted
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
       user system elapsed
NeuCA 21.72  16.11   16.39
* 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: 1 ERROR, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/NeuCA.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/NeuCA_1.0.0.tar.gz && rm -rf NeuCA.buildbin-libdir && mkdir NeuCA.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=NeuCA.buildbin-libdir NeuCA_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL NeuCA_1.0.0.zip && rm NeuCA_1.0.0.tar.gz NeuCA_1.0.0.zip
###
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install for i386

* installing *source* package 'NeuCA' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'NeuCA'
    finding HTML links ... done
    Baron_counts                            html  
    NeuCA                                   html  
    Seg_counts                              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

install for x64

* installing *source* package 'NeuCA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'NeuCA' as NeuCA_1.0.0.zip
* DONE (NeuCA)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'NeuCA' successfully unpacked and MD5 sums checked