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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scAlign.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scAlign_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/scAlign.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scAlign/DESCRIPTION’ ... OK
* this is package ‘scAlign’ version ‘1.8.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'SingleCellExperiment', 'Seurat', 'tensorflow', 'purrr', 'irlba',
  'Rtsne', 'ggplot2', 'FNN'
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 for sufficient/correct file permissions ... OK
* checking whether package ‘scAlign’ 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 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
.check_all_args: no visible global function definition for ‘metadata’
.check_all_args: no visible global function definition for ‘assays’
.data_setup: no visible global function definition for ‘assays’
.data_setup: no visible global function definition for ‘assay’
PlotTSNE: no visible global function definition for ‘assays’
PlotTSNE: no visible binding for global variable ‘scAlignHSC’
PlotTSNE: no visible global function definition for ‘assay’
scAlign: no visible global function definition for ‘metadata’
scAlign: no visible global function definition for ‘metadata<-’
scAlignCreateObject: no visible global function definition for
  ‘colData<-’
scAlignCreateObject: no visible global function definition for
  ‘metadata’
scAlignCreateObject: no visible global function definition for
  ‘metadata<-’
scAlignCreateObject: no visible global function definition for ‘assays’
scAlignCreateObject: no visible global function definition for ‘assay’
scAlignCreateObject: no visible global function definition for
  ‘GetCellEmbeddings’
scAlignCreateObject: no visible global function definition for
  ‘GetGeneLoadings’
scAlignCreateObject : <anonymous>: no visible global function
  definition for ‘assay’
scAlignMulti: no visible global function definition for ‘metadata’
scAlignMulti: no visible global function definition for ‘metadata<-’
scAlignMulti: no visible global function definition for ‘assays’
scAlignMulti: no visible global function definition for ‘assay’
Undefined global functions or variables:
  GetCellEmbeddings GetGeneLoadings assay assays colData<- metadata
  metadata<- scAlignHSC
* 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 ... WARNING
Files not of a type allowed in a ‘data’ directory:
  ‘DESCRIPTION’ ‘LICENSE’ ‘NAMESPACE’ ‘NEWS’ ‘README.md’
Please use e.g. ‘inst/extdata’ for non-R data files

* checking data for non-ASCII characters ... 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 ... ERROR
Running examples in ‘scAlign-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gaussianKernel
> ### Title: Computes gaussian kernel matrix
> ### Aliases: gaussianKernel
> 
> ### ** Examples
> 
> 
> ## Input data, 100 cells x 10 features
> data = matrix(sample.int(1000, 100*10, TRUE), 100, 10)
> rownames(data) = paste0("cell", seq_len(100))
> colnames(data) = paste0("gene", seq_len(10))
> 
> result = gaussianKernel(data, nrow(data))
Error in py_call_impl(callable, dots$args, dots$keywords) : 
  ValueError: Tried to convert 'shape' to a tensor and failed. Error: Cannot convert a partially known TensorShape to a Tensor: (None, 1)

Detailed traceback:
  File "/usr/local/lib/python3.8/site-packages/tensorflow/python/util/dispatch.py", line 201, in wrapper
    return target(*args, **kwargs)
  File "/usr/local/lib/python3.8/site-packages/tensorflow/python/ops/array_ops.py", line 195, in reshape
    result = gen_array_ops.reshape(tensor, shape, name)
  File "/usr/local/lib/python3.8/site-packages/tensorflow/python/ops/gen_array_ops.py", line 8233, in reshape
    _, _, _op, _outputs = _op_def_library._apply_op_helper(
  File "/usr/local/lib/python3.8/site-packages/tensorflow/python/framework/op_def_library.py", line 486, in _apply_op_helper
    raise ValueError(
Calls: gaussianKernel ... tryCatchList -> force -> <Anonymous> -> py_call_impl
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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: 1 ERROR, 1 WARNING, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/scAlign.Rcheck/00check.log’
for details.