* using log directory 'd:/RCompile/CRANincoming/R-devel/gen3DNet.Rcheck'
* using R Under development (unstable) (2024-05-16 r86559 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'gen3DNet/DESCRIPTION' ... OK
* this is package 'gen3DNet' version '1.0.0.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Shamim Mollah <samollah1@gmail.com>'

New submission

Non-FOSS package license (file LICENSE)
* 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 serialization versions ... OK
* checking whether package 'gen3DNet' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... NOTE
Author field differs from that derived from Authors@R
  Author:    'Paul Morrison, Tina Tang, Charles Lu, Shamim Mollah'
  Authors@R: 'Paul Morrison [aut], Tina Tang [aut] (<https://orcid.org/0009-0002-0820-4545>), Charles Lu [aut] (<https://orcid.org/0000-0003-3450-1682>), Shamim Mollah [aut, cre] (<https://orcid.org/0000-0001-9178-8339>)'

Maintainer field differs from that derived from Authors@R
  Maintainer: 'Shamim Mollah <samollah1@gmail.com>'
  Authors@R:  'Shamim Mollah <samollah1@gmail.com>>'

* checking top-level files ... NOTE
Non-standard files/directories found at top level:
  'LICENSE.md' 'gen3DNet-manual.pdf'
* 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 loading without being on the library search path ... OK
* checking use of S3 registration ... 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
Found if() conditions comparing class() to string:
File 'gen3DNet/R/gen3DNet.R': if (class(object) == "data.frame") ...
File 'gen3DNet/R/gen3DNet.R': if (class(object) == "list") ...
Use inherits() (or maybe is()) instead.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 examples ... [21s] ERROR
Running examples in 'gen3DNet-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: create_gen3DNet
> ### Title: Create a general 3D network.
> ### Aliases: create_gen3DNet
> 
> ### ** Examples
> 
> 
> library("gen3DNet")
> histon_path <- system.file("extdata", "histon_data.csv", package="gen3DNet")
> phospho_path <- system.file("extdata", "phospho_data.csv", package="gen3DNet")
> result <- gen3DNet(
+    histon_path,
+    phospho_path,
+    nmf_nrun = 10,
+    p_val_threshold = 0.01, 
+    # k_picker = max_cophenetic
+    # k_picker = kneedle_silhouette_consensus
+    # k_picker = kneedle_cophenetic 
+    # k_picker = max_silhouette_consensus
+    # k_picker = max_cophenetic
+    # k_picker = max_ward_kl
+    k_picker = max_ward_kl
+ )
✔ Generating 3D network
✔ Running NMF
ℹ  Picking k from [ 2 , 30 ].
ℹ  Using k = 4
✔ Running PLSR
✔ Merging data...
✔ Writing to D:\temp\Rtmpqw62h2_gen3DNet_2024-05-17_23-25-55
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/D:\temp\Rtmpqw62h2_gen3DNet_2024-05-17_23-25-55/plsr/p_list.csv': Invalid argument
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: gen3DNet ... write.csv -> eval.parent -> eval -> eval -> <Anonymous> -> file
Execution halted
* checking PDF version of manual ... [13s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 ERROR, 4 NOTEs