* using log directory ‘/home/omnipath/testing/cosmosR/bioc-3.14/2022-04-20_1310/cosmosR/cosmosR.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘cosmosR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cosmosR’ version ‘1.2.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘cosmosR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   2.1Mb
* 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
* 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 dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘scales’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘cosmosR-Ex.R’ failed
The error most likely occurred in:

> ### Name: run_COSMOS_metabolism_to_signaling
> ### Title: run COSMOS metabolism to signaling
> ### Aliases: run_COSMOS_metabolism_to_signaling
> 
> ### ** Examples
> 
> CARNIVAL_options <- cosmosR::default_CARNIVAL_options()
> CARNIVAL_options$solver <- "lpSolve"
> data(toy_network)
> data(toy_signaling_input)
> data(toy_metabolic_input)
> data(toy_RNA)
> test_back <- preprocess_COSMOS_metabolism_to_signaling(meta_network = toy_network,
+ signaling_data = toy_signaling_input,
+ metabolic_data = toy_metabolic_input,
+ diff_expression_data = toy_RNA,
+ maximum_network_depth = 15,
+ remove_unexpressed_nodes = TRUE,
+ CARNIVAL_options = CARNIVAL_options
+ )
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
[1] "COSMOS: all 3 signaling nodes from data were found in the meta PKN"
[1] "COSMOS: all 3 metabolic nodes from data were found in the meta PKN"
[1] "COSMOS: 4660 of the 15919 genes in expression data were found as transcription factor target"
[1] "COSMOS: 4660 of the 5312 transcription factor targets were found in expression data"
[1] "COSMOS: removing unexpressed nodes from PKN..."
[1] "COSMOS: 0 interactions removed"
[1] "COSMOS: removing nodes that are not reachable from inputs within 15 steps"
[1] "COSMOS: 105 from  115 interactions are removed from the PKN"
[1] "COSMOS: 2 input/measured nodes are not in PKN any more: X4790, X5062 and 0 more."
[1] "COSMOS: 2 input/measured nodes are not in PKN any more: XMetab__65359___c____, XMetab__107738___m____ and 0 more."
[1] "COSMOS: removing nodes that are not observable by measurements within 15 steps"
[1] "COSMOS: 5 from  10 interactions are removed from the PKN"
[1] "COSMOS:  0 interactions are removed from the PKN based on consistency check between TF activity and gene expression"
[1] "lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers."
[1] "lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers."
--- Start of the CARNIVAL pipeline ---
13:11:14 20.04.2022 Carnival flavour: vanilla
13:11:14 20.04.2022 Generating variables for lp problem
13:11:14 20.04.2022 Done: generating variables for lp problem
Saving preprocessed data.
Done: saving parsed data: /home/omnipath/testing/cosmosR/bioc-3.14/2022-04-20_1310/cosmosR/cosmosR.Rcheck//parsedData_t13_11_14d20_04_2022n68.RData
13:11:14 20.04.2022 Generating formulation for LP problem
13:11:14 20.04.2022 Done: generating formulation for LP problem.
Saving LP file
Done: Saving LP file: /home/omnipath/testing/cosmosR/bioc-3.14/2022-04-20_1310/cosmosR/cosmosR.Rcheck//lpFile_t13_11_14d20_04_2022n68.lp
13:11:14 20.04.2022 Solving LP problem
Parsing .lp file for lpSolve
Rows: 602 Columns: 1
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (1): X1

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Error in f.obj[idx] <- coefficients : 
  NAs are not allowed in subscripted assignments
Calls: preprocess_COSMOS_metabolism_to_signaling ... prepareLPMatrixSingle -> transformObjectiveFunction
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 ...
  ‘tutorial.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/omnipath/testing/cosmosR/bioc-3.14/2022-04-20_1310/cosmosR/cosmosR.Rcheck/00check.log’
for details.