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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:scMultiSim.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings scMultiSim_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/scMultiSim.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘scMultiSim/DESCRIPTION’ ... OK
* this is package ‘scMultiSim’ version ‘1.2.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* 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:
  inst/shiny-app/www/.prettierrc
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 ‘scMultiSim’ 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 loading without being on the library search path ... 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
.SpatialGrid: no visible global function definition for ‘new’
.amplifyOneCell: no visible binding for global variable ‘len2nfrag’
.atacSeq: no visible binding for global variable ‘dens_nonzero’
.check_opt: no visible binding for global variable ‘val’
.check_opt: no visible binding for global variable ‘checker’
.check_opt: no visible binding for global variable ‘desc’
.check_opt: no visible binding for global variable ‘check’
.check_opt: no visible binding for global variable ‘err_msg’
.check_opt: no visible global function definition for ‘check’
.continuousCIFParamNormal : <anonymous>: no visible binding for global
  variable ‘.’
.continuousCIFParamNormal : <anonymous>: no visible binding for global
  variable ‘tips’
.continuousCIFParamNormal : <anonymous>: no visible binding for global
  variable ‘internal’
.continuousCIFParamNormal : <anonymous> : <anonymous>: no visible
  global function definition for ‘Impulsecifpertip’
.continuousCIFParamNormal : <anonymous> : <anonymous>: no visible
  binding for global variable ‘tips’
.continuousCIFParamNormal : <anonymous> : <anonymous>: no visible
  binding for global variable ‘internal’
.continuousCIFParamSpatial: no visible binding for global variable
  ‘max_layers’
.continuousCIFParamSpatial: no visible binding for global variable
  ‘paths’
.continuousCIFParamSpatial: no visible binding for global variable
  ‘cell_path’
.continuousCIFParamSpatial: no visible binding for global variable
  ‘path_len’
.continuousCIFParamSpatial: no visible binding for global variable
  ‘i_cell’
.continuousCIFParamSpatial : <anonymous>: no visible binding for global
  variable ‘.’
.continuousCIFParamSpatial : <anonymous>: no visible binding for global
  variable ‘i_cell’
.continuousCIFParamSpatial : <anonymous>: no visible binding for global
  variable ‘tips’
.continuousCIFParamSpatial : <anonymous>: no visible binding for global
  variable ‘internal’
.continuousCIFParamSpatial : <anonymous> : <anonymous>: no visible
  global function definition for ‘Impulsecifpertip’
.continuousCIFParamSpatial : <anonymous> : <anonymous>: no visible
  binding for global variable ‘tips’
.continuousCIFParamSpatial : <anonymous> : <anonymous>: no visible
  binding for global variable ‘internal’
.continuousCIFParamSpatial : <anonymous>: no visible binding for global
  variable ‘max_layers’
.continuousCIFParamSpatial : <anonymous>: no visible binding for global
  variable ‘paths’
.continuousCIFParamSpatial: no visible binding for global variable ‘id’
.continuousCIFParamSpatial: no visible binding for global variable
  ‘from’
.continuousCIFParamSpatial: no visible binding for global variable ‘to’
.continuousCIFParamSpatial: no visible binding for global variable
  ‘len’
.discreteCIF : <anonymous>: no visible binding for global variable ‘.’
.discreteCIFSpatial : <anonymous>: no visible binding for global
  variable ‘.’
.dynGRN: no visible global function definition for ‘new’
.geneEffectsByRegulator: no visible binding for global variable
  ‘target’
.geneEffectsByRegulator: no visible binding for global variable
  ‘regulator’
.geneEffectsByRegulator: no visible binding for global variable
  ‘effect’
.getPaths: no visible binding for global variable ‘tips’
.getPaths: no visible binding for global variable ‘internal’
.identityVectors: no visible binding for global variable ‘.’
.print_opt: no visible binding for global variable ‘val’
.print_opt: no visible binding for global variable ‘checker’
.print_opt: no visible binding for global variable ‘desc’
.processVelocity : get_velo: no visible binding for global variable
  ‘vx_normalized’
.processVelocity : get_velo: no visible binding for global variable
  ‘vy_normalized’
.processVelocity : get_velo: no visible binding for global variable
  ‘vx_knn_normalized’
.processVelocity : get_velo: no visible binding for global variable
  ‘vy_knn_normalized’
.regionToGeneMatrix: no visible binding for global variable ‘.’
.rnaSeq: no visible binding for global variable ‘tips’
.rnaSeq: no visible binding for global variable ‘internal’
.rnaSeq: no visible binding for global variable ‘.’
.rnaSeq: no visible binding for global variable ‘parent’
.rnaSeq: no visible binding for global variable ‘child’
.rnaSeqSpatial: no visible binding for global variable ‘tips’
.rnaSeqSpatial: no visible binding for global variable ‘internal’
.rnaVelocityCosine: no visible binding for global variable
  ‘current_counts_s_tsne’
.rnaVelocityCosine: no visible binding for global variable
  ‘future_counts_s_tsne’
.rnaVelocityCosine: no visible binding for global variable ‘vx_raw’
.rnaVelocityCosine: no visible binding for global variable ‘vy_raw’
.rnaVelocityCosine: no visible binding for global variable
  ‘vx_normalized’
.rnaVelocityCosine: no visible binding for global variable
  ‘vy_normalized’
.rnaVelocityCosine: no visible binding for global variable ‘vx_knn’
.rnaVelocityCosine: no visible binding for global variable ‘vy_knn’
.rnaVelocityCosine: no visible binding for global variable
  ‘vx_knn_normalized’
.rnaVelocityCosine: no visible binding for global variable
  ‘vy_knn_normalized’
.rnaVelocityCosine: no visible binding for global variable
  ‘future_counts_s_tsne2’
.rnaVelocityCosine: no visible binding for global variable ‘vx_raw2’
.rnaVelocityCosine: no visible binding for global variable ‘vy_raw2’
.rnaVelocityCosine: no visible binding for global variable
  ‘vx_normalized2’
.rnaVelocityCosine: no visible binding for global variable
  ‘vy_normalized2’
.rnaVelocityCosine: no visible binding for global variable ‘vx_knn2’
.rnaVelocityCosine: no visible binding for global variable ‘vy_knn2’
.rnaVelocityCosine: no visible binding for global variable
  ‘vx_knn_normalized2’
.rnaVelocityCosine: no visible binding for global variable
  ‘vy_knn_normalized2’
.rnaVelocityCosine : <anonymous>: no visible binding for global
  variable ‘vx_knn_normalized’
.rnaVelocityCosine : <anonymous>: no visible binding for global
  variable ‘vy_knn_normalized’
.rnaVelocityCosine : <anonymous>: no visible binding for global
  variable ‘vx_knn_normalized2’
.rnaVelocityCosine : <anonymous>: no visible binding for global
  variable ‘vy_knn_normalized2’
.rnaVelocityCosine: no visible binding for global variable ‘x’
.rnaVelocityCosine: no visible binding for global variable ‘y’
.summarizeExp: no visible global function definition for ‘metadata<-’
SampleDen: no visible global function definition for ‘rmultinom’
add_expr_noise: no visible binding for global variable ‘gene_len_pool’
add_outliers: no visible global function definition for ‘rowVars’
cci_cell_type_params: no visible binding for global variable ‘tips’
cci_cell_type_params: no visible binding for global variable ‘internal’
gene_coexpr_cci: no visible binding for global variable ‘name’
gene_coexpr_cci: no visible binding for global variable ‘value’
gene_corr_cci: no visible binding for global variable ‘name’
gene_corr_cci: no visible binding for global variable ‘value’
gene_corr_regulator: no visible binding for global variable ‘.’
generateSpatialLoc: no visible binding for global variable ‘paths’
generateSpatialLoc: no visible binding for global variable ‘max_layers’
generateSpatialLoc: no visible binding for global variable ‘id’
generateSpatialLoc: no visible binding for global variable ‘from’
generateSpatialLoc: no visible binding for global variable ‘to’
generateSpatialLoc: no visible binding for global variable ‘len’
generateSpatialLoc: no visible binding for global variable ‘meta’
plot_cell_loc: no visible binding for global variable ‘x’
plot_cell_loc: no visible binding for global variable ‘y’
plot_cell_loc: no visible binding for global variable ‘cell_type’
plot_cell_loc: no visible binding for global variable ‘xend’
plot_cell_loc: no visible binding for global variable ‘yend’
plot_grid: no visible binding for global variable ‘x’
plot_grid: no visible binding for global variable ‘y’
plot_grid: no visible binding for global variable ‘index’
plot_rna_velocity: no visible binding for global variable
  ‘current_counts_s_tsne’
plot_rna_velocity: no visible binding for global variable
  ‘future_counts_s_tsne’
plot_rna_velocity: no visible binding for global variable ‘vx_raw’
plot_rna_velocity: no visible binding for global variable ‘vy_raw’
plot_rna_velocity: no visible binding for global variable
  ‘vx_normalized’
plot_rna_velocity: no visible binding for global variable
  ‘vy_normalized’
plot_rna_velocity: no visible binding for global variable ‘vx_knn’
plot_rna_velocity: no visible binding for global variable ‘vy_knn’
plot_rna_velocity: no visible binding for global variable
  ‘vx_knn_normalized’
plot_rna_velocity: no visible binding for global variable
  ‘vy_knn_normalized’
plot_rna_velocity: no visible binding for global variable ‘index’
plot_tsne: no visible global function definition for ‘prcomp’
plot_tsne: no visible binding for global variable ‘x’
plot_tsne: no visible binding for global variable ‘y’
plot_tsne: no visible binding for global variable ‘index’
rna_velo_knn: no visible global function definition for ‘paired_simil’
rna_velo_knn : <anonymous>: no visible global function definition for
  ‘distMat.KernelKnn’
sim_example: no visible binding for global variable ‘GRN_params_100’
sim_example_spatial: no visible binding for global variable
  ‘GRN_params_100’
sim_true_counts: no visible binding for global variable ‘.rn_sp’
sim_true_counts: no visible binding for global variable ‘paths’
sim_true_counts: no visible binding for global variable ‘total_ncell’
Undefined global functions or variables:
  . .rn_sp GRN_params_100 Impulsecifpertip cell_path cell_type check
  checker child current_counts_s_tsne dens_nonzero desc
  distMat.KernelKnn effect err_msg from future_counts_s_tsne
  future_counts_s_tsne2 gene_len_pool i_cell id index internal len
  len2nfrag max_layers meta metadata<- name new paired_simil parent
  path_len paths prcomp regulator rmultinom rowVars target tips to
  total_ncell val value vx_knn vx_knn2 vx_knn_normalized
  vx_knn_normalized2 vx_normalized vx_normalized2 vx_raw vx_raw2 vy_knn
  vy_knn2 vy_knn_normalized vy_knn_normalized2 vy_normalized
  vy_normalized2 vy_raw vy_raw2 x xend y yend
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "prcomp", "rmultinom")
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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/scMultiSim.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL scMultiSim
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘scMultiSim’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Note: wrong number of arguments to 'sqrt' 
** 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 (scMultiSim)

R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(scMultiSim)
> 
> test_check("scMultiSim")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
  6.676   0.314   6.980