Hechen Li
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/scMultiSim |
| git_branch: RELEASE_3_20 |
| git_last_commit: 92f9425 |
| git_last_commit_date: 2024-10-29 11:30:13 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1887/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scMultiSim 1.2.0 (landing page) Hechen Li
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the scMultiSim package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scMultiSim.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: scMultiSim |
| Version: 1.2.0 |
| Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scMultiSim.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings scMultiSim_1.2.0.tar.gz |
| StartedAt: 2024-12-20 05:44:39 -0500 (Fri, 20 Dec 2024) |
| EndedAt: 2024-12-20 05:48:52 -0500 (Fri, 20 Dec 2024) |
| EllapsedTime: 252.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: scMultiSim.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scMultiSim.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings scMultiSim_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/scMultiSim.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.3.0
GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* 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 ... 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 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 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
'F:/biocbuild/bbs-3.20-bioc/meat/scMultiSim.Rcheck/00check.log'
for details.
scMultiSim.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL scMultiSim ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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)
scMultiSim.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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
8.18 0.56 10.28
scMultiSim.Rcheck/scMultiSim-Ex.timings
| name | user | system | elapsed | |
| GRN_params_100 | 0.00 | 0.01 | 0.02 | |
| GRN_params_1139 | 0.00 | 0.02 | 0.02 | |
| Get_1region_ATAC_correlation | 0 | 0 | 0 | |
| Get_ATAC_correlation | 0.89 | 0.05 | 0.94 | |
| Phyla1 | 0 | 0 | 0 | |
| Phyla3 | 0 | 0 | 0 | |
| Phyla5 | 0 | 0 | 0 | |
| True2ObservedATAC | 0.29 | 0.08 | 0.36 | |
| True2ObservedCounts | 0 | 0 | 0 | |
| add_expr_noise | 3.20 | 0.18 | 3.39 | |
| cci_cell_type_params | 0.01 | 0.04 | 0.05 | |
| dens_nonzero | 0.00 | 0.01 | 0.01 | |
| divide_batches | 2.55 | 0.08 | 2.63 | |
| gen_clutter | 0 | 0 | 0 | |
| gene_corr_cci | 2.63 | 0.17 | 2.86 | |
| gene_corr_regulator | 0.47 | 0.13 | 0.59 | |
| gene_len_pool | 0.00 | 0.03 | 0.03 | |
| len2nfrag | 1.40 | 0.08 | 1.49 | |
| match_params | 0.02 | 0.00 | 0.01 | |
| plot_cell_loc | 2.42 | 0.14 | 2.57 | |
| plot_gene_module_cor_heatmap | 0.61 | 0.04 | 0.67 | |
| plot_grid | 2.39 | 0.10 | 2.48 | |
| plot_grn | 0.11 | 0.00 | 0.11 | |
| plot_phyla | 0.25 | 0.01 | 0.26 | |
| plot_rna_velocity | 1.11 | 0.05 | 1.19 | |
| plot_tsne | 0.37 | 0.03 | 0.41 | |
| scmultisim_help | 0.03 | 0.00 | 0.03 | |
| sim_example | 0.30 | 0.02 | 0.31 | |
| sim_example_spatial | 2.23 | 0.04 | 2.28 | |
| sim_true_counts | 0.80 | 0.03 | 2.14 | |