Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-08-27 11:46 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
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 1863/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scMultiSim 1.1.3 (landing page) Hechen i
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
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: 1.1.3 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scMultiSim.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scMultiSim_1.1.3.tar.gz |
StartedAt: 2024-08-27 00:10:47 -0400 (Tue, 27 Aug 2024) |
EndedAt: 2024-08-27 00:12:01 -0400 (Tue, 27 Aug 2024) |
EllapsedTime: 73.8 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: scMultiSim.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scMultiSim.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scMultiSim_1.1.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/scMultiSim.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘scMultiSim/DESCRIPTION’ ... OK * this is package ‘scMultiSim’ version ‘1.1.3’ * 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 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 dependencies in R code ... WARNING '::' or ':::' import not declared from: ‘BiocParallel’ 'library' or 'require' call not declared from: ‘BiocParallel’ 'library' or 'require' call to ‘BiocParallel’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * 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: 1 WARNING, 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/scMultiSim.Rcheck/00check.log’ for details.
scMultiSim.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL scMultiSim ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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 2.670 0.107 2.780
scMultiSim.Rcheck/scMultiSim-Ex.timings
name | user | system | elapsed | |
GRN_params_100 | 0.001 | 0.001 | 0.001 | |
GRN_params_1139 | 0.001 | 0.001 | 0.002 | |
Get_1region_ATAC_correlation | 0 | 0 | 0 | |
Get_ATAC_correlation | 0.098 | 0.004 | 0.103 | |
Phyla1 | 0.001 | 0.000 | 0.001 | |
Phyla3 | 0 | 0 | 0 | |
Phyla5 | 0.001 | 0.000 | 0.000 | |
True2ObservedATAC | 0.279 | 0.010 | 0.290 | |
True2ObservedCounts | 0 | 0 | 0 | |
add_expr_noise | 0.893 | 0.020 | 0.913 | |
cci_cell_type_params | 0.004 | 0.018 | 0.022 | |
dens_nonzero | 0.000 | 0.000 | 0.001 | |
divide_batches | 0.663 | 0.023 | 0.687 | |
gen_clutter | 0 | 0 | 0 | |
gene_corr_cci | 0.682 | 0.031 | 0.712 | |
gene_corr_regulator | 0.119 | 0.012 | 0.130 | |
gene_len_pool | 0.005 | 0.001 | 0.007 | |
len2nfrag | 0.330 | 0.002 | 0.332 | |
match_params | 0.008 | 0.001 | 0.008 | |
plot_cell_loc | 0.881 | 0.034 | 0.917 | |
plot_gene_module_cor_heatmap | 0.137 | 0.015 | 0.151 | |
plot_grid | 0.607 | 0.029 | 0.637 | |
plot_grn | 0.046 | 0.003 | 0.049 | |
plot_phyla | 0.080 | 0.006 | 0.086 | |
plot_rna_velocity | 0.357 | 0.011 | 0.369 | |
plot_tsne | 0.105 | 0.003 | 0.109 | |
scmultisim_help | 0.006 | 0.000 | 0.007 | |
sim_example | 0.065 | 0.003 | 0.068 | |
sim_example_spatial | 0.568 | 0.029 | 0.600 | |
sim_true_counts | 0.300 | 0.015 | 0.316 | |