Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:06 -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 1028/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
infercnv 1.22.0 (landing page) Christophe Georgescu
| 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 infercnv package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/infercnv.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: infercnv |
Version: 1.22.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:infercnv.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings infercnv_1.22.0.tar.gz |
StartedAt: 2024-12-20 04:51:39 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 05:08:30 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 1011.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: infercnv.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:infercnv.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings infercnv_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/infercnv.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-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 Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘infercnv/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘infercnv’ version ‘1.22.0’ * 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 ‘infercnv’ 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 ... NOTE Unexported object imported by a ':::' call: ‘HiddenMarkov:::makedensity’ See the note in ?`:::` about the use of this operator. * 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 ... NOTE checkRd: (-1) run.Rd:268: Lost braces; missing escapes or markup? 268 | \item{require_DE_all_normals}{If mask_nonDE_genes is set, those genes will be masked only if they are are found as DE according to test.use and mask_nonDE_pval in each of the comparisons to normal cells options: {"any", "most", "all"} (default: "any") | ^ * 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed inferCNVBayesNet 364.175 6.785 356.034 run 21.292 0.817 22.947 apply_median_filtering 13.955 0.155 15.792 plot_subclusters 1.750 3.382 5.508 * 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 ‘/Users/biocbuild/bbs-3.20-bioc/meat/infercnv.Rcheck/00check.log’ for details.
infercnv.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL infercnv ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘infercnv’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** 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 (infercnv)
infercnv.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-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. > #!/usr/bin/env Rscript > > library(testthat) > library(infercnv) > > test_check("infercnv") INFO [2024-12-20 05:08:15] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE INFO [2024-12-20 05:08:15] subtracting mean(normal) per gene per cell across all data INFO [2024-12-20 05:08:15] -subtracting expr per gene, use_bounds=TRUE INFO [2024-12-20 05:08:15] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE INFO [2024-12-20 05:08:15] subtracting mean(normal) per gene per cell across all data INFO [2024-12-20 05:08:15] -subtracting expr per gene, use_bounds=TRUE INFO [2024-12-20 05:08:15] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE INFO [2024-12-20 05:08:15] subtracting mean(normal) per gene per cell across all data INFO [2024-12-20 05:08:15] -subtracting expr per gene, use_bounds=TRUE INFO [2024-12-20 05:08:15] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE INFO [2024-12-20 05:08:15] subtracting mean(normal) per gene per cell across all data INFO [2024-12-20 05:08:15] -subtracting expr per gene, use_bounds=TRUE INFO [2024-12-20 05:08:15] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE INFO [2024-12-20 05:08:15] subtracting mean(normal) per gene per cell across all data INFO [2024-12-20 05:08:15] -subtracting expr per gene, use_bounds=TRUE INFO [2024-12-20 05:08:15] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE INFO [2024-12-20 05:08:15] subtracting mean(normal) per gene per cell across all data INFO [2024-12-20 05:08:15] -subtracting expr per gene, use_bounds=TRUE WARN [2024-12-20 05:08:15] window length < 2, returning original unmodified data WARN [2024-12-20 05:08:15] window length < 2, returning original unmodified data INFO [2024-12-20 05:08:15] ::remove_outlier_norm:Start out_method: average_bound lower_bound: -1 upper_bound: 30 INFO [2024-12-20 05:08:15] ::remove_outlier_norm: using hard thresholds: lower_bound: -1 upper_bound: 30 INFO [2024-12-20 05:08:15] ::remove_outlier_norm:Start out_method: average_bound lower_bound: 5 upper_bound: 15 INFO [2024-12-20 05:08:15] ::remove_outlier_norm: using hard thresholds: lower_bound: 5 upper_bound: 15 INFO [2024-12-20 05:08:16] ::remove_outlier_norm:Start out_method: average_bound lower_bound: NA upper_bound: NA INFO [2024-12-20 05:08:16] ::remove_outlier_norm using method: average_bound for defining outliers. INFO [2024-12-20 05:08:16] outlier bounds defined between: -0.5 - 17.75 INFO [2024-12-20 05:08:16] ::order_reduce:Start. INFO [2024-12-20 05:08:16] ::order_reduce:Start. INFO [2024-12-20 05:08:16] .order_reduce(): expr and order match. INFO [2024-12-20 05:08:16] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 10,2 Total=110 Min=1 Max=10. INFO [2024-12-20 05:08:16] ::order_reduce:Start. INFO [2024-12-20 05:08:16] .order_reduce(): expr and order match. INFO [2024-12-20 05:08:16] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 10,2 Total=110 Min=1 Max=10. INFO [2024-12-20 05:08:16] ::order_reduce:Start. INFO [2024-12-20 05:08:16] ::process_data:order_reduce:The position file and the expression file row (gene) names do not match. [ FAIL 0 | WARN 0 | SKIP 3 | PASS 39 ] ══ Skipped tests (3) ═══════════════════════════════════════════════════════════ • empty test (3): 'test_infer_cnv.R:343:1', 'test_infer_cnv.R:349:1', 'test_infer_cnv.R:355:1' [ FAIL 0 | WARN 0 | SKIP 3 | PASS 39 ] > > proc.time() user system elapsed 26.208 1.767 28.502
infercnv.Rcheck/infercnv-Ex.timings
name | user | system | elapsed | |
CreateInfercnvObject | 0.153 | 0.012 | 0.174 | |
apply_median_filtering | 13.955 | 0.155 | 15.792 | |
color.palette | 0.004 | 0.001 | 0.005 | |
filterHighPNormals | 0.023 | 0.003 | 0.028 | |
inferCNVBayesNet | 364.175 | 6.785 | 356.034 | |
plot_cnv | 0.677 | 0.116 | 0.828 | |
plot_per_group | 1.643 | 0.204 | 1.967 | |
plot_subclusters | 1.750 | 3.382 | 5.508 | |
run | 21.292 | 0.817 | 22.947 | |
sample_object | 0.042 | 0.005 | 0.047 | |