Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-23 11:45 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4372 |
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 1021/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
infercnv 1.23.0 (landing page) Christophe Georgescu
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: 1.23.0 |
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_1.23.0.tar.gz |
StartedAt: 2024-12-22 19:50:22 -0500 (Sun, 22 Dec 2024) |
EndedAt: 2024-12-22 19:53:01 -0500 (Sun, 22 Dec 2024) |
EllapsedTime: 158.9 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_1.23.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/infercnv.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * 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 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘infercnv/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘infercnv’ version ‘1.23.0’ * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 31 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 49.274 1.371 44.535 * 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-3.21-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/4.5-arm64/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 Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 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. > #!/usr/bin/env Rscript > > library(testthat) > library(infercnv) > > test_check("infercnv") INFO [2024-12-22 19:52:57] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE INFO [2024-12-22 19:52:57] subtracting mean(normal) per gene per cell across all data INFO [2024-12-22 19:52:57] -subtracting expr per gene, use_bounds=TRUE INFO [2024-12-22 19:52:57] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE INFO [2024-12-22 19:52:57] subtracting mean(normal) per gene per cell across all data INFO [2024-12-22 19:52:57] -subtracting expr per gene, use_bounds=TRUE INFO [2024-12-22 19:52:57] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE INFO [2024-12-22 19:52:57] subtracting mean(normal) per gene per cell across all data INFO [2024-12-22 19:52:57] -subtracting expr per gene, use_bounds=TRUE INFO [2024-12-22 19:52:57] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE INFO [2024-12-22 19:52:57] subtracting mean(normal) per gene per cell across all data INFO [2024-12-22 19:52:57] -subtracting expr per gene, use_bounds=TRUE INFO [2024-12-22 19:52:57] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE INFO [2024-12-22 19:52:57] subtracting mean(normal) per gene per cell across all data INFO [2024-12-22 19:52:57] -subtracting expr per gene, use_bounds=TRUE INFO [2024-12-22 19:52:57] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE INFO [2024-12-22 19:52:57] subtracting mean(normal) per gene per cell across all data INFO [2024-12-22 19:52:57] -subtracting expr per gene, use_bounds=TRUE WARN [2024-12-22 19:52:57] window length < 2, returning original unmodified data WARN [2024-12-22 19:52:57] window length < 2, returning original unmodified data INFO [2024-12-22 19:52:57] ::remove_outlier_norm:Start out_method: average_bound lower_bound: -1 upper_bound: 30 INFO [2024-12-22 19:52:57] ::remove_outlier_norm: using hard thresholds: lower_bound: -1 upper_bound: 30 INFO [2024-12-22 19:52:57] ::remove_outlier_norm:Start out_method: average_bound lower_bound: 5 upper_bound: 15 INFO [2024-12-22 19:52:57] ::remove_outlier_norm: using hard thresholds: lower_bound: 5 upper_bound: 15 INFO [2024-12-22 19:52:57] ::remove_outlier_norm:Start out_method: average_bound lower_bound: NA upper_bound: NA INFO [2024-12-22 19:52:57] ::remove_outlier_norm using method: average_bound for defining outliers. INFO [2024-12-22 19:52:57] outlier bounds defined between: -0.5 - 17.75 INFO [2024-12-22 19:52:57] ::order_reduce:Start. INFO [2024-12-22 19:52:57] ::order_reduce:Start. INFO [2024-12-22 19:52:57] .order_reduce(): expr and order match. INFO [2024-12-22 19:52:57] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 10,2 Total=110 Min=1 Max=10. INFO [2024-12-22 19:52:57] ::order_reduce:Start. INFO [2024-12-22 19:52:57] .order_reduce(): expr and order match. INFO [2024-12-22 19:52:57] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 10,2 Total=110 Min=1 Max=10. INFO [2024-12-22 19:52:57] ::order_reduce:Start. INFO [2024-12-22 19:52:57] ::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 4.721 0.286 5.040
infercnv.Rcheck/infercnv-Ex.timings
name | user | system | elapsed | |
CreateInfercnvObject | 0.028 | 0.005 | 0.033 | |
apply_median_filtering | 1.391 | 0.033 | 1.423 | |
color.palette | 0.001 | 0.000 | 0.001 | |
filterHighPNormals | 0.003 | 0.001 | 0.005 | |
inferCNVBayesNet | 49.274 | 1.371 | 44.535 | |
plot_cnv | 0.147 | 0.031 | 0.180 | |
plot_per_group | 0.318 | 0.056 | 0.374 | |
plot_subclusters | 0.256 | 0.336 | 0.601 | |
run | 4.772 | 0.204 | 4.984 | |
sample_object | 0.010 | 0.002 | 0.011 | |