Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-04 11:38:53 -0500 (Mon, 04 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4676 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4441 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4417 |
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 154/2251 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
benchdamic 1.9.1 (landing page) Matteo Calgaro
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the benchdamic package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/benchdamic.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: benchdamic |
Version: 1.9.1 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings benchdamic_1.9.1.tar.gz |
StartedAt: 2024-03-02 00:33:06 -0500 (Sat, 02 Mar 2024) |
EndedAt: 2024-03-02 01:05:48 -0500 (Sat, 02 Mar 2024) |
EllapsedTime: 1962.8 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: benchdamic.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings benchdamic_1.9.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/benchdamic.Rcheck’ * using R Under development (unstable) (2024-01-16 r85808) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘benchdamic/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘benchdamic’ version ‘1.9.1’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘benchdamic’ 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 R 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 ... OK * 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘benchdamic-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: DA_Seurat > ### Title: DA_Seurat > ### Aliases: DA_Seurat > > ### ** Examples > > set.seed(1) > # Create a very simple phyloseq object > counts <- matrix(rnbinom(n = 60, size = 3, prob = 0.5), nrow = 10, ncol = 6) > metadata <- data.frame("Sample" = c("S1", "S2", "S3", "S4", "S5", "S6"), + "group" = as.factor(c("A", "A", "A", "B", "B", "B"))) > ps <- phyloseq::phyloseq(phyloseq::otu_table(counts, taxa_are_rows = TRUE), + phyloseq::sample_data(metadata)) > > # Differential abundance > DA_Seurat(object = ps, contrast = c("group","B","A")) Warning: Data is of class matrix. Coercing to dgCMatrix. Setting A the reference level for group variable. Extracting results for group variable, B / A Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| For a (much!) faster implementation of the Wilcoxon Rank Sum Test, (default method for FindMarkers) please install the presto package -------------------------------------------- install.packages('devtools') devtools::install_github('immunogenomics/presto') -------------------------------------------- After installation of presto, Seurat will automatically use the more efficient implementation (no further action necessary). This message will be shown once per session $pValMat rawP adjP sp1 0.1904303 1.000000 sp2 1.0000000 1.000000 sp3 0.6625206 1.000000 sp4 0.1840386 1.000000 sp5 0.6625206 1.000000 sp6 0.3827331 1.000000 sp7 0.3827331 1.000000 sp8 1.0000000 1.000000 sp9 0.0808556 0.808556 sp10 1.0000000 1.000000 $statInfo p_val avg_log2FC pct.1 pct.2 p_val_adj sp1 0.1904303 -1.09264009 0.667 1.000 1.000000 sp2 1.0000000 0.04134924 1.000 1.000 1.000000 sp3 0.6625206 -0.66334771 1.000 0.667 1.000000 sp4 0.1840386 -1.36463577 0.333 1.000 1.000000 sp5 0.6625206 0.90884814 0.667 1.000 1.000000 sp6 0.3827331 0.71678480 1.000 1.000 1.000000 sp7 0.3827331 -0.35805875 1.000 1.000 1.000000 sp8 1.0000000 0.04608187 1.000 0.667 1.000000 sp9 0.0808556 0.89057297 1.000 0.667 0.808556 sp10 1.0000000 -0.41820485 1.000 1.000 1.000000 $name [1] "Seurat.LogNormalize.SF10000.wilcox" > > # Perform a simple Wilcoxon test using Seurat on raw data > DA_Seurat(object = ps, contrast = c("group","B","A"), norm = "none", + test = "wilcox") Warning: Data is of class matrix. Coercing to dgCMatrix. Setting A the reference level for group variable. Extracting results for group variable, B / A Warning: Layer ‘data’ is empty Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'rowSums': subscript out of bounds Calls: DA_Seurat ... callGeneric -> eval -> eval -> [ -> [ -> .subscript.2ary Execution halted * 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 ERROR See ‘/Users/biocbuild/bbs-3.19-bioc/meat/benchdamic.Rcheck/00check.log’ for details.
benchdamic.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL benchdamic ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘benchdamic’ ... ** 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 (benchdamic)
benchdamic.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 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. > library(testthat) > library(benchdamic) > > test_check("benchdamic") |------------(25%)----------(50%)----------(75%)----------| |------------(25%)----------(50%)----------(75%)----------| |------------(25%)----------(50%)----------(75%)----------| |------------(25%)----------(50%)----------(75%)----------| |------------(25%)----------(50%)----------(75%)----------| [ FAIL 0 | WARN 0 | SKIP 1 | PASS 310 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'test_DA_paired.R:3:1' [ FAIL 0 | WARN 0 | SKIP 1 | PASS 310 ] > > proc.time() user system elapsed 407.567 22.181 648.824
benchdamic.Rcheck/benchdamic-Ex.timings
name | user | system | elapsed | |
CAT | 0.008 | 0.002 | 0.012 | |
DA_ALDEx2 | 12.060 | 2.167 | 33.550 | |
DA_ANCOM | 8.745 | 0.207 | 9.964 | |
DA_DESeq2 | 6.152 | 0.097 | 6.815 | |
DA_MAST | 3.198 | 0.082 | 3.825 | |
DA_Maaslin2 | 0.514 | 0.079 | 0.740 | |
DA_NOISeq | 1.903 | 0.049 | 2.084 | |