Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:44 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
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" | 4373 |
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 266/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
cardelino 1.9.0 (landing page) Davis McCarthy
| 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 cardelino package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cardelino.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: cardelino |
Version: 1.9.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cardelino.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cardelino_1.9.0.tar.gz |
StartedAt: 2024-12-23 18:28:42 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 18:31:26 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 164.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: cardelino.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cardelino.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cardelino_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/cardelino.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 ‘cardelino/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘cardelino’ version ‘1.9.0’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘cardelino’ 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 ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: plot_tree.Rd: ggtree vc_heatmap.Rd: pheatmap Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed vc_heatmap 21.063 6.164 27.529 clone_id 4.548 0.968 5.583 * 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 NOTE See ‘/Users/biocbuild/bbs-3.21-bioc/meat/cardelino.Rcheck/00check.log’ for details.
cardelino.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL cardelino ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘cardelino’ ... ** using staged installation ** R ** data ** 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 (cardelino)
cardelino.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. > Sys.setenv("R_TESTS" = "") > library(testthat) > library(cardelino) > > test_check("cardelino") [1] "Total iterations: 11" 98.9% converged. 99.8% converged. [1] "Converged in 300 iterations." DIC: 4657.21 D_mean: 2475.12 D_post: 2353.26 logLik_var: 575.99 [,1] [,2] [,3] [,4] [1,] 1 2 3 4 [1] "58 samples have multiple labels." Scanning file to determine attributes. File attributes: meta lines: 37 header_line: 38 variant count: 112 column count: 86 Meta line 37 read in. All meta lines processed. gt matrix initialized. Character matrix gt created. Character matrix gt rows: 112 Character matrix gt cols: 86 skip: 0 nrows: 112 row_num: 0 Processed variant: 112 All variants processed [1] "112 out of 112 SNPs passed." Scanning file to determine attributes. File attributes: meta lines: 37 header_line: 38 variant count: 112 column count: 86 Meta line 37 read in. All meta lines processed. gt matrix initialized. Character matrix gt created. Character matrix gt rows: 112 Character matrix gt cols: 86 skip: 0 nrows: 112 row_num: 0 Processed variant: 112 All variants processed [ FAIL 0 | WARN 2 | SKIP 0 | PASS 20 ] [ FAIL 0 | WARN 2 | SKIP 0 | PASS 20 ] > > # check test coverage with covr in Rstudio > # covr::package_coverage() > > proc.time() user system elapsed 8.812 0.619 9.584
cardelino.Rcheck/cardelino-Ex.timings
name | user | system | elapsed | |
assign_cells_to_clones | 0.018 | 0.002 | 0.021 | |
binaryPRC | 0.003 | 0.001 | 0.003 | |
binaryROC | 0.002 | 0.001 | 0.002 | |
clone_id | 4.548 | 0.968 | 5.583 | |
colMatch | 0.000 | 0.001 | 0.000 | |
get_snp_matrices | 4.551 | 0.309 | 4.906 | |
get_tree | 0.112 | 0.002 | 0.115 | |
heat_matrix | 0.181 | 0.007 | 0.189 | |
load_GT_vcf | 0.082 | 0.010 | 0.095 | |
load_cellSNP_vcf | 0.008 | 0.001 | 0.009 | |
mixBinom | 0.003 | 0.000 | 0.003 | |
mtx_to_df | 0.000 | 0.000 | 0.001 | |
plot_config_diffs | 0.040 | 0.001 | 0.041 | |
plot_tree | 0.069 | 0.001 | 0.070 | |
predMixBinom | 0.003 | 0.000 | 0.003 | |
prob_heatmap | 0.018 | 0.001 | 0.019 | |
pub.theme | 0.009 | 0.000 | 0.009 | |
read_vcf | 1.118 | 0.203 | 1.325 | |
rowArgmax | 0.000 | 0.000 | 0.001 | |
rowMax | 0 | 0 | 0 | |
sample_seq_depth | 0.519 | 0.023 | 0.543 | |
sample_tree_SNV | 0.001 | 0.000 | 0.003 | |
sim_read_count | 0.332 | 0.011 | 0.343 | |
vc_heatmap | 21.063 | 6.164 | 27.529 | |