Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:37 -0000 (Wed, 01 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
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To the developers/maintainers of the cardelino package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 249/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
cardelino 1.1.1 (landing page) Davis McCarthy
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
Package: cardelino |
Version: 1.1.1 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:cardelino.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings cardelino_1.1.1.tar.gz |
StartedAt: 2023-02-27 22:36:04 -0000 (Mon, 27 Feb 2023) |
EndedAt: 2023-02-27 22:46:00 -0000 (Mon, 27 Feb 2023) |
EllapsedTime: 595.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: cardelino.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:cardelino.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings cardelino_1.1.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/cardelino.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘cardelino/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘cardelino’ version ‘1.1.1’ * 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 ‘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 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 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 123.670 0.944 124.616 clone_id 22.855 0.412 23.267 get_snp_matrices 22.087 1.092 23.182 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘vignette-cloneid.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
cardelino.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL cardelino ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (64-bit) 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" 99.4% converged. 100% converged. [1] "Converged in 300 iterations." DIC: 2925.2 D_mean: 2558.89 D_post: 2417.74 logLik_var: 126.87 [,1] [,2] [,3] [,4] [1,] 1 2 3 4 [1] "61 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 31.553 0.979 32.518
cardelino.Rcheck/cardelino-Ex.timings
name | user | system | elapsed | |
assign_cells_to_clones | 0.111 | 0.012 | 0.123 | |
binaryPRC | 0.006 | 0.005 | 0.009 | |
binaryROC | 0.007 | 0.003 | 0.010 | |
clone_id | 22.855 | 0.412 | 23.267 | |
colMatch | 0.001 | 0.000 | 0.001 | |
get_snp_matrices | 22.087 | 1.092 | 23.182 | |
get_tree | 0.397 | 0.012 | 0.410 | |
heat_matrix | 0.782 | 0.012 | 0.794 | |
load_GT_vcf | 0.289 | 0.024 | 0.323 | |
load_cellSNP_vcf | 0.023 | 0.000 | 0.024 | |
mixBinom | 0.017 | 0.000 | 0.018 | |
mtx_to_df | 0.002 | 0.000 | 0.002 | |
plot_config_diffs | 0.174 | 0.004 | 0.178 | |
plot_tree | 0.300 | 0.008 | 0.307 | |
predMixBinom | 0.013 | 0.003 | 0.017 | |
prob_heatmap | 0.084 | 0.004 | 0.088 | |
pub.theme | 0.033 | 0.000 | 0.033 | |
read_vcf | 3.921 | 0.664 | 4.584 | |
rowArgmax | 0.001 | 0.000 | 0.000 | |
rowMax | 0.001 | 0.000 | 0.001 | |
sample_seq_depth | 0.015 | 0.000 | 0.014 | |
sample_tree_SNV | 0.006 | 0.000 | 0.006 | |
sim_read_count | 3.921 | 0.048 | 3.969 | |
vc_heatmap | 123.670 | 0.944 | 124.616 | |