Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:14:56 -0000 (Wed, 08 Feb 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" | 4164 |
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To the developers/maintainers of the CIMICE package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CIMICE.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 325/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CIMICE 1.7.0 (landing page) Nicolò Rossi
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
Package: CIMICE |
Version: 1.7.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:CIMICE.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings CIMICE_1.7.0.tar.gz |
StartedAt: 2023-02-06 21:07:11 -0000 (Mon, 06 Feb 2023) |
EndedAt: 2023-02-06 21:09:38 -0000 (Mon, 06 Feb 2023) |
EllapsedTime: 146.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CIMICE.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:CIMICE.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings CIMICE_1.7.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/CIMICE.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 ‘CIMICE/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CIMICE’ version ‘1.7.0’ * 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 ... NOTE Found the following hidden files and directories: .git.bfg-report These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘CIMICE’ 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 files in ‘vignettes’ ... OK * checking examples ... OK * 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 ... ‘CIMICER.Rmd’ using ‘UTF-8’... OK ‘CIMICE_SHORT.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.17-bioc/meat/CIMICE.Rcheck/00check.log’ for details.
CIMICE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL CIMICE ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘CIMICE’ ... ** using staged installation ** R ** 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 (CIMICE)
CIMICE.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. > library(testthat) > library(CIMICE) > > test_check("CIMICE") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ] > > proc.time() user system elapsed 3.389 0.193 3.938
CIMICE.Rcheck/CIMICE-Ex.timings
name | user | system | elapsed | |
annotate_mutational_matrix | 0.029 | 0.000 | 0.030 | |
binary_radix_sort | 0.042 | 0.000 | 0.042 | |
build_subset_graph | 0.096 | 0.008 | 0.110 | |
build_topology_subset | 0.060 | 0.000 | 0.077 | |
chunk_reader | 0.010 | 0.000 | 0.025 | |
compact_dataset | 0.022 | 0.000 | 0.022 | |
computeDWNW | 0.082 | 0.000 | 0.083 | |
computeUPW | 0.071 | 0.000 | 0.148 | |
compute_weights_default | 0.083 | 0.004 | 0.136 | |
corrplot_from_mutational_matrix | 0.435 | 0.004 | 0.444 | |
corrplot_genes | 0.477 | 0.005 | 0.523 | |
corrplot_samples | 0.191 | 0.024 | 0.216 | |
dataset_preprocessing | 0.034 | 0.004 | 0.038 | |
dataset_preprocessing_population | 0.025 | 0.000 | 0.025 | |
draw_ggraph | 0.339 | 0.024 | 0.519 | |
draw_networkD3 | 0.174 | 0.004 | 0.183 | |
draw_visNetwork | 0.086 | 0.004 | 0.125 | |
example_dataset | 0.013 | 0.000 | 0.021 | |
example_dataset_withFreqs | 0.012 | 0.000 | 0.012 | |
finalize_generator | 0.297 | 0.000 | 0.298 | |
fix_clonal_genotype | 0.035 | 0.000 | 0.035 | |
format_labels | 0.000 | 0.000 | 0.001 | |
gene_mutations_hist | 0.173 | 0.000 | 0.206 | |
get_no_of_children | 0.059 | 0.008 | 0.069 | |
graph_non_transitive_subset_topology | 0.052 | 0.000 | 0.052 | |
make_dataset | 0.002 | 0.000 | 0.002 | |
make_generator_stub | 0.140 | 0.000 | 0.141 | |
make_labels | 0.067 | 0.000 | 0.067 | |
normalizeDWNW | 0.073 | 0.000 | 0.074 | |
normalizeUPW | 0.066 | 0.002 | 0.069 | |
perturb_dataset | 0.442 | 0.008 | 0.450 | |
plot_generator | 0.518 | 0.000 | 0.519 | |
prepare_generator_edge_set_command | 0.187 | 0.000 | 0.188 | |
prepare_labels | 0.033 | 0.000 | 0.034 | |
quick_run | 0.056 | 0.000 | 0.057 | |
read | 0.818 | 0.211 | 1.111 | |
read_CAPRI | 0.866 | 0.160 | 1.062 | |
read_CAPRI_string | 0.005 | 0.000 | 0.005 | |
read_CAPRIpop | 0.005 | 0.000 | 0.007 | |
read_CAPRIpop_string | 0.005 | 0.000 | 0.005 | |
read_MAF | 0.268 | 0.016 | 0.356 | |
read_matrix | 0.004 | 0.000 | 0.004 | |
remove_transitive_edges | 0.000 | 0.000 | 0.001 | |
sample_mutations_hist | 0.196 | 0.000 | 0.196 | |
select_genes_on_mutations | 0.024 | 0.000 | 0.024 | |
select_samples_on_mutations | 0.047 | 0.003 | 0.051 | |
set_generator_edges | 0.199 | 0.000 | 0.199 | |
simulate_generator | 0.177 | 0.004 | 0.181 | |
to_dot | 0.062 | 0.000 | 0.062 | |
update_df | 0.017 | 0.000 | 0.017 | |