Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-03-18 11:07:11 -0400 (Fri, 18 Mar 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
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 |
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 317/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CIMICE 1.3.1 (landing page) Nicolò Rossi
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
Package: CIMICE |
Version: 1.3.1 |
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CIMICE.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CIMICE_1.3.1.tar.gz |
StartedAt: 2022-03-17 18:43:31 -0400 (Thu, 17 Mar 2022) |
EndedAt: 2022-03-17 18:44:49 -0400 (Thu, 17 Mar 2022) |
EllapsedTime: 77.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CIMICE.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CIMICE.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CIMICE_1.3.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/CIMICE.Rcheck' * using R Under development (unstable) (2021-11-21 r81221) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'CIMICE/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'CIMICE' version '1.3.1' * 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 ... 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 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 ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See 'D:/biocbuild/bbs-3.15-bioc/meat/CIMICE.Rcheck/00check.log' for details.
CIMICE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL CIMICE ### ############################################################################## ############################################################################## * installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library' * installing *source* package 'CIMICE' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'CIMICE' finding HTML links ... done CIMICE html annotate_mutational_matrix html binary_radix_sort html build_subset_graph html build_topology_subset html chunk_reader html compact_dataset html computeDWNW html computeDWNW_aux html computeUPW html computeUPW_aux html compute_weights_default html corrplot_from_mutational_matrix html corrplot_genes html corrplot_samples html dataset_preprocessing html dataset_preprocessing_population html draw_ggraph html draw_networkD3 html draw_visNetwork html example_dataset html example_dataset_withFreqs html finalize_generator html fix_clonal_genotype html format_labels html gene_mutations_hist html get_no_of_children html graph_non_transitive_subset_topology html make_dataset html make_generator_stub html make_labels html normalizeDWNW html normalizeUPW html perturb_dataset html plot_generator html prepare_generator_edge_set_command html prepare_labels html quick_run html read html read_CAPRI html read_CAPRI_string html read_CAPRIpop html read_CAPRIpop_string html read_MAF html read_matrix html remove_transitive_edges html sample_mutations_hist html select_genes_on_mutations html select_samples_on_mutations html set_generator_edges html simulate_generator html to_dot html update_df html ** 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) Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") : DESCRIPTION file of package 'iBBiG' is missing or broken done
CIMICE.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (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 2.14 0.23 2.35
CIMICE.Rcheck/CIMICE-Ex.timings
name | user | system | elapsed | |
annotate_mutational_matrix | 0.03 | 0.00 | 0.04 | |
binary_radix_sort | 0.03 | 0.00 | 0.03 | |
build_subset_graph | 0.06 | 0.00 | 0.07 | |
build_topology_subset | 0.03 | 0.00 | 0.03 | |
chunk_reader | 0 | 0 | 0 | |
compact_dataset | 0.02 | 0.00 | 0.01 | |
computeDWNW | 0.05 | 0.00 | 0.05 | |
computeUPW | 0.03 | 0.00 | 0.03 | |
compute_weights_default | 0.04 | 0.00 | 0.05 | |
corrplot_from_mutational_matrix | 0.16 | 0.03 | 0.18 | |
corrplot_genes | 0.36 | 0.00 | 0.36 | |
corrplot_samples | 0.08 | 0.04 | 0.11 | |
dataset_preprocessing | 0.03 | 0.00 | 0.03 | |
dataset_preprocessing_population | 0.00 | 0.01 | 0.02 | |
draw_ggraph | 0.19 | 0.03 | 0.22 | |
draw_networkD3 | 0.08 | 0.00 | 0.08 | |
draw_visNetwork | 0.03 | 0.00 | 0.86 | |
example_dataset | 0.01 | 0.00 | 0.02 | |
example_dataset_withFreqs | 0 | 0 | 0 | |
finalize_generator | 0.19 | 0.00 | 0.19 | |
fix_clonal_genotype | 0.03 | 0.00 | 0.03 | |
format_labels | 0 | 0 | 0 | |
gene_mutations_hist | 0.08 | 0.00 | 0.07 | |
get_no_of_children | 0.04 | 0.00 | 0.03 | |
graph_non_transitive_subset_topology | 0.03 | 0.00 | 0.03 | |
make_dataset | 0 | 0 | 0 | |
make_generator_stub | 0.11 | 0.00 | 0.11 | |
make_labels | 0.03 | 0.00 | 0.03 | |
normalizeDWNW | 0.03 | 0.00 | 0.03 | |
normalizeUPW | 0.04 | 0.00 | 0.03 | |
perturb_dataset | 0.09 | 0.00 | 0.10 | |
plot_generator | 0.23 | 0.01 | 0.25 | |
prepare_generator_edge_set_command | 0.11 | 0.00 | 0.11 | |
prepare_labels | 0.01 | 0.00 | 0.02 | |
quick_run | 0.04 | 0.00 | 0.03 | |
read | 0.51 | 0.29 | 0.79 | |
read_CAPRI | 0.50 | 0.29 | 0.80 | |
read_CAPRI_string | 0 | 0 | 0 | |
read_CAPRIpop | 0.02 | 0.00 | 0.02 | |
read_CAPRIpop_string | 0 | 0 | 0 | |
read_MAF | 0.14 | 0.02 | 0.15 | |
read_matrix | 0.01 | 0.00 | 0.02 | |
remove_transitive_edges | 0 | 0 | 0 | |
sample_mutations_hist | 0.10 | 0.00 | 0.09 | |
select_genes_on_mutations | 0.01 | 0.00 | 0.02 | |
select_samples_on_mutations | 0.03 | 0.00 | 0.03 | |
set_generator_edges | 0.14 | 0.00 | 0.14 | |
simulate_generator | 0.10 | 0.00 | 0.09 | |
to_dot | 0.03 | 0.00 | 0.03 | |
update_df | 0 | 0 | 0 | |