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This page was generated on 2023-05-31 05:44:31 -0000 (Wed, 31 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4219 |
| 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 | ||||
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To the developers/maintainers of the CIMICE package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 339/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CIMICE 1.9.0 (landing page) Nicolò Rossi
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: CIMICE |
| Version: 1.9.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:CIMICE.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings CIMICE_1.9.0.tar.gz |
| StartedAt: 2023-05-30 03:27:55 -0000 (Tue, 30 May 2023) |
| EndedAt: 2023-05-30 03:29:40 -0000 (Tue, 30 May 2023) |
| EllapsedTime: 105.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CIMICE.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:CIMICE.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings CIMICE_1.9.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/CIMICE.Rcheck’
* using R version 4.3.0 (2023-04-21)
* 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 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘CIMICE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CIMICE’ 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 ... 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 loading without being on the library search path ... 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-3.18-bioc/meat/CIMICE.Rcheck/00check.log’
for details.
CIMICE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL CIMICE ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-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 version 4.3.0 (2023-04-21) -- "Already Tomorrow"
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
3.418 0.201 3.603
CIMICE.Rcheck/CIMICE-Ex.timings
| name | user | system | elapsed | |
| annotate_mutational_matrix | 0.029 | 0.004 | 0.033 | |
| binary_radix_sort | 0.040 | 0.000 | 0.041 | |
| build_subset_graph | 0.090 | 0.007 | 0.097 | |
| build_topology_subset | 0.059 | 0.000 | 0.059 | |
| chunk_reader | 0.009 | 0.000 | 0.010 | |
| compact_dataset | 0.021 | 0.000 | 0.021 | |
| computeDWNW | 0.076 | 0.000 | 0.076 | |
| computeUPW | 0.063 | 0.000 | 0.063 | |
| compute_weights_default | 0.077 | 0.002 | 0.080 | |
| corrplot_from_mutational_matrix | 0.458 | 0.009 | 0.466 | |
| corrplot_genes | 0.476 | 0.031 | 0.508 | |
| corrplot_samples | 0.22 | 0.00 | 0.22 | |
| dataset_preprocessing | 0.037 | 0.000 | 0.038 | |
| dataset_preprocessing_population | 0.022 | 0.004 | 0.026 | |
| draw_ggraph | 0.312 | 0.020 | 0.332 | |
| draw_networkD3 | 0.162 | 0.003 | 0.167 | |
| draw_visNetwork | 0.083 | 0.000 | 0.089 | |
| example_dataset | 0.012 | 0.000 | 0.012 | |
| example_dataset_withFreqs | 0.009 | 0.000 | 0.009 | |
| finalize_generator | 0.239 | 0.000 | 0.239 | |
| fix_clonal_genotype | 0.035 | 0.000 | 0.035 | |
| format_labels | 0.001 | 0.000 | 0.001 | |
| gene_mutations_hist | 0.171 | 0.000 | 0.171 | |
| get_no_of_children | 0.060 | 0.000 | 0.061 | |
| graph_non_transitive_subset_topology | 0.05 | 0.00 | 0.05 | |
| make_dataset | 0.002 | 0.000 | 0.002 | |
| make_generator_stub | 0.109 | 0.000 | 0.109 | |
| make_labels | 0.053 | 0.000 | 0.053 | |
| normalizeDWNW | 0.064 | 0.004 | 0.068 | |
| normalizeUPW | 0.074 | 0.000 | 0.074 | |
| perturb_dataset | 0.382 | 0.000 | 0.382 | |
| plot_generator | 0.473 | 0.000 | 0.474 | |
| prepare_generator_edge_set_command | 0.124 | 0.000 | 0.124 | |
| prepare_labels | 0.034 | 0.000 | 0.034 | |
| quick_run | 0.055 | 0.000 | 0.054 | |
| read | 0.873 | 0.252 | 1.126 | |
| read_CAPRI | 0.832 | 0.220 | 1.052 | |
| read_CAPRI_string | 0.006 | 0.000 | 0.005 | |
| read_CAPRIpop | 0.004 | 0.000 | 0.006 | |
| read_CAPRIpop_string | 0.000 | 0.004 | 0.005 | |
| read_MAF | 0.251 | 0.028 | 0.277 | |
| read_matrix | 0.003 | 0.000 | 0.004 | |
| remove_transitive_edges | 0 | 0 | 0 | |
| sample_mutations_hist | 0.2 | 0.0 | 0.2 | |
| select_genes_on_mutations | 0.025 | 0.000 | 0.025 | |
| select_samples_on_mutations | 0.051 | 0.000 | 0.052 | |
| set_generator_edges | 0.164 | 0.008 | 0.172 | |
| simulate_generator | 0.173 | 0.000 | 0.173 | |
| to_dot | 0.065 | 0.000 | 0.066 | |
| update_df | 0.016 | 0.003 | 0.019 | |