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This page was generated on 2025-09-03 12:07 -0400 (Wed, 03 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4826
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4616
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4563
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
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 357/2321HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CIMICE 1.17.0  (landing page)
Nicolò Rossi
Snapshot Date: 2025-09-02 13:45 -0400 (Tue, 02 Sep 2025)
git_url: https://git.bioconductor.org/packages/CIMICE
git_branch: devel
git_last_commit: 1f095cb
git_last_commit_date: 2025-04-15 12:23:50 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for CIMICE on taishan

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.
- 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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: CIMICE
Version: 1.17.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:CIMICE.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings CIMICE_1.17.0.tar.gz
StartedAt: 2025-09-02 05:18:27 -0000 (Tue, 02 Sep 2025)
EndedAt: 2025-09-02 05:19:53 -0000 (Tue, 02 Sep 2025)
EllapsedTime: 86.0 seconds
RetCode: 0
Status:   OK  
CheckDir: CIMICE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:CIMICE.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings CIMICE_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/CIMICE.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CIMICE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CIMICE’ version ‘1.17.0’
* 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 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 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 ... 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
  ‘/home/biocbuild/bbs-3.22-bioc/meat/CIMICE.Rcheck/00check.log’
for details.


Installation output

CIMICE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL CIMICE
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘CIMICE’ ...
** this is package ‘CIMICE’ version ‘1.17.0’
** 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)

Tests output

CIMICE.Rcheck/tests/testthat.Rout


R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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 2 | SKIP 0 | PASS 1 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
  3.571   0.210   3.778 

Example timings

CIMICE.Rcheck/CIMICE-Ex.timings

nameusersystemelapsed
annotate_mutational_matrix0.0340.0000.034
binary_radix_sort0.0200.0040.023
build_subset_graph0.0620.0000.062
build_topology_subset0.0540.0000.054
chunk_reader0.0090.0000.012
compact_dataset0.0150.0000.014
computeDWNW0.1800.0040.184
computeUPW0.0840.0000.084
compute_weights_default0.0860.0000.086
corrplot_from_mutational_matrix0.3320.0040.337
corrplot_genes0.4210.0000.422
corrplot_samples0.2220.0000.223
dataset_preprocessing0.0290.0000.029
dataset_preprocessing_population0.0180.0000.018
draw_ggraph0.4860.0000.492
draw_networkD30.4070.0080.419
draw_visNetwork0.1100.0000.134
example_dataset0.0030.0000.003
example_dataset_withFreqs0.0030.0000.003
finalize_generator0.2090.0160.225
fix_clonal_genotype0.0330.0000.033
format_labels0.0010.0000.001
gene_mutations_hist0.1590.0320.191
get_no_of_children0.0610.0080.069
graph_non_transitive_subset_topology0.0410.0080.050
make_dataset0.0040.0000.004
make_generator_stub0.1220.0160.138
make_labels0.0790.0040.084
normalizeDWNW0.0880.0200.109
normalizeUPW0.0840.0040.089
perturb_dataset0.2510.0120.264
plot_generator0.5000.0080.509
prepare_generator_edge_set_command0.1230.0040.127
prepare_labels0.0250.0040.029
quick_run0.0850.0000.085
read0.7350.1230.863
read_CAPRI0.7440.1160.863
read_CAPRI_string0.0060.0000.005
read_CAPRIpop0.0050.0000.005
read_CAPRIpop_string0.0050.0000.005
read_MAF0.2720.0280.300
read_matrix0.0040.0000.004
remove_transitive_edges0.0010.0000.000
sample_mutations_hist0.2170.0080.225
select_genes_on_mutations0.0080.0000.008
select_samples_on_mutations0.0240.0040.028
set_generator_edges0.1690.0000.170
simulate_generator0.1490.0000.150
to_dot0.1020.0000.102
update_df0.0170.0000.017