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This page was generated on 2025-01-25 15:37 -0500 (Sat, 25 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4658
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" 4455
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4408
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 348/2286HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CIMICE 1.15.0  (landing page)
Nicolò Rossi
Snapshot Date: 2025-01-24 13:40 -0500 (Fri, 24 Jan 2025)
git_url: https://git.bioconductor.org/packages/CIMICE
git_branch: devel
git_last_commit: 93f6739
git_last_commit_date: 2024-10-29 10:57:21 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for CIMICE on nebbiolo1

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.

raw results


Summary

Package: CIMICE
Version: 1.15.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:CIMICE.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings CIMICE_1.15.0.tar.gz
StartedAt: 2025-01-24 20:54:07 -0500 (Fri, 24 Jan 2025)
EndedAt: 2025-01-24 20:55:32 -0500 (Fri, 24 Jan 2025)
EllapsedTime: 85.1 seconds
RetCode: 0
Status:   OK  
CheckDir: CIMICE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:CIMICE.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings CIMICE_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/CIMICE.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘CIMICE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CIMICE’ version ‘1.15.0’
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/CIMICE.Rcheck/00check.log’
for details.


Installation output

CIMICE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL CIMICE
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘CIMICE’ ...
** this is package ‘CIMICE’ version ‘1.15.0’
** 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 Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 
  2.619   0.230   2.837 

Example timings

CIMICE.Rcheck/CIMICE-Ex.timings

nameusersystemelapsed
annotate_mutational_matrix0.0200.0020.022
binary_radix_sort0.020.000.02
build_subset_graph0.0430.0020.046
build_topology_subset0.0240.0000.024
chunk_reader0.0080.0010.009
compact_dataset0.0080.0000.008
computeDWNW0.1240.0050.128
computeUPW0.050.000.05
compute_weights_default0.0580.0010.058
corrplot_from_mutational_matrix0.2640.0380.303
corrplot_genes0.2950.0030.299
corrplot_samples0.1510.0000.152
dataset_preprocessing0.0190.0000.020
dataset_preprocessing_population0.0120.0010.013
draw_ggraph0.6260.0250.654
draw_networkD30.1220.0040.127
draw_visNetwork0.0660.0150.083
example_dataset0.0030.0010.003
example_dataset_withFreqs0.0020.0010.003
finalize_generator0.1490.0270.176
fix_clonal_genotype0.0200.0040.024
format_labels0.0000.0000.001
gene_mutations_hist0.1310.0150.146
get_no_of_children0.0480.0000.048
graph_non_transitive_subset_topology0.0320.0020.034
make_dataset0.0030.0000.004
make_generator_stub0.0770.0010.078
make_labels0.0520.0000.052
normalizeDWNW0.0730.0040.076
normalizeUPW0.0540.0000.054
perturb_dataset0.1610.0030.163
plot_generator0.3250.0020.327
prepare_generator_edge_set_command0.0800.0020.082
prepare_labels0.0180.0010.019
quick_run0.0520.0000.052
read0.5770.6001.179
read_CAPRI0.5960.6111.207
read_CAPRI_string0.0030.0020.004
read_CAPRIpop0.0030.0010.003
read_CAPRIpop_string0.0020.0020.004
read_MAF0.2080.0650.239
read_matrix0.0030.0000.003
remove_transitive_edges0.0010.0000.000
sample_mutations_hist0.1310.0050.135
select_genes_on_mutations0.0050.0020.006
select_samples_on_mutations0.0200.0010.021
set_generator_edges0.1110.0060.117
simulate_generator0.1050.0020.106
to_dot0.0530.0010.053
update_df0.0140.0010.015