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This page was generated on 2025-03-17 11:38 -0400 (Mon, 17 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4545
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4576
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4528
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4459
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 355/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CIMICE 1.15.0  (landing page)
Nicolò Rossi
Snapshot Date: 2025-03-16 13:40 -0400 (Sun, 16 Mar 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 -0400 (Tue, 29 Oct 2024)
palomino7Windows Server 2022 Datacenter / x64  OK    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 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for CIMICE on lconway

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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CIMICE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CIMICE_1.15.0.tar.gz
StartedAt: 2025-03-16 19:53:46 -0400 (Sun, 16 Mar 2025)
EndedAt: 2025-03-16 19:55:14 -0400 (Sun, 16 Mar 2025)
EllapsedTime: 87.4 seconds
RetCode: 0
Status:   OK  
CheckDir: CIMICE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CIMICE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CIMICE_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/CIMICE.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CIMICE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CIMICE’ version ‘1.15.0’
* 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 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
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/CIMICE.Rcheck/00check.log’
for details.


Installation output

CIMICE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CIMICE
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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) (2025-03-02 r87868) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 
  3.082   0.301   3.399 

Example timings

CIMICE.Rcheck/CIMICE-Ex.timings

nameusersystemelapsed
annotate_mutational_matrix0.0260.0020.029
binary_radix_sort0.0200.0010.021
build_subset_graph0.0530.0020.055
build_topology_subset0.0440.0020.047
chunk_reader0.0080.0020.011
compact_dataset0.0100.0000.011
computeDWNW0.1510.0040.155
computeUPW0.0870.0030.089
compute_weights_default0.0790.0010.082
corrplot_from_mutational_matrix0.2970.0120.311
corrplot_genes0.3730.0030.378
corrplot_samples0.1800.0030.183
dataset_preprocessing0.0270.0020.029
dataset_preprocessing_population0.0200.0020.021
draw_ggraph0.3220.0040.328
draw_networkD30.2590.0110.275
draw_visNetwork0.1040.0210.130
example_dataset0.0040.0000.005
example_dataset_withFreqs0.0020.0000.003
finalize_generator0.2040.0050.210
fix_clonal_genotype0.0320.0020.034
format_labels0.0010.0000.001
gene_mutations_hist0.4060.0030.411
get_no_of_children0.0660.0030.069
graph_non_transitive_subset_topology0.0420.0020.046
make_dataset0.0020.0000.003
make_generator_stub0.0880.0090.098
make_labels0.0570.0050.062
normalizeDWNW0.0860.0080.094
normalizeUPW0.0620.0050.068
perturb_dataset0.1810.0180.201
plot_generator0.3700.0060.376
prepare_generator_edge_set_command0.1040.0030.107
prepare_labels0.0280.0020.029
quick_run0.0470.0010.048
read0.8080.5221.352
read_CAPRI0.7900.5391.336
read_CAPRI_string0.0040.0000.005
read_CAPRIpop0.0040.0010.005
read_CAPRIpop_string0.0050.0010.005
read_MAF0.2120.0580.270
read_matrix0.0030.0010.003
remove_transitive_edges000
sample_mutations_hist0.1540.0020.158
select_genes_on_mutations0.0060.0010.007
select_samples_on_mutations0.0270.0010.029
set_generator_edges0.1230.0030.127
simulate_generator0.1160.0030.120
to_dot0.0700.0020.074
update_df0.0190.0010.020