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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 353/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CIMICE 1.14.0  (landing page)
Nicolò Rossi
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/CIMICE
git_branch: RELEASE_3_20
git_last_commit: d6b750a
git_last_commit_date: 2024-10-29 10:57:21 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for CIMICE on merida1

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: 1.14.0
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_1.14.0.tar.gz
StartedAt: 2024-12-20 01:07:51 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 01:10:27 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 156.0 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_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/CIMICE.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* 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 ‘1.14.0’
* 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-3.20-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/4.4-x86_64/Resources/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)

Tests output

CIMICE.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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 
  5.958   0.486   6.461 

Example timings

CIMICE.Rcheck/CIMICE-Ex.timings

nameusersystemelapsed
annotate_mutational_matrix0.0540.0040.062
binary_radix_sort0.0410.0020.043
build_subset_graph0.1000.0040.104
build_topology_subset0.0660.0030.070
chunk_reader0.0150.0030.018
compact_dataset0.0200.0020.022
computeDWNW0.3280.0060.337
computeUPW0.1230.0040.130
compute_weights_default0.1430.0020.151
corrplot_from_mutational_matrix0.5730.0200.624
corrplot_genes0.7320.0050.738
corrplot_samples0.3500.0030.353
dataset_preprocessing0.0460.0030.049
dataset_preprocessing_population0.0260.0030.029
draw_ggraph0.7630.0050.771
draw_networkD30.6070.0150.626
draw_visNetwork0.1840.0450.234
example_dataset0.0060.0020.008
example_dataset_withFreqs0.0060.0020.006
finalize_generator0.3480.0410.391
fix_clonal_genotype0.0460.0050.051
format_labels0.0010.0010.002
gene_mutations_hist0.2780.0330.312
get_no_of_children0.1160.0060.123
graph_non_transitive_subset_topology0.0700.0020.072
make_dataset0.0040.0000.006
make_generator_stub0.1690.0040.175
make_labels0.1160.0010.118
normalizeDWNW0.1570.0030.161
normalizeUPW0.1350.0040.139
perturb_dataset0.3480.0040.352
plot_generator0.7350.0080.745
prepare_generator_edge_set_command0.1970.0050.204
prepare_labels0.0410.0020.043
quick_run0.1290.0020.131
read1.8351.4903.671
read_CAPRI1.8732.3324.285
read_CAPRI_string0.0090.0020.009
read_CAPRIpop0.0060.0020.008
read_CAPRIpop_string0.0080.0020.009
read_MAF0.4710.1540.614
read_matrix0.0060.0010.006
remove_transitive_edges0.0010.0000.001
sample_mutations_hist0.3290.0030.351
select_genes_on_mutations0.0140.0010.015
select_samples_on_mutations0.0440.0030.049
set_generator_edges0.2590.0060.297
simulate_generator0.2540.0070.261
to_dot0.1450.0020.154
update_df0.0250.0020.026