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This page was generated on 2024-06-11 14:40 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4522
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4468
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 353/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CIMICE 1.12.0  (landing page)
Nicolò Rossi
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/CIMICE
git_branch: RELEASE_3_19
git_last_commit: 5c11705
git_last_commit_date: 2024-04-30 11:32:27 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows 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 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for CIMICE on palomino3

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: 1.12.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CIMICE.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings CIMICE_1.12.0.tar.gz
StartedAt: 2024-06-10 01:50:51 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 01:52:57 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 126.0 seconds
RetCode: 0
Status:   OK  
CheckDir: CIMICE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CIMICE.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings CIMICE_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/CIMICE.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'CIMICE/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CIMICE' version '1.12.0'
* 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 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
  'F:/biocbuild/bbs-3.19-bioc/meat/CIMICE.Rcheck/00check.log'
for details.


Installation output

CIMICE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL CIMICE
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 
   2.81    1.35    4.09 

Example timings

CIMICE.Rcheck/CIMICE-Ex.timings

nameusersystemelapsed
annotate_mutational_matrix0.030.010.05
binary_radix_sort0.000.020.01
build_subset_graph0.030.010.05
build_topology_subset0.020.000.02
chunk_reader0.010.000.03
compact_dataset0.000.020.01
computeDWNW0.050.040.10
computeUPW0.040.020.07
compute_weights_default0.070.020.07
corrplot_from_mutational_matrix0.310.030.35
corrplot_genes0.340.000.34
corrplot_samples0.130.020.14
dataset_preprocessing0.030.000.03
dataset_preprocessing_population0.010.000.02
draw_ggraph0.390.000.39
draw_networkD30.380.000.51
draw_visNetwork0.080.030.80
example_dataset000
example_dataset_withFreqs000
finalize_generator0.230.060.30
fix_clonal_genotype0.030.010.04
format_labels000
gene_mutations_hist0.190.050.24
get_no_of_children0.070.030.11
graph_non_transitive_subset_topology0.040.030.06
make_dataset000
make_generator_stub0.140.000.14
make_labels0.050.000.04
normalizeDWNW0.050.050.11
normalizeUPW0.080.030.11
perturb_dataset0.270.000.29
plot_generator0.500.050.55
prepare_generator_edge_set_command0.140.010.16
prepare_labels0.030.020.05
quick_run0.050.000.05
read1.370.442.12
read_CAPRI1.250.421.69
read_CAPRI_string000
read_CAPRIpop0.000.010.01
read_CAPRIpop_string000
read_MAF0.270.050.32
read_matrix000
remove_transitive_edges000
sample_mutations_hist0.190.000.18
select_genes_on_mutations0.010.000.02
select_samples_on_mutations0.020.020.03
set_generator_edges0.110.010.13
simulate_generator0.110.000.11
to_dot0.030.000.03
update_df0.010.020.03