Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:20:05 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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

CHECK results for CIMICE on nebbiolo1


To the developers/maintainers of the CIMICE package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 327/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CIMICE 1.4.0  (landing page)
Nicolò Rossi
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/CIMICE
git_branch: RELEASE_3_15
git_last_commit: 474cda8
git_last_commit_date: 2022-04-26 12:14:06 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 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
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CIMICE
Version: 1.4.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:CIMICE.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings CIMICE_1.4.0.tar.gz
StartedAt: 2022-10-18 19:02:33 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 19:03:45 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 71.1 seconds
RetCode: 0
Status:   OK  
CheckDir: CIMICE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:CIMICE.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings CIMICE_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/CIMICE.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CIMICE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CIMICE’ version ‘1.4.0’
* 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 R 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 in ‘inst/doc’ ... 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-3.15-bioc/meat/CIMICE.Rcheck/00check.log’
for details.



Installation output

CIMICE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL CIMICE
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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 
  2.744   0.172   2.901 

Example timings

CIMICE.Rcheck/CIMICE-Ex.timings

nameusersystemelapsed
annotate_mutational_matrix0.0280.0040.031
binary_radix_sort0.0380.0080.046
build_subset_graph0.0810.0000.082
build_topology_subset0.0500.0040.054
chunk_reader0.0040.0030.010
compact_dataset0.0160.0000.017
computeDWNW0.0830.0190.103
computeUPW0.0480.0110.061
compute_weights_default0.0700.0010.071
corrplot_from_mutational_matrix0.3350.0000.335
corrplot_genes0.3660.0030.371
corrplot_samples0.1140.0170.131
dataset_preprocessing0.0270.0000.027
dataset_preprocessing_population0.0190.0020.021
draw_ggraph0.2200.0160.236
draw_networkD30.1100.0030.115
draw_visNetwork0.0540.0070.065
example_dataset0.0090.0000.009
example_dataset_withFreqs0.0060.0000.006
finalize_generator0.1930.0040.196
fix_clonal_genotype0.0420.0000.042
format_labels0.0010.0000.000
gene_mutations_hist0.1180.0000.118
get_no_of_children0.0480.0000.047
graph_non_transitive_subset_topology0.0410.0000.040
make_dataset0.0020.0000.001
make_generator_stub0.0940.0000.094
make_labels0.0350.0000.035
normalizeDWNW0.0490.0000.049
normalizeUPW0.0560.0000.056
perturb_dataset0.1100.0040.115
plot_generator0.3350.0030.339
prepare_generator_edge_set_command0.1060.0050.110
prepare_labels0.0210.0030.024
quick_run0.0350.0000.035
read0.6000.6761.279
read_CAPRI0.5520.7361.288
read_CAPRI_string0.0060.0000.006
read_CAPRIpop0.0040.0000.004
read_CAPRIpop_string0.0050.0000.004
read_MAF0.2100.0710.240
read_matrix0.0030.0000.003
remove_transitive_edges000
sample_mutations_hist0.1360.0040.140
select_genes_on_mutations0.0150.0040.020
select_samples_on_mutations0.0410.0000.041
set_generator_edges0.1450.0040.147
simulate_generator0.1090.0040.114
to_dot0.0420.0000.042
update_df0.0160.0000.016