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This page was generated on 2025-09-15 12:03 -0400 (Mon, 15 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4719
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4538
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4522
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4543
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 1095/2327HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
KBoost 1.17.0  (landing page)
Luis F. Iglesias-Martinez
Snapshot Date: 2025-09-14 13:45 -0400 (Sun, 14 Sep 2025)
git_url: https://git.bioconductor.org/packages/KBoost
git_branch: devel
git_last_commit: f39db19
git_last_commit_date: 2025-04-15 12:31:52 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  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 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for KBoost on nebbiolo2

To the developers/maintainers of the KBoost package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/KBoost.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: KBoost
Version: 1.17.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:KBoost.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings KBoost_1.17.0.tar.gz
StartedAt: 2025-09-15 00:51:24 -0400 (Mon, 15 Sep 2025)
EndedAt: 2025-09-15 00:52:00 -0400 (Mon, 15 Sep 2025)
EllapsedTime: 36.0 seconds
RetCode: 0
Status:   OK  
CheckDir: KBoost.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:KBoost.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings KBoost_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/KBoost.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘KBoost/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘KBoost’ version ‘1.17.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘KBoost’ 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 ... NOTE
Problems with news in ‘NEWS.md’:
No news entries found.
* 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 ... NOTE
check_input: no visible global function definition for ‘is’
net_summary_bin: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
d4_mfac 5.845   0.01   5.855
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/KBoost.Rcheck/00check.log’
for details.


Installation output

KBoost.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL KBoost
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘KBoost’ ...
** this is package ‘KBoost’ version ‘1.17.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (KBoost)

Tests output

KBoost.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
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(KBoost)
> 
> test_check("KBoost")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 7 ]
> 
> proc.time()
   user  system elapsed 
  0.686   0.070   0.744 

Example timings

KBoost.Rcheck/KBoost-Ex.timings

nameusersystemelapsed
AUPR_AUROC_matrix1.1590.0581.219
D4_multi_10.0000.0000.001
D4_multi_20.0010.0000.000
D4_multi_30.0010.0010.000
D4_multi_40.0000.0010.000
D4_multi_5000
G_D4_multi_10.0010.0010.000
G_D4_multi_20.0000.0000.001
G_D4_multi_30.0000.0000.001
G_D4_multi_40.0000.0000.001
G_D4_multi_5000
Gerstein_Prior_ENET_2000
Human_TFs0.0010.0000.000
IRMA_Gold0.0010.0010.000
KBoost_human_symbol0.0210.0000.022
KPC0.0030.0000.004
RBF_K0.0000.0000.001
add_names0.4950.0010.496
d4_mfac5.8450.0105.855
get_prior_Gerstein0.0030.0000.003
get_tfs_human0.0010.0000.000
grid_search_kboost0.1400.0000.141
irma_check0.010.000.01
irma_off0.0000.0010.000
irma_on0.0010.0000.000
kboost0.550.000.55
kernel_normal0.0000.0000.001
kernel_pc_boosting0.3420.0000.343
net_dist_bin0.5230.0010.524
net_refine0.0030.0000.003
net_summary_bin0.5270.0000.527
tab_2_matrix_D40.0010.0000.001
write_GRN_D40.6120.0010.614