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This page was generated on 2023-06-06 11:00:34 -0000 (Tue, 06 Jun 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.0 (2023-04-21) -- "Already Tomorrow" 4366
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 KBoost on kunpeng2


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.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 1031/2199HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
KBoost 1.9.0  (landing page)
Luis F. Iglesias-Martinez
Snapshot Date: 2023-06-05 06:35:06 -0000 (Mon, 05 Jun 2023)
git_url: https://git.bioconductor.org/packages/KBoost
git_branch: devel
git_last_commit: 07b8d5e
git_last_commit_date: 2023-04-25 15:30:12 -0000 (Tue, 25 Apr 2023)
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

Summary

Package: KBoost
Version: 1.9.0
Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:KBoost.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings KBoost_1.9.0.tar.gz
StartedAt: 2023-06-06 00:51:17 -0000 (Tue, 06 Jun 2023)
EndedAt: 2023-06-06 00:52:11 -0000 (Tue, 06 Jun 2023)
EllapsedTime: 54.1 seconds
RetCode: 0
Status:   OK  
CheckDir: KBoost.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:KBoost.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings KBoost_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/KBoost.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘KBoost/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘KBoost’ version ‘1.9.0’
* 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 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 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 16.441  0.008  16.481
* 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 ...
  ‘KBoost.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/KBoost.Rcheck/00check.log’
for details.



Installation output

KBoost.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL KBoost
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’
* installing *source* package ‘KBoost’ ...
** 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 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(KBoost)
> 
> test_check("KBoost")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 7 ]
> 
> proc.time()
   user  system elapsed 
  0.842   0.054   0.884 

Example timings

KBoost.Rcheck/KBoost-Ex.timings

nameusersystemelapsed
AUPR_AUROC_matrix3.3070.0233.337
D4_multi_10.0010.0000.001
D4_multi_20.0010.0000.001
D4_multi_3000
D4_multi_40.0010.0000.001
D4_multi_50.0010.0000.001
G_D4_multi_10.0010.0000.001
G_D4_multi_2000
G_D4_multi_30.0010.0000.001
G_D4_multi_40.0010.0000.001
G_D4_multi_50.0010.0000.001
Gerstein_Prior_ENET_2000
Human_TFs0.0010.0000.001
IRMA_Gold0.0010.0000.001
KBoost_human_symbol0.0220.0000.022
KPC0.0110.0000.011
RBF_K0.0010.0000.001
add_names0.8520.0000.854
d4_mfac16.441 0.00816.481
get_prior_Gerstein0.0030.0000.004
get_tfs_human000
grid_search_kboost0.1830.0000.184
irma_check0.0190.0000.019
irma_off0.0010.0000.001
irma_on0.0000.0010.001
kboost0.8230.0020.827
kernel_normal0.0020.0000.001
kernel_pc_boosting0.5070.0080.516
net_dist_bin0.8300.0040.836
net_refine0.0060.0000.006
net_summary_bin0.8380.0120.852
tab_2_matrix_D40.0010.0000.001
write_GRN_D41.0050.0001.007