Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:05:31 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 nebbiolo2


To the developers/maintainers of the KBoost package:
- Please 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 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 976/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
KBoost 1.2.0  (landing page)
Luis F. Iglesias-Martinez
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/KBoost
git_branch: RELEASE_3_14
git_last_commit: a207b80
git_last_commit_date: 2021-10-26 13:10:17 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: KBoost
Version: 1.2.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:KBoost.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings KBoost_1.2.0.tar.gz
StartedAt: 2022-04-12 07:57:47 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 07:58:15 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 27.6 seconds
RetCode: 0
Status:   OK  
CheckDir: KBoost.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:KBoost.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings KBoost_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/KBoost.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘KBoost/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘KBoost’ version ‘1.2.0’
* 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 ... 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 ... 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 5.117  0.008   5.125
* 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-3.14-bioc/meat/KBoost.Rcheck/00check.log’
for details.



Installation output

KBoost.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL KBoost
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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 4.1.3 (2022-03-10) -- "One Push-Up"
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(KBoost)
> 
> test_check("KBoost")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 7 ]
> 
> proc.time()
   user  system elapsed 
  0.609   0.054   0.643 

Example timings

KBoost.Rcheck/KBoost-Ex.timings

nameusersystemelapsed
AUPR_AUROC_matrix0.9890.0451.034
D4_multi_10.0010.0000.001
D4_multi_20.0010.0000.000
D4_multi_3000
D4_multi_40.0010.0000.000
D4_multi_50.0000.0010.000
G_D4_multi_10.0000.0010.000
G_D4_multi_20.0000.0010.001
G_D4_multi_30.0000.0010.001
G_D4_multi_40.0000.0000.001
G_D4_multi_50.0000.0000.001
Gerstein_Prior_ENET_20.0000.0000.001
Human_TFs0.0000.0000.001
IRMA_Gold0.0000.0000.001
KBoost_human_symbol0.0150.0000.015
KPC0.0030.0000.003
RBF_K000
add_names0.4590.0000.459
d4_mfac5.1170.0085.125
get_prior_Gerstein0.0030.0000.002
get_tfs_human000
grid_search_kboost0.1190.0000.120
irma_check0.0090.0000.009
irma_off0.0000.0000.001
irma_on0.0000.0000.001
kboost0.4310.0000.432
kernel_normal0.0000.0000.001
kernel_pc_boosting0.3030.0000.303
net_dist_bin0.4530.0000.454
net_refine0.0030.0000.003
net_summary_bin0.4600.0000.459
tab_2_matrix_D40.0010.0000.000
write_GRN_D40.5500.0030.553