Multiple platform build/check report for BioC 3.14 - CHECK results for KBoost on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (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*

Package: KBoost

Version: 1.2.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:KBoost.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings KBoost_1.2.0.tar.gz

StartedAt: 2022-04-12 21:50:50 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 21:51:51 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 61.8 seconds

RetCode: 0

Status: OK

CheckDir: KBoost.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:KBoost.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings KBoost_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/KBoost.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
        user system elapsed
d4_mfac 5.25      0    5.25
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
        user system elapsed
d4_mfac 5.22   0.04    5.26
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/KBoost.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/KBoost_1.2.0.tar.gz && rm -rf KBoost.buildbin-libdir && mkdir KBoost.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=KBoost.buildbin-libdir KBoost_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL KBoost_1.2.0.zip && rm KBoost_1.2.0.tar.gz KBoost_1.2.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 90  492k   90  444k    0     0   698k      0 --:--:-- --:--:-- --:--:--  699k
100  492k  100  492k    0     0   730k      0 --:--:-- --:--:-- --:--:--  731k

install for i386

* 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
  converting help for package 'KBoost'
    finding HTML links ... done
    AUPR_AUROC_matrix                       html  
    D4_multi_1                              html  
    D4_multi_2                              html  
    D4_multi_3                              html  
    D4_multi_4                              html  
    D4_multi_5                              html  
    G_D4_multi_1                            html  
    G_D4_multi_2                            html  
    G_D4_multi_3                            html  
    G_D4_multi_4                            html  
    G_D4_multi_5                            html  
    Gerstein_Prior_ENET_2                   html  
    Human_TFs                               html  
    IRMA_Gold                               html  
    KBoost_human_symbol                     html  
    KPC                                     html  
    RBF_K                                   html  
    add_names                               html  
    d4_mfac                                 html  
    get_prior_Gerstein                      html  
    get_tfs_human                           html  
    grid_search_kboost                      html  
    irma_check                              html  
    irma_off                                html  
    irma_on                                 html  
    kboost                                  html  
    kernel_normal                           html  
    kernel_pc_boosting                      html  
    net_dist_bin                            html  
    net_refine                              html  
    net_summary_bin                         html  
    tab_2_matrix_D4                         html  
    write_GRN_D4                            html  
** 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

install for x64

* installing *source* package 'KBoost' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'KBoost' as KBoost_1.2.0.zip
* DONE (KBoost)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'KBoost' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
   0.98    0.09    1.06


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
   0.90    0.09    0.98

name	user	system	elapsed
AUPR_AUROC_matrix	1.40	0.06	1.58
D4_multi_1	0.00	0.02	0.01
D4_multi_2	0	0	0
D4_multi_3	0	0	0
D4_multi_4	0	0	0
D4_multi_5	0	0	0
G_D4_multi_1	0	0	0
G_D4_multi_2	0.00	0.02	0.01
G_D4_multi_3	0	0	0
G_D4_multi_4	0	0	0
G_D4_multi_5	0	0	0
Gerstein_Prior_ENET_2	0	0	0
Human_TFs	0.02	0.00	0.02
IRMA_Gold	0	0	0
KBoost_human_symbol	0.01	0.00	0.02
KPC	0	0	0
RBF_K	0.02	0.00	0.01
add_names	0.58	0.00	0.58
d4_mfac	5.25	0.00	5.25
get_prior_Gerstein	0	0	0
get_tfs_human	0	0	0
grid_search_kboost	0.11	0.00	0.10
irma_check	0.02	0.00	0.02
irma_off	0	0	0
irma_on	0	0	0
kboost	0.51	0.00	0.52
kernel_normal	0	0	0
kernel_pc_boosting	0.39	0.00	0.39
net_dist_bin	0.52	0.00	0.51
net_refine	0	0	0
net_summary_bin	0.53	0.00	0.53
tab_2_matrix_D4	0	0	0
write_GRN_D4	0.72	0.00	0.72

name	user	system	elapsed
AUPR_AUROC_matrix	1.19	0.09	1.31
D4_multi_1	0.02	0.00	0.02
D4_multi_2	0.00	0.02	0.01
D4_multi_3	0	0	0
D4_multi_4	0	0	0
D4_multi_5	0	0	0
G_D4_multi_1	0.00	0.01	0.02
G_D4_multi_2	0	0	0
G_D4_multi_3	0	0	0
G_D4_multi_4	0	0	0
G_D4_multi_5	0	0	0
Gerstein_Prior_ENET_2	0	0	0
Human_TFs	0	0	0
IRMA_Gold	0	0	0
KBoost_human_symbol	0.02	0.00	0.02
KPC	0.00	0.02	0.01
RBF_K	0	0	0
add_names	0.53	0.00	0.54
d4_mfac	5.22	0.04	5.26
get_prior_Gerstein	0	0	0
get_tfs_human	0	0	0
grid_search_kboost	0.14	0.00	0.14
irma_check	0	0	0
irma_off	0	0	0
irma_on	0	0	0
kboost	0.50	0.02	0.51
kernel_normal	0	0	0
kernel_pc_boosting	0.41	0.00	0.41
net_dist_bin	0.53	0.00	0.53
net_refine	0	0	0
net_summary_bin	0.55	0.00	0.55
tab_2_matrix_D4	0	0	0
write_GRN_D4	0.69	0.00	0.69

CHECK results for KBoost on tokay2

Summary

Command output

Installation output

Tests output

Example timings