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This page was generated on 2021-06-17 12:05:33 -0400 (Thu, 17 Jun 2021).

CHECK results for GRridge on riesling1

To the developers/maintainers of the GRridge package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GRridge.git to
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raw results

Package 792/1993HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GRridge 1.17.0  (landing page)
Mark A. van de Wiel
Snapshot Date: 2021-06-16 14:50:06 -0400 (Wed, 16 Jun 2021)
URL: https://git.bioconductor.org/packages/GRridge
Branch: master
Last Commit: 26c8069
Last Changed Date: 2021-05-19 12:24:38 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: GRridge
Version: 1.17.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GRridge.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GRridge_1.17.0.tar.gz
StartedAt: 2021-06-17 00:19:13 -0400 (Thu, 17 Jun 2021)
EndedAt: 2021-06-17 00:22:16 -0400 (Thu, 17 Jun 2021)
EllapsedTime: 183.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: GRridge.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GRridge.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GRridge_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/GRridge.Rcheck'
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GRridge/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GRridge' version '1.17.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'penalized', 'Iso', 'survival', 'graph', 'glmnet', 'mvtnorm'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'GRridge' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.2Mb
  sub-directories of 1Mb or more:
    data   8.8Mb
* 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  predict.grridge
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.grridgelin: no visible binding for global variable 'datapred'
predict.grridge: no visible binding for global variable 'samout'
Undefined global functions or variables:
  datapred samout
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented data sets:
  'Y' 'part5' 'simdata'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 data for ASCII and uncompressed saves ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                    old_size new_size compress
  dataFarkas.rda       3.4Mb    2.5Mb    bzip2
  dataWurdinger.rda    2.0Mb    1.2Mb       xz
* 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
dataSimlin 15.65   0.26   17.58
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
dataSimlin 14.58   0.33   15.39
* 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: 2 WARNINGs, 4 NOTEs
See
  'D:/biocbuild/bbs-3.14-bioc/meat/GRridge.Rcheck/00check.log'
for details.



Installation output

GRridge.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/GRridge_1.17.0.tar.gz && rm -rf GRridge.buildbin-libdir && mkdir GRridge.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GRridge.buildbin-libdir GRridge_1.17.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL GRridge_1.17.0.zip && rm GRridge_1.17.0.tar.gz GRridge_1.17.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 31 8975k   31 2790k    0     0  7156k      0  0:00:01 --:--:--  0:00:01 7138k
100 8975k  100 8975k    0     0   9.9M      0 --:--:-- --:--:-- --:--:--  9.9M

install for i386

* installing *source* package 'GRridge' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GRridge'
    finding HTML links ... done
    CreatePartition                         html  
    GRridge-package                         html  
    PartitionsSelection                     html  
    auc                                     html  
    dataFarkas                              html  
    dataSimlin                              html  
    dataVerlaat                             html  
    dataWurdinger                           html  
    grridge                                 html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.14-bioc/meat/GRridge.buildbin-libdir/00LOCK-GRridge/00new/GRridge/help/grridge.html
    grridgeCV                               html  
    hello                                   html  
    matchGeneSets                           html  
    mergeGroups                             html  
    predict.grridge                         html  
    roc                                     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 'GRridge' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GRridge' as GRridge_1.17.0.zip
* DONE (GRridge)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'GRridge' successfully unpacked and MD5 sums checked

Tests output

GRridge.Rcheck/tests_i386/testthat.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 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("GRridge")
Loading required package: penalized
Loading required package: survival
Welcome to penalized. For extended examples, see vignette("penalized").
Loading required package: Iso
Iso 0.0-18.1
Loading required package: graph
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following object is masked from 'package:penalized':

    as.data.frame

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: glmnet
Loading required package: Matrix
Loaded glmnet 4.1-1
Loading required package: mvtnorm
> 
> testthat::test_check("GRridge")
[1] "Summary of group sizes:"
 VarIn VarOut 
    50     50 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
   1.82    0.12    2.42 

GRridge.Rcheck/tests_x64/testthat.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 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("GRridge")
Loading required package: penalized
Loading required package: survival
Welcome to penalized. For extended examples, see vignette("penalized").
Loading required package: Iso
Iso 0.0-18.1
Loading required package: graph
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following object is masked from 'package:penalized':

    as.data.frame

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: glmnet
Loading required package: Matrix
Loaded glmnet 4.1-1
Loading required package: mvtnorm
> 
> testthat::test_check("GRridge")
[1] "Summary of group sizes:"
 VarIn VarOut 
    50     50 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
   1.87    0.20    2.03 

Example timings

GRridge.Rcheck/examples_i386/GRridge-Ex.timings

nameusersystemelapsed
CreatePartition0.020.010.04
PartitionsSelection0.000.020.01
auc0.060.020.08
dataFarkas0.060.000.06
dataSimlin15.65 0.2617.58
dataVerlaat0.040.000.03
dataWurdinger1.230.021.29
grridge0.130.000.13
grridgeCV0.140.000.17
hello000
matchGeneSets0.900.040.95
mergeGroups0.630.050.67
predict.grridge000
roc0.840.051.46

GRridge.Rcheck/examples_x64/GRridge-Ex.timings

nameusersystemelapsed
CreatePartition0.080.000.10
PartitionsSelection000
auc0.100.020.11
dataFarkas0.110.000.11
dataSimlin14.58 0.3315.39
dataVerlaat0.030.000.03
dataWurdinger1.150.001.36
grridge0.070.000.06
grridgeCV0.040.030.08
hello000
matchGeneSets0.740.040.78
mergeGroups1.030.051.19
predict.grridge000
roc0.890.000.89