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This page was generated on 2024-03-27 11:35:54 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4667
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4403
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4426
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 906/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GRridge 1.26.0  (landing page)
Mark A. van de Wiel
Snapshot Date: 2024-03-25 14:05:07 -0400 (Mon, 25 Mar 2024)
git_url: https://git.bioconductor.org/packages/GRridge
git_branch: RELEASE_3_18
git_last_commit: d07ed8f
git_last_commit_date: 2023-10-24 10:54:19 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino4Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for GRridge on nebbiolo2


To the developers/maintainers of the GRridge package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GRridge.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: GRridge
Version: 1.26.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:GRridge.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings GRridge_1.26.0.tar.gz
StartedAt: 2024-03-25 22:55:48 -0400 (Mon, 25 Mar 2024)
EndedAt: 2024-03-25 22:57:29 -0400 (Mon, 25 Mar 2024)
EllapsedTime: 100.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: GRridge.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:GRridge.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings GRridge_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/GRridge.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘GRridge/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GRridge’ version ‘1.26.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘GRridge’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'GRridge' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.18-bioc/meat/GRridge.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  9.1Mb
  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
* 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 startup messages can be suppressed ... 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
.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:
  ‘CpGannFarkas’ ‘datcenFarkas’ ‘respFarkas’ ‘Y’ ‘part5’ ‘simdata’
  ‘CpGann’ ‘datcenVerlaat’ ‘diffmeanFarkas’ ‘pvalFarkas’ ‘respVerlaat’
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 ... OK
* 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 ...
  ‘GRridge.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! LaTeX Error: Something's wrong--perhaps a missing \item.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
* checking PDF version of manual without index ... ERROR
* DONE

Status: 1 ERROR, 4 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/GRridge.Rcheck/00check.log’
for details.


Installation output

GRridge.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL GRridge
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘GRridge’ ...
** using staged installation
** R
** data
** 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
Warning: Package 'GRridge' is deprecated and will be removed from Bioconductor
  version 3.19
** testing if installed package can be loaded from final location
Warning: Package 'GRridge' is deprecated and will be removed from Bioconductor
  version 3.19
** testing if installed package keeps a record of temporary installation path
* DONE (GRridge)

Tests output

GRridge.Rcheck/tests/testthat.Rout


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 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("GRridge")
Loading required package: penalized
Loading required package: survival
Welcome to penalized. For extended examples, see vignette("penalized").
Loading required package: Iso
Iso 0.0-21

     An "infelicity" in the function ufit() (whereby 
     it was all too easy to conflate the location of 
     the mode with its index in the entries of the 
     "x" argument) has been corrected.  To this end, 
     ufit() now has arguments "lmode" (the location 
     of the mode), and "imode" (its index).  At most 
     one of these arguments should be specified.  See 
     the help for ufit().
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, aperm, 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 4.1-8
Loading required package: mvtnorm
Warning message:
Package 'GRridge' is deprecated and will be removed from Bioconductor
  version 3.19 
> 
> 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 
  1.990   0.140   2.119 

Example timings

GRridge.Rcheck/GRridge-Ex.timings

nameusersystemelapsed
CreatePartition0.0520.0000.052
PartitionsSelection000
auc0.1020.0040.106
dataWurdinger1.1570.0721.229
grridge0.3180.0040.322
grridgeCV0.0780.0120.090
hello000
matchGeneSets0.7780.0480.826
mergeGroups0.9040.0440.948
predict.grridge000
roc1.0230.0161.039