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This page was generated on 2024-05-21 11:38:37 -0400 (Tue, 21 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4751
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4485
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4515
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 2166/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TimiRGeN 1.14.0  (landing page)
Krutik Patel
Snapshot Date: 2024-05-20 14:00:15 -0400 (Mon, 20 May 2024)
git_url: https://git.bioconductor.org/packages/TimiRGeN
git_branch: RELEASE_3_19
git_last_commit: 1b922fc
git_last_commit_date: 2024-04-30 11:26:47 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for TimiRGeN on lconway


To the developers/maintainers of the TimiRGeN package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TimiRGeN.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: TimiRGeN
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TimiRGeN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TimiRGeN_1.14.0.tar.gz
StartedAt: 2024-05-21 00:23:56 -0400 (Tue, 21 May 2024)
EndedAt: 2024-05-21 00:35:53 -0400 (Tue, 21 May 2024)
EllapsedTime: 716.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: TimiRGeN.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TimiRGeN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TimiRGeN_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/TimiRGeN.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TimiRGeN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TimiRGeN’ version ‘1.14.0’
* 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 ‘TimiRGeN’ 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 code 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 whether 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 ... OK
* 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 ... NOTE
  Note: found 3 marked UTF-8 strings
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘TimiRGeN-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dloadGmt
> ### Title: dloadGmt
> ### Aliases: dloadGmt
> 
> ### ** Examples
> 
> MAE <- MultiAssayExperiment()
> 
> MAE <- dloadGmt(MAE, species = "Homo sapiens")
Error in rWikiPathways::downloadPathwayArchive(organism = species, format = "gmt") : 
  Could not find a file matching your specifications. Try browsing https://data.wikipathways.org.
trying URL 'https://data.wikipathways.org/20230110/gmt/wikipathways-20230110-gmt-Homo_sapiens.gmt'
Warning in download.file(url, paste(destpath, filename, sep = "/"), "auto") :
  downloaded length 0 != reported length 9379
Warning in download.file(url, paste(destpath, filename, sep = "/"), "auto") :
  cannot open URL 'https://data.wikipathways.org/20230110/gmt/wikipathways-20230110-gmt-Homo_sapiens.gmt': HTTP status was '404 Not Found'
Error in download.file(url, paste(destpath, filename, sep = "/"), "auto") : 
  cannot open URL 'https://data.wikipathways.org/20230110/gmt/wikipathways-20230110-gmt-Homo_sapiens.gmt'
Calls: dloadGmt -> <Anonymous> -> download.file
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/TimiRGeN.Rcheck/00check.log’
for details.


Installation output

TimiRGeN.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TimiRGeN
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘TimiRGeN’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** 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 in fun(libname, pkgname) :
  Package 'TimiRGeN' is deprecated and will be removed from Bioconductor
  version 3.20
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'TimiRGeN' is deprecated and will be removed from Bioconductor
  version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (TimiRGeN)

Tests output

TimiRGeN.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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.

> #unit test check
> library(testthat)
> library(TimiRGeN)
Loading required package: Mfuzz
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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, table, tapply,
    union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: e1071

Attaching package: 'DynDoc'

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

    path

Loading required package: MultiAssayExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

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

    rowMedians

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb

Warning message:
In fun(libname, pkgname) :
  Package 'TimiRGeN' is deprecated and will be removed from Bioconductor
  version 3.20
> test_check(package = "TimiRGeN")
[ FAIL 0 | WARN 49 | SKIP 0 | PASS 124 ]

[ FAIL 0 | WARN 49 | SKIP 0 | PASS 124 ]
> 
> proc.time()
   user  system elapsed 
 38.471  11.722  51.581 

Example timings

TimiRGeN.Rcheck/TimiRGeN-Ex.timings

nameusersystemelapsed
UUO_data0.0050.0020.008
addIds 6.696 1.42814.739
addPrefix0.8250.2401.103
clusterCheck4.1561.1907.062
clusterList 8.060 1.67510.032
combineGenes0.5200.1330.664
createClusters3.9071.1046.321
createClusters21.0390.3201.399
cytoMake0.0000.0010.000
diffExpressRes5.8141.1447.305