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This page was generated on 2023-03-29 11:05:21 -0400 (Wed, 29 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4482
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4278
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4306
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 TimiRGeN on nebbiolo2


To the developers/maintainers of the TimiRGeN package:
- Please 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 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 2053/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TimiRGeN 1.8.0  (landing page)
Krutik Patel
Snapshot Date: 2023-03-27 14:00:04 -0400 (Mon, 27 Mar 2023)
git_url: https://git.bioconductor.org/packages/TimiRGeN
git_branch: RELEASE_3_16
git_last_commit: 6150789
git_last_commit_date: 2022-11-01 11:22:47 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: TimiRGeN
Version: 1.8.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:TimiRGeN.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings TimiRGeN_1.8.0.tar.gz
StartedAt: 2023-03-28 00:39:15 -0400 (Tue, 28 Mar 2023)
EndedAt: 2023-03-28 00:47:22 -0400 (Tue, 28 Mar 2023)
EllapsedTime: 486.5 seconds
RetCode: 0
Status:   OK  
CheckDir: TimiRGeN.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:TimiRGeN.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings TimiRGeN_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/TimiRGeN.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘TimiRGeN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TimiRGeN’ version ‘1.8.0’
* 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 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 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
wikiMrna    5.811  0.931  11.240
makeDynamic 3.858  0.643   5.034
addIds      2.998  0.402   5.163
* 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 ...
  ‘TimiRGeN_tutorial.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/TimiRGeN.Rcheck/00check.log’
for details.



Installation output

TimiRGeN.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL TimiRGeN
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (TimiRGeN)

Tests output

TimiRGeN.Rcheck/tests/testthat.Rout


R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 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.

> #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, sort, 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 objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb

> 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 
 29.959   4.051  34.474 

Example timings

TimiRGeN.Rcheck/TimiRGeN-Ex.timings

nameusersystemelapsed
UUO_data0.0040.0010.004
addIds2.9980.4025.163
addPrefix1.4090.2341.618
clusterCheck0.6930.2061.562
clusterList3.1000.6414.203
combineGenes0.3270.0660.379
createClusters0.7240.1771.533
createClusters20.6420.1420.749
cytoMake000
diffExpressRes2.5940.4313.470
dloadGmt1.2610.2372.037
dloadMirdb000
dloadMirtarbase0.2980.0330.320
dloadTargetscan000
eNames2.6270.3923.535
e_list_mouse0.0010.0010.002
enrichWiki1.8650.2782.651
genesList0.6460.0930.713
getIdsMir0.7890.0810.854
getIdsMrna1.7080.3022.535
gmtEnsembl1.2380.1831.965
hs_mRNA0.0000.0010.001
hs_miR0.0000.0010.001
hs_probes0.0000.0010.001
linearRegr3.2770.5654.262
long_data0.0000.0030.003
makeDynamic3.8580.6435.034
makeMapp2.3770.5113.326
makeNet0.0460.0220.066
matrixFilter0.2630.0460.299
miRTarBase0.0020.0000.001
mirMrnaInt0.2230.0460.256
mm_mRNA0.0010.0000.001
mm_miR0.0010.0000.001
multiReg2.9630.5823.981
quickBar1.6640.2322.366
quickCrossCorr2.8680.5343.835
quickDMap3.1300.6824.260
quickDendro3.1100.5534.303
quickFuzz0.7010.1951.575
quickHClust3.2730.6254.410
quickMap0.2670.0500.306
quickNet0.1270.0220.143
quickPathwayTC3.0170.6204.248
quickReg3.1830.6684.284
quickTC3.0660.6024.303
quickTCPred3.3580.5964.448
reduceWiki0.2760.0420.306
returnCluster1.0730.1571.802
significantVals0.3170.0410.344
startObject0.1310.0090.135
turnPercent0.4760.0770.534
w_list_mouse0.0010.0000.001
wikiMatrix0.2120.0410.245
wikiMrna 5.811 0.93111.240