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CHECK report for TimiRGeN on malbec1

This page was generated on 2021-05-06 12:29:27 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the TimiRGeN package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1865/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TimiRGeN 1.0.6  (landing page)
Krutik Patel
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/TimiRGeN
Branch: RELEASE_3_12
Last Commit: ef00328
Last Changed Date: 2021-04-28 08:21:03 -0400 (Wed, 28 Apr 2021)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: TimiRGeN
Version: 1.0.6
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:TimiRGeN.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings TimiRGeN_1.0.6.tar.gz
StartedAt: 2021-05-06 06:41:26 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 06:50:02 -0400 (Thu, 06 May 2021)
EllapsedTime: 516.3 seconds
RetCode: 0
Status:   OK  
CheckDir: TimiRGeN.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:TimiRGeN.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings TimiRGeN_1.0.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/TimiRGeN.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TimiRGeN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TimiRGeN’ version ‘1.0.6’
* 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 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 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       6.216  0.248   9.986
quickTCPred    6.112  0.280   8.262
clusterList    5.964  0.284  11.288
quickTC        5.764  0.264   7.904
addIds         5.560  0.376   7.682
quickPathwayTC 5.472  0.296   7.425
quickHClust    5.436  0.332   7.545
quickCrossCorr 5.524  0.228   7.731
makeDynamic    5.336  0.224   7.392
linearRegr     5.260  0.300   8.929
quickDMap      5.100  0.272   7.102
quickDendro    4.880  0.288   6.873
quickReg       4.812  0.260   6.817
multiReg       4.820  0.240   7.649
makeMapp       4.844  0.184   7.208
eNames         4.656  0.232   6.919
diffExpressRes 4.592  0.208   8.369
enrichWiki     4.480  0.200   5.692
getIdsMrna     3.064  0.128   7.257
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/TimiRGeN.Rcheck/00check.log’
for details.



Installation output

TimiRGeN.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL TimiRGeN
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

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:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb

> test_check(package = "TimiRGeN")
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 125 ]
> 
> proc.time()
   user  system elapsed 
 28.676   1.956  32.383 

Example timings

TimiRGeN.Rcheck/TimiRGeN-Ex.timings

nameusersystemelapsed
UUO_data0.0080.0000.005
addIds5.5600.3767.682
addPrefix0.9360.0641.010
clusterCheck1.4320.0962.006
clusterList 5.964 0.28411.288
combineGenes0.5120.0280.536
createClusters1.2240.0761.737
createClusters20.9520.1161.057
cytoMake0.0040.0000.000
diffExpressRes4.5920.2088.369
dloadGmt2.4080.0643.424
dloadMirdb000
dloadMirtarbase0.3360.0200.357
dloadTargetscan000
eNames4.6560.2326.919
e_list_mouse0.0000.0000.002
enrichWiki4.4800.2005.692
genesList0.9760.0881.059
getIdsMir1.0600.0641.118
getIdsMrna3.0640.1287.257
gmtEnsembl1.9400.0643.016
hs_mRNA0.0000.0000.001
hs_miR0.0000.0000.001
hs_probes0.0000.0040.001
linearRegr5.2600.3008.929
long_data0.0040.0000.005
makeDynamic5.3360.2247.392
makeMapp4.8440.1847.208
makeNet0.0920.0000.091
matrixFilter0.3280.0120.346
miRTarBase0.0000.0000.002
mirMrnaInt0.5120.0400.557
mm_mRNA0.0000.0000.002
mm_miR0.0040.0000.002
multiReg4.8200.2407.649
quickBar2.4680.1643.569
quickCrossCorr5.5240.2287.731
quickDMap5.1000.2727.102
quickDendro4.8800.2886.873
quickFuzz1.3400.0841.858
quickHClust5.4360.3327.545
quickMap0.3800.0040.383
quickNet0.1760.0080.187
quickPathwayTC5.4720.2967.425
quickReg4.8120.2606.817
quickTC5.7640.2647.904
quickTCPred6.1120.2808.262
reduceWiki0.5240.0400.559
returnCluster1.4800.1282.037
significantVals0.5560.0200.587
startObject0.1680.0120.179
turnPercent0.5600.0560.621
w_list_mouse0.0040.0000.001
wikiMatrix0.3320.0120.346
wikiMrna6.2160.2489.986