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This page was generated on 2022-06-27 11:10:10 -0400 (Mon, 27 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
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 nebbiolo1


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 2012/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TimiRGeN 1.6.0  (landing page)
Krutik Patel
Snapshot Date: 2022-06-26 13:55:11 -0400 (Sun, 26 Jun 2022)
git_url: https://git.bioconductor.org/packages/TimiRGeN
git_branch: RELEASE_3_15
git_last_commit: 55f72bc
git_last_commit_date: 2022-04-26 12:08:12 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: TimiRGeN
Version: 1.6.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:TimiRGeN.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings TimiRGeN_1.6.0.tar.gz
StartedAt: 2022-06-26 22:16:00 -0400 (Sun, 26 Jun 2022)
EndedAt: 2022-06-26 22:23:38 -0400 (Sun, 26 Jun 2022)
EllapsedTime: 457.7 seconds
RetCode: 0
Status:   OK  
CheckDir: TimiRGeN.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:TimiRGeN.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings TimiRGeN_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/TimiRGeN.Rcheck’
* using R version 4.2.0 (2022-04-22)
* 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 ‘1.6.0’
* 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 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
quickTCPred    7.129  0.918  12.444
quickHClust    6.746  0.766   8.462
quickDendro    6.435  0.799   8.727
makeMapp       5.856  0.571   9.821
wikiMrna       5.452  0.815   8.189
makeDynamic    5.564  0.568   9.872
clusterList    5.324  0.775   7.019
quickReg       4.514  0.583   5.825
quickPathwayTC 4.418  0.655   6.048
linearRegr     4.203  0.692   5.634
quickTC        4.184  0.627   5.604
quickDMap      4.074  0.619   5.520
multiReg       3.897  0.547   5.330
quickCrossCorr 3.761  0.529   5.040
addIds         3.804  0.294   5.621
* 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-3.15-bioc/meat/TimiRGeN.Rcheck/00check.log’
for details.



Installation output

TimiRGeN.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL TimiRGeN
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-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 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 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, 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 
 24.297   3.761  27.062 

Example timings

TimiRGeN.Rcheck/TimiRGeN-Ex.timings

nameusersystemelapsed
UUO_data0.0010.0050.006
addIds3.8040.2945.621
addPrefix0.6530.1370.761
clusterCheck0.9070.3191.657
clusterList5.3240.7757.019
combineGenes0.3980.1030.488
createClusters0.8140.1931.411
createClusters20.7590.1530.874
cytoMake0.0000.0000.001
diffExpressRes3.0090.4764.259
dloadGmt2.1900.4113.572
dloadMirdb0.0000.0000.001
dloadMirtarbase0.3420.0320.364
dloadTargetscan000
eNames3.5350.4424.755
e_list_mouse0.0020.0000.002
enrichWiki1.8570.3272.804
genesList0.8400.1390.947
getIdsMir0.8260.1730.975
getIdsMrna2.2960.3053.419
gmtEnsembl1.4210.3112.239
hs_mRNA0.0000.0010.002
hs_miR0.0000.0010.001
hs_probes0.0000.0010.001
linearRegr4.2030.6925.634
long_data0.0040.0000.004
makeDynamic5.5640.5689.872
makeMapp5.8560.5719.821
makeNet0.1450.0120.152
matrixFilter0.4640.0620.512
miRTarBase0.0020.0000.002
mirMrnaInt0.2980.0410.328
mm_mRNA0.0020.0000.001
mm_miR0.0020.0000.001
multiReg3.8970.5475.330
quickBar1.9950.2402.701
quickCrossCorr3.7610.5295.040
quickDMap4.0740.6195.520
quickDendro6.4350.7998.727
quickFuzz1.7810.2062.429
quickHClust6.7460.7668.462
quickMap0.4940.0740.558
quickNet0.1800.0240.198
quickPathwayTC4.4180.6556.048
quickReg4.5140.5835.825
quickTC4.1840.6275.604
quickTCPred 7.129 0.91812.444
reduceWiki0.7000.0750.776
returnCluster1.9270.2302.637
significantVals0.7030.0880.792
startObject0.2690.0190.287
turnPercent0.7590.1330.881
w_list_mouse0.0020.0000.002
wikiMatrix0.3210.0580.371
wikiMrna5.4520.8158.189