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This page was generated on 2022-06-27 11:05:33 -0400 (Mon, 27 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
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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 1992/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TimiRGeN 1.7.0  (landing page)
Krutik Patel
Snapshot Date: 2022-06-26 14:00:03 -0400 (Sun, 26 Jun 2022)
git_url: https://git.bioconductor.org/packages/TimiRGeN
git_branch: master
git_last_commit: f5d5c1d
git_last_commit_date: 2022-04-26 12:08:12 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: TimiRGeN
Version: 1.7.0
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/library --no-vignettes --timings TimiRGeN_1.7.0.tar.gz
StartedAt: 2022-06-26 22:06:07 -0400 (Sun, 26 Jun 2022)
EndedAt: 2022-06-26 22:13:33 -0400 (Sun, 26 Jun 2022)
EllapsedTime: 445.9 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/library --no-vignettes --timings TimiRGeN_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/TimiRGeN.Rcheck’
* using R version 4.2.0 Patched (2022-06-02 r82447)
* 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 ‘1.7.0’
* 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
linearRegr     8.206  0.942  12.391
clusterList    6.201  0.934   9.488
quickDMap      6.262  0.814  10.108
quickDendro    5.780  0.740   8.105
makeDynamic    5.136  0.617   6.768
diffExpressRes 4.459  0.610   6.715
wikiMrna       3.987  0.624   6.036
quickReg       3.796  0.811   5.416
quickTCPred    3.699  0.777   5.418
quickPathwayTC 3.702  0.707   5.221
quickTC        3.695  0.659   5.227
quickHClust    3.602  0.606   5.035
addIds         3.207  0.414   5.167
* 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-3.16-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/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 Patched (2022-06-02 r82447) -- "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 
 24.658   4.236  27.897 

Example timings

TimiRGeN.Rcheck/TimiRGeN-Ex.timings

nameusersystemelapsed
UUO_data0.0020.0040.006
addIds3.2070.4145.167
addPrefix0.6830.1240.779
clusterCheck1.1570.2351.894
clusterList6.2010.9349.488
combineGenes0.6880.0790.767
createClusters1.6420.2382.870
createClusters21.3630.1941.850
cytoMake0.0000.0010.000
diffExpressRes4.4590.6106.715
dloadGmt1.5030.2573.077
dloadMirdb000
dloadMirtarbase0.3650.0200.376
dloadTargetscan000
eNames3.0040.3474.248
e_list_mouse0.0010.0000.001
enrichWiki2.1590.2542.932
genesList0.9800.1381.078
getIdsMir1.1350.1191.229
getIdsMrna2.0250.3583.295
gmtEnsembl1.8070.2092.498
hs_mRNA0.0000.0030.003
hs_miR0.0030.0000.002
hs_probes0.0020.0000.002
linearRegr 8.206 0.94212.391
long_data0.0020.0040.006
makeDynamic5.1360.6176.768
makeMapp2.8940.4474.234
makeNet0.0790.0250.101
matrixFilter0.2700.0690.329
miRTarBase0.0010.0010.002
mirMrnaInt0.3540.0570.400
mm_mRNA0.0010.0000.001
mm_miR0.0010.0000.001
multiReg3.4750.5294.938
quickBar1.6540.2572.368
quickCrossCorr3.2430.4854.563
quickDMap 6.262 0.81410.108
quickDendro5.7800.7408.105
quickFuzz1.5230.1952.029
quickHClust3.6020.6065.035
quickMap0.3520.0370.378
quickNet0.2300.0370.259
quickPathwayTC3.7020.7075.221
quickReg3.7960.8115.416
quickTC3.6950.6595.227
quickTCPred3.6990.7775.418
reduceWiki0.4120.0620.459
returnCluster1.1490.2331.685
significantVals0.3940.0370.414
startObject0.1480.0330.174
turnPercent0.5000.0910.569
w_list_mouse0.0010.0000.001
wikiMatrix0.3400.0860.412
wikiMrna3.9870.6246.036