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This page was generated on 2022-06-24 12:08:15 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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 merida1


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: 2022-06-23 13:55:15 -0400 (Thu, 23 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
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    NA  

Summary

Package: TimiRGeN
Version: 1.6.0
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_1.6.0.tar.gz
StartedAt: 2022-06-24 09:55:30 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 10:11:49 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 978.9 seconds
RetCode: 0
Status:   OK  
CheckDir: TimiRGeN.Rcheck
Warnings: 0

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_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/TimiRGeN.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-apple-darwin17.0 (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
wikiMrna       13.836  3.965  19.559
clusterList    11.202  1.081  13.311
quickTCPred    10.053  1.061  11.952
quickHClust     9.924  1.037  18.828
quickReg        9.747  1.086  11.739
quickDMap       9.667  0.994  17.635
multiReg        9.663  0.992  19.320
quickTC         9.534  0.973  11.423
quickDendro     9.503  0.995  13.125
linearRegr      9.456  1.007  11.850
quickPathwayTC  9.320  0.925  11.321
quickCrossCorr  9.088  0.882  17.823
makeDynamic     9.010  0.935  11.136
addIds          8.709  1.008  10.806
eNames          7.838  0.723  10.225
makeMapp        7.702  0.699  12.621
diffExpressRes  7.565  0.711   9.231
getIdsMrna      5.596  0.409   7.241
enrichWiki      3.923  0.554   5.848
quickBar        3.818  0.473   5.918
* 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
  ‘/Users/biocbuild/bbs-3.15-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/4.2/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
** 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-apple-darwin17.0 (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 
 49.948  10.521  60.901 

Example timings

TimiRGeN.Rcheck/TimiRGeN-Ex.timings

nameusersystemelapsed
UUO_data0.0080.0050.013
addIds 8.709 1.00810.806
addPrefix1.4540.3011.791
clusterCheck2.0330.4272.844
clusterList11.202 1.08113.311
combineGenes0.9380.1581.141
createClusters1.8330.3192.498
createClusters21.7430.3362.090
cytoMake0.0000.0000.001
diffExpressRes7.5650.7119.231
dloadGmt3.5550.3534.773
dloadMirdb0.0000.0000.001
dloadMirtarbase0.7330.1121.074
dloadTargetscan0.0000.0000.001
eNames 7.838 0.72310.225
e_list_mouse0.0020.0020.005
enrichWiki3.9230.5545.848
genesList1.9590.3032.649
getIdsMir1.9550.2402.650
getIdsMrna5.5960.4097.241
gmtEnsembl2.8500.3514.335
hs_mRNA0.0020.0040.005
hs_miR0.0020.0030.006
hs_probes0.0020.0030.006
linearRegr 9.456 1.00711.850
long_data0.0050.0030.009
makeDynamic 9.010 0.93511.136
makeMapp 7.702 0.69912.621
makeNet0.2600.0350.626
matrixFilter0.6660.1021.490
miRTarBase0.0020.0030.006
mirMrnaInt0.7020.1091.592
mm_mRNA0.0020.0030.005
mm_miR0.0020.0030.005
multiReg 9.663 0.99219.320
quickBar3.8180.4735.918
quickCrossCorr 9.088 0.88217.823
quickDMap 9.667 0.99417.635
quickDendro 9.503 0.99513.125
quickFuzz1.9920.3394.455
quickHClust 9.924 1.03718.828
quickMap0.7790.1240.939
quickNet0.4100.0640.483
quickPathwayTC 9.320 0.92511.321
quickReg 9.747 1.08611.739
quickTC 9.534 0.97311.423
quickTCPred10.053 1.06111.952
reduceWiki0.9210.1511.075
returnCluster2.5570.4173.338
significantVals0.8660.1471.018
startObject0.3890.0590.449
turnPercent1.1840.1901.403
w_list_mouse0.0020.0030.007
wikiMatrix0.7500.1240.897
wikiMrna13.836 3.96519.559