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This page was generated on 2022-01-25 11:07:32 -0500 (Tue, 25 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4164
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4059
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4001
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4118
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 isomiRs on riesling1


To the developers/maintainers of the isomiRs package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/isomiRs.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 964/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
isomiRs 1.23.1  (landing page)
Lorena Pantano
Snapshot Date: 2022-01-24 13:55:18 -0500 (Mon, 24 Jan 2022)
git_url: https://git.bioconductor.org/packages/isomiRs
git_branch: master
git_last_commit: 1e62c9a
git_last_commit_date: 2021-11-21 00:21:43 -0500 (Sun, 21 Nov 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'SummarizedExperiment' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: isomiRs
Version: 1.23.1
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:isomiRs.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings isomiRs_1.23.1.tar.gz
StartedAt: 2022-01-24 19:12:48 -0500 (Mon, 24 Jan 2022)
EndedAt: 2022-01-24 19:16:30 -0500 (Mon, 24 Jan 2022)
EllapsedTime: 222.2 seconds
RetCode: 0
Status:   OK  
CheckDir: isomiRs.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:isomiRs.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings isomiRs_1.23.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/isomiRs.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'isomiRs/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'isomiRs' version '1.23.1'
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'isomiRs' 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 ... NOTE
.clean_noise: no visible binding for global variable 'total'
.clean_noise: no visible binding for global variable 'hits'
.remove_gt_n_changes: no visible binding for global variable 'changes'
isoAnnotate: no visible binding for global variable 'pct'
isoCounts: no visible global function definition for 'as.tibble'
isoPlot: no visible binding for global variable 'iso_sample'
isoPlotPosition: no visible binding for global variable 'iso_sample'
mirna2targetscan: no visible binding for global variable
  'targetscan.Hs.egMIRNA'
mirna2targetscan: no visible binding for global variable
  'targetscan.Hs.egMIRBASE2FAMILY'
mirna2targetscan: no visible binding for global variable
  'targetscan.Hs.egTARGETS'
mirna2targetscan: no visible binding for global variable
  'targetscan.Hs.egTARGETSFULL'
mirna2targetscan: no visible binding for global variable
  'targetscan.Mm.egMIRNA'
mirna2targetscan: no visible binding for global variable
  'targetscan.Mm.egMIRBASE2FAMILY'
mirna2targetscan: no visible binding for global variable
  'targetscan.Mm.egTARGETS'
mirna2targetscan: no visible binding for global variable
  'targetscan.Mm.egTARGETSFULL'
Undefined global functions or variables:
  as.tibble changes hits iso_sample pct targetscan.Hs.egMIRBASE2FAMILY
  targetscan.Hs.egMIRNA targetscan.Hs.egTARGETS
  targetscan.Hs.egTARGETSFULL targetscan.Mm.egMIRBASE2FAMILY
  targetscan.Mm.egMIRNA targetscan.Mm.egTARGETS
  targetscan.Mm.egTARGETSFULL total
* 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 ... OK
* 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
isoNetwork  5.6   0.05    5.65
* 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: 2 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/isomiRs.Rcheck/00check.log'
for details.



Installation output

isomiRs.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL isomiRs
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'isomiRs' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
Registered S3 method overwritten by 'GGally':
  method from   
  +.gg   ggplot2
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'isomiRs'
    finding HTML links ... done
    IsomirDataSeq                           html  
    IsomirDataSeqFromFiles                  html  
    IsomirDataSeqFromMirtop                 html  
    IsomirDataSeqFromRawData                html  
    counts                                  html  
    dat286.long                             html  
    design                                  html  
    ego                                     html  
    findTargets                             html  
    gene_ex_rse                             html  
    isoAnnotate                             html  
    isoCounts                               html  
    isoDE                                   html  
    isoNetwork                              html  
    isoNorm                                 html  
    isoPLSDA                                html  
    isoPLSDAplot                            html  
    isoPlot                                 html  
    isoPlotNet                              html  
    isoPlotPosition                         html  
    isoSelect                               html  
    isoTop                                  html  
    isomiRs-package                         html  
    ma_ex                                   html  
    mirData                                 html  
    mirTritation                            html  
    mirna2targetscan                        html  
    mirna_ex_rse                            html  
    updateIsomirDataSeq                     html  
** 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 (isomiRs)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'rtracklayer' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'TPP2D' is missing or broken
 done

Tests output

isomiRs.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.

> library(testthat)
> library(isomiRs)
Loading required package: DiscriMiner
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

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

Loading required package: GenomicRanges
Loading required package: stats4
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

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

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

    anyMissing, rowMedians

> 
> test_check("isomiRs")
Dimmension of cor matrix: 20 20 
Dimmension of cor matrix: 3 2 
Dimmension of cor matrix: 3 2 
Dimmension of cor matrix: 0 0 
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 28 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 28 ]
> 
> proc.time()
   user  system elapsed 
  17.75    1.10   19.20 

Example timings

isomiRs.Rcheck/isomiRs-Ex.timings

nameusersystemelapsed
IsomirDataSeq0.970.251.14
IsomirDataSeqFromFiles0.890.060.90
IsomirDataSeqFromMirtop0.390.050.44
IsomirDataSeqFromRawData0.860.090.86
counts0.060.030.09
design0.720.020.74
findTargets0.060.000.06
isoAnnotate3.850.083.92
isoCounts0.450.030.49
isoDE3.840.013.85
isoNetwork5.600.055.65
isoNorm1.510.001.51
isoPLSDA1.750.061.81
isoPLSDAplot1.830.051.88
isoPlot0.500.030.53
isoPlotPosition0.440.000.44
isoSelect0.220.020.23
isoTop0.200.010.22
mirna2targetscan1.620.051.67