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This page was generated on 2021-10-15 15:06:20 -0400 (Fri, 15 Oct 2021).

CHECK results for RNAmodR on tokay2

To the developers/maintainers of the RNAmodR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RNAmodR.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 1603/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RNAmodR 1.6.0  (landing page)
Felix G.M. Ernst
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/RNAmodR
git_branch: RELEASE_3_13
git_last_commit: c7b25bf
git_last_commit_date: 2021-05-19 12:44:18 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: RNAmodR
Version: 1.6.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RNAmodR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings RNAmodR_1.6.0.tar.gz
StartedAt: 2021-10-15 04:40:49 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 04:57:48 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 1019.4 seconds
RetCode: 0
Status:   OK  
CheckDir: RNAmodR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RNAmodR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings RNAmodR_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/RNAmodR.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RNAmodR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RNAmodR' 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 whether package 'RNAmodR' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Unexported objects imported by ':::' calls:
  'BiocGenerics:::replaceSlots' 'Biostrings:::XString'
  'IRanges:::.valid.CompressedList' 'IRanges:::coerceToCompressedList'
  'S4Vectors:::.valid.DataFrame' 'S4Vectors:::labeledLine'
  'S4Vectors:::make_zero_col_DataFrame'
  'S4Vectors:::prepare_objects_to_bind'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.get_inosine_score'
* 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
stats                          45.67   1.60  109.94
CoverageSequenceData-class     20.42   4.05   26.24
ModInosine                     13.03   0.45   14.39
PileupSequenceData-class       11.53   0.42   13.05
EndSequenceData-class          10.78   0.43   12.27
ProtectedEndSequenceData-class 10.59   0.54   12.09
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
stats                          47.05   1.56  105.75
CoverageSequenceData-class     19.92   1.66   23.36
ModInosine                     14.22   0.39   15.53
EndSequenceData-class          13.09   0.34   14.43
ProtectedEndSequenceData-class 12.32   0.31   13.56
PileupSequenceData-class       11.96   0.35   13.38
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/RNAmodR.Rcheck/00check.log'
for details.

Installation output

RNAmodR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/RNAmodR_1.6.0.tar.gz && rm -rf RNAmodR.buildbin-libdir && mkdir RNAmodR.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RNAmodR.buildbin-libdir RNAmodR_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL RNAmodR_1.6.0.zip && rm RNAmodR_1.6.0.tar.gz RNAmodR_1.6.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  543k  100  543k    0     0  1568k      0 --:--:-- --:--:-- --:--:-- 1572k

install for i386

* installing *source* package 'RNAmodR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RNAmodR'
    finding HTML links ... done
    CoverageSequenceData-class              html  
    EndSequenceData-class                   html  
    ModInosine-functions                    html  
    ModInosine-internals                    html  
    ModInosine                              html  
    Modifier-class                          html  
    Modifier-functions                      html  
    ModifierSet-class                       html  
    NormEndSequenceData-class               html  
    PileupSequenceData-class                html  
    ProtectedEndSequenceData-class          html  
    RNAmodR-datasets                        html  
    RNAmodR-development                     html  
    RNAmodR-internals                       html  
    RNAmodR                                 html  
    SequenceData-class                      html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/RNAmodR.buildbin-libdir/00LOCK-RNAmodR/00new/RNAmodR/help/SequenceData.html
    SequenceData-functions                  html  
    SequenceDataFrame-class                 html  
    SequenceDataList-class                  html  
    SequenceDataSet-class                   html  
    SequenceModDNAStringSetTrack-class      html  
    SequenceModRNAStringSetTrack-class      html  
    aggregate                               html  
    compareByCoord                          html  
    modify                                  html  
    plotData                                html  
    plotROC                                 html  
    settings                                html  
    stats                                   html  
    subsetByCoord                           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

install for x64

* installing *source* package 'RNAmodR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RNAmodR' as RNAmodR_1.6.0.zip
* DONE (RNAmodR)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'RNAmodR' successfully unpacked and MD5 sums checked

Tests output

RNAmodR.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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(RNAmodR)
Loading required package: S4Vectors
Loading required package: stats4
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


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: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: Modstrings
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit


Attaching package: 'RNAmodR'

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

    compare

> 
> test_check("RNAmodR")
== Skipped tests ===============================================================
* On Bioconductor (9)

[ FAIL 0 | WARN 0 | SKIP 9 | PASS 192 ]
> 
> proc.time()
   user  system elapsed 
  53.46    5.46   60.84

RNAmodR.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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(RNAmodR)
Loading required package: S4Vectors
Loading required package: stats4
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


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: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: Modstrings
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit


Attaching package: 'RNAmodR'

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

    compare

> 
> test_check("RNAmodR")
== Skipped tests ===============================================================
* On Bioconductor (9)

[ FAIL 0 | WARN 0 | SKIP 9 | PASS 192 ]
> 
> proc.time()
   user  system elapsed 
  58.40    3.65   63.78

Example timings

RNAmodR.Rcheck/examples_i386/RNAmodR-Ex.timings

nameusersystemelapsed
CoverageSequenceData-class20.42 4.0526.24
EndSequenceData-class10.78 0.4312.27
ModInosine-functions0.620.050.68
ModInosine13.03 0.4514.39
Modifier-functions0.240.080.31
NormEndSequenceData-class000
PileupSequenceData-class11.53 0.4213.05
ProtectedEndSequenceData-class10.59 0.5412.09
RNAmodR-development0.060.000.06
SequenceData-functions0.090.040.14
SequenceDataFrame-class0.110.070.17
SequenceDataList-class0.160.100.27
SequenceDataSet-class0.090.130.22
SequenceModDNAStringSetTrack-class1.230.001.23
SequenceModRNAStringSetTrack-class0.130.000.13
aggregate0.550.140.69
compareByCoord2.150.062.22
modify0.630.100.71
plotData2.150.072.25
plotROC1.600.051.65
settings0.170.030.20
stats 45.67 1.60109.94
subsetByCoord0.550.070.62

RNAmodR.Rcheck/examples_x64/RNAmodR-Ex.timings

nameusersystemelapsed
CoverageSequenceData-class19.92 1.6623.36
EndSequenceData-class13.09 0.3414.43
ModInosine-functions0.800.070.86
ModInosine14.22 0.3915.53
Modifier-functions0.250.040.29
NormEndSequenceData-class000
PileupSequenceData-class11.96 0.3513.38
ProtectedEndSequenceData-class12.32 0.3113.56
RNAmodR-development0.130.000.12
SequenceData-functions0.090.130.22
SequenceDataFrame-class0.110.070.19
SequenceDataList-class0.170.130.29
SequenceDataSet-class0.100.110.21
SequenceModDNAStringSetTrack-class1.310.001.31
SequenceModRNAStringSetTrack-class0.110.000.11
aggregate0.450.120.58
compareByCoord1.920.031.95
modify0.600.020.61
plotData1.930.082.02
plotROC1.610.061.67
settings0.130.050.17
stats 47.05 1.56105.75
subsetByCoord0.780.030.82