Multiple platform build/check report for BioC 3.12 - CHECK report for RNAmodR on tokay1

Package: RNAmodR

Version: 1.4.2

Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RNAmodR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings RNAmodR_1.4.2.tar.gz

StartedAt: 2021-05-06 06:20:00 -0400 (Thu, 06 May 2021)

EndedAt: 2021-05-06 06:39:06 -0400 (Thu, 06 May 2021)

EllapsedTime: 1145.8 seconds

RetCode: 0

Status: OK

CheckDir: RNAmodR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RNAmodR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings RNAmodR_1.4.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/RNAmodR.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.4.2'
* 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                          46.56   1.90  125.38
CoverageSequenceData-class     19.45   2.82   26.18
ModInosine                     13.82   0.64   15.89
ProtectedEndSequenceData-class 13.22   0.38   14.86
EndSequenceData-class          12.92   0.43   14.74
PileupSequenceData-class       12.70   0.53   14.56
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
stats                          53.70   1.78  119.77
CoverageSequenceData-class     20.19   1.70   23.49
ModInosine                     19.47   0.30   21.09
PileupSequenceData-class       16.75   0.52   18.49
ProtectedEndSequenceData-class 14.59   0.42   16.18
EndSequenceData-class          13.58   0.33   15.04
* 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-3.12-bioc/meat/RNAmodR.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/RNAmodR_1.4.2.tar.gz && rm -rf RNAmodR.buildbin-libdir && mkdir RNAmodR.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RNAmodR.buildbin-libdir RNAmodR_1.4.2.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL RNAmodR_1.4.2.zip && rm RNAmodR_1.4.2.tar.gz RNAmodR_1.4.2.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  542k  100  542k    0     0  23.8M      0 --:--:-- --:--:-- --:--:-- 25.2M

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  
    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_1.4.2.zip
* DONE (RNAmodR)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'RNAmodR' successfully unpacked and MD5 sums checked


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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 object is masked from 'package:base':

    expand.grid

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")
Error in (function (x)  : attempt to apply non-function
== Skipped tests ===============================================================
* On Bioconductor (9)

[ FAIL 0 | WARN 0 | SKIP 9 | PASS 187 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
  70.62    6.67   80.56


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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 object is masked from 'package:base':

    expand.grid

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 187 ]
> 
> proc.time()
   user  system elapsed 
  58.92    2.85   65.31

name	user	system	elapsed
CoverageSequenceData-class	19.45	2.82	26.18
EndSequenceData-class	12.92	0.43	14.74
ModInosine-functions	0.74	0.11	0.85
ModInosine	13.82	0.64	15.89
Modifier-functions	0.27	0.05	0.31
NormEndSequenceData-class	0	0	0
PileupSequenceData-class	12.70	0.53	14.56
ProtectedEndSequenceData-class	13.22	0.38	14.86
RNAmodR-development	0.11	0.00	0.11
SequenceData-functions	0.11	0.06	0.19
SequenceDataFrame-class	0.11	0.09	0.20
SequenceDataList-class	0.15	0.11	0.27
SequenceDataSet-class	0.11	0.11	0.22
SequenceModDNAStringSetTrack-class	1.35	0.00	1.34
SequenceModRNAStringSetTrack-class	0.11	0.00	0.11
aggregate	0.61	0.11	0.71
compareByCoord	2.35	0.06	2.41
modify	0.62	0.10	0.72
plotData	2.02	0.11	2.12
plotROC	1.45	0.06	1.52
settings	0.16	0.05	0.20
stats	46.56	1.90	125.38
subsetByCoord	0.66	0.07	0.72

name	user	system	elapsed
CoverageSequenceData-class	20.19	1.70	23.49
EndSequenceData-class	13.58	0.33	15.04
ModInosine-functions	1.95	0.07	2.03
ModInosine	19.47	0.30	21.09
Modifier-functions	0.25	0.08	0.33
NormEndSequenceData-class	0	0	0
PileupSequenceData-class	16.75	0.52	18.49
ProtectedEndSequenceData-class	14.59	0.42	16.18
RNAmodR-development	0.08	0.00	0.08
SequenceData-functions	0.09	0.04	0.14
SequenceDataFrame-class	0.07	0.07	0.13
SequenceDataList-class	0.21	0.16	0.38
SequenceDataSet-class	0.18	0.08	0.25
SequenceModDNAStringSetTrack-class	1.70	0.01	1.72
SequenceModRNAStringSetTrack-class	0.14	0.00	0.14
aggregate	0.91	0.08	0.98
compareByCoord	2.84	0.11	2.95
modify	0.98	0.06	1.05
plotData	2.43	0.10	2.52
plotROC	2.23	0.06	2.29
settings	0.11	0.08	0.19
stats	53.70	1.78	119.77
subsetByCoord	0.69	0.03	0.72

CHECK report for RNAmodR on tokay1

Summary

Command output

Installation output

Tests output

Example timings