Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-24 15:06:10 -0400 (Fri, 24 Sep 2021).

CHECK results for FRASER on tokay2

To the developers/maintainers of the FRASER package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/FRASER.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 674/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FRASER 1.4.0  (landing page)
Christian Mertes
Snapshot Date: 2021-09-23 04:50:12 -0400 (Thu, 23 Sep 2021)
git_url: https://git.bioconductor.org/packages/FRASER
git_branch: RELEASE_3_13
git_last_commit: 926f313
git_last_commit_date: 2021-05-19 12:51:54 -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: FRASER
Version: 1.4.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FRASER.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings FRASER_1.4.0.tar.gz
StartedAt: 2021-09-23 22:29:40 -0400 (Thu, 23 Sep 2021)
EndedAt: 2021-09-23 22:52:57 -0400 (Thu, 23 Sep 2021)
EllapsedTime: 1397.8 seconds
RetCode: 0
Status:   OK  
CheckDir: FRASER.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FRASER.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings FRASER_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/FRASER.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 'FRASER/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'FRASER' version '1.4.0'
* 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 'FRASER' 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 object imported by a ':::' call: 'S4Vectors:::selectSome'
  See the note in ?`:::` about the use of this operator.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/FRASER/libs/i386/FRASER.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/FRASER/libs/x64/FRASER.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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
plotFunctions              125.53   0.07  125.62
FRASER                      61.41   1.83   63.67
counts                      38.23   0.33   40.21
annotateRanges              20.81   0.30   27.45
optimHyperParams            17.66   0.08   17.74
injectOutliers              10.63   0.02   10.64
mergeExternalData            6.97   1.81   13.06
results                      5.90   0.07    5.97
makeSimulatedFraserDataSet   5.06   0.00    5.06
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
plotFunctions              136.22   0.16  136.37
FRASER                      70.46   0.49   71.59
counts                      39.86   0.17   40.17
optimHyperParams            16.80   0.04   16.85
annotateRanges              15.31   0.11   19.72
injectOutliers              10.88   0.02   10.89
mergeExternalData            7.28   2.05   14.51
results                      6.97   0.03    7.00
makeSimulatedFraserDataSet   5.65   0.00    5.66
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/FRASER.Rcheck/00check.log'
for details.



Installation output

FRASER.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/FRASER_1.4.0.tar.gz && rm -rf FRASER.buildbin-libdir && mkdir FRASER.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=FRASER.buildbin-libdir FRASER_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL FRASER_1.4.0.zip && rm FRASER_1.4.0.tar.gz FRASER_1.4.0.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  953k  100  953k    0     0  1518k      0 --:--:-- --:--:-- --:--:-- 1520k

install for i386

* installing *source* package 'FRASER' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include'   -I"c:/extsoft/include"  -fopenmp -DARMA_DONT_USE_OPENMP   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include'   -I"c:/extsoft/include"  -fopenmp -DARMA_DONT_USE_OPENMP   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o FRASER.dll tmp.def RcppExports.o loss_n_gradient_functions.o -fopenmp -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/FRASER.buildbin-libdir/00LOCK-FRASER/00new/FRASER/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'FRASER'
    finding HTML links ... done
    FRASER                                  html  
    FraserDataSet-class                     html  
    FraserDataSet                           html  
    annotateRanges                          html  
    assayNames-FraserDataSet-method         html  
    assays-FraserDataSet-method             html  
    calculatePSIValues                      html  
    countRNA                                html  
    counts                                  html  
    createTestFraserDataSet                 html  
    fds-methods                             html  
    filtering                               html  
    fit                                     html  
    getter_setter_functions                 html  
    injectOutliers                          html  
    length-FraserDataSet-method             html  
    loadFraserDataSet                       html  
    makeSimulatedFraserDataSet              html  
    mergeExternalData                       html  
    optimHyperParams                        html  
    plotFunctions                           html  
    finding level-2 HTML links ... done

    psiTypes                                html  
    results                                 html  
    subset                                  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 'FRASER' ...
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_DONT_USE_OPENMP   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_DONT_USE_OPENMP   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o FRASER.dll tmp.def RcppExports.o loss_n_gradient_functions.o -fopenmp -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/FRASER.buildbin-libdir/FRASER/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'FRASER' as FRASER_1.4.0.zip
* DONE (FRASER)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'FRASER' successfully unpacked and MD5 sums checked

Tests output

FRASER.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(FRASER)
Loading required package: BiocParallel
Loading required package: data.table
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
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

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:data.table':

    first, second

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:data.table':

    shift

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

    windows

Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

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: 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


Attaching package: 'FRASER'

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

    samples

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

    mapSeqlevels

> 
> # to speed up the testing on windows do it in serial mode
> if(.Platform$OS.type != "unix") {
+     register(SerialParam())
+ }
> 
> test_check("FRASER")

        ==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
       Rsubread 2.6.4

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                                                                            ||
||                           sample3.bam                                      ||
||                                                                            ||
||              Paired-end : yes                                              ||
||        Count read pairs : yes                                              ||
||              Annotation : R data.frame                                     ||
||      Dir for temp files : C:/Users/biocbuild/bbs-3.13-bioc/tmpdir/Rtmp ... ||
||                 Threads : 1                                                ||
||                   Level : meta-feature level                               ||
||      Multimapping reads : counted                                          ||
|| Multi-overlapping reads : counted                                          ||
||   Min overlapping bases : 10                                               ||
||                                                                            ||
\\============================================================================//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid11556 ...         ||
||    Features : 87                                                           ||
||    Meta-features : 87                                                      ||
||    Chromosomes/contigs : 2                                                 ||
||                                                                            ||
|| Process BAM file sample3.bam...                                            ||
||    Strand specific : stranded                                              ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 1918                                                 ||
||    Successfully assigned alignments : 241 (12.6%)                          ||
||    Running time : 0.00 minutes                                             ||
||                                                                            ||
|| Write the final count table.                                               ||
|| Write the read assignment summary.                                         ||
||                                                                            ||
\\============================================================================//


        ==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
       Rsubread 2.6.4

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                                                                            ||
||                           sample1.bam                                      ||
||                                                                            ||
||              Paired-end : yes                                              ||
||        Count read pairs : yes                                              ||
||              Annotation : R data.frame                                     ||
||      Dir for temp files : C:/Users/biocbuild/bbs-3.13-bioc/tmpdir/Rtmp ... ||
||                 Threads : 1                                                ||
||                   Level : meta-feature level                               ||
||      Multimapping reads : counted                                          ||
|| Multi-overlapping reads : counted                                          ||
||   Min overlapping bases : 10                                               ||
||                                                                            ||
\\============================================================================//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid11556 ...         ||
||    Features : 77                                                           ||
||    Meta-features : 77                                                      ||
||    Chromosomes/contigs : 2                                                 ||
||                                                                            ||
|| Process BAM file sample1.bam...                                            ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 474                                                  ||
||    Successfully assigned alignments : 145 (30.6%)                          ||
||    Running time : 0.00 minutes                                             ||
||                                                                            ||
|| Write the final count table.                                               ||
|| Write the read assignment summary.                                         ||
||                                                                            ||
\\============================================================================//


        ==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
       Rsubread 2.6.4

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                                                                            ||
||                           sample2.bam                                      ||
||                                                                            ||
||              Paired-end : yes                                              ||
||        Count read pairs : yes                                              ||
||              Annotation : R data.frame                                     ||
||      Dir for temp files : C:/Users/biocbuild/bbs-3.13-bioc/tmpdir/Rtmp ... ||
||                 Threads : 1                                                ||
||                   Level : meta-feature level                               ||
||      Multimapping reads : counted                                          ||
|| Multi-overlapping reads : counted                                          ||
||   Min overlapping bases : 10                                               ||
||                                                                            ||
\\============================================================================//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid11556 ...         ||
||    Features : 77                                                           ||
||    Meta-features : 77                                                      ||
||    Chromosomes/contigs : 2                                                 ||
||                                                                            ||
|| Process BAM file sample2.bam...                                            ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 2455                                                 ||
||    Successfully assigned alignments : 826 (33.6%)                          ||
||    Running time : 0.00 minutes                                             ||
||                                                                            ||
|| Write the final count table.                                               ||
|| Write the read assignment summary.                                         ||
||                                                                            ||
\\============================================================================//


        ==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
       Rsubread 2.6.4

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                                                                            ||
||                           sample3.bam                                      ||
||                                                                            ||
||              Paired-end : yes                                              ||
||        Count read pairs : yes                                              ||
||              Annotation : R data.frame                                     ||
||      Dir for temp files : C:/Users/biocbuild/bbs-3.13-bioc/tmpdir/Rtmp ... ||
||                 Threads : 1                                                ||
||                   Level : meta-feature level                               ||
||      Multimapping reads : counted                                          ||
|| Multi-overlapping reads : counted                                          ||
||   Min overlapping bases : 10                                               ||
||                                                                            ||
\\============================================================================//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid11556 ...         ||
||    Features : 77                                                           ||
||    Meta-features : 77                                                      ||
||    Chromosomes/contigs : 2                                                 ||
||                                                                            ||
|| Process BAM file sample3.bam...                                            ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 1918                                                 ||
||    Successfully assigned alignments : 703 (36.7%)                          ||
||    Running time : 0.00 minutes                                             ||
||                                                                            ||
|| Write the final count table.                                               ||
|| Write the read assignment summary.                                         ||
||                                                                            ||
\\============================================================================//

[ FAIL 0 | WARN 10 | SKIP 0 | PASS 55 ]
> 
> proc.time()
   user  system elapsed 
 139.68    4.20  149.01 

FRASER.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(FRASER)
Loading required package: BiocParallel
Loading required package: data.table
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
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

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:data.table':

    first, second

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:data.table':

    shift

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

    windows

Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

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: 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


Attaching package: 'FRASER'

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

    samples

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

    mapSeqlevels

> 
> # to speed up the testing on windows do it in serial mode
> if(.Platform$OS.type != "unix") {
+     register(SerialParam())
+ }
> 
> test_check("FRASER")

        ==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
       Rsubread 2.6.4

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                                                                            ||
||                           sample3.bam                                      ||
||                                                                            ||
||              Paired-end : yes                                              ||
||        Count read pairs : yes                                              ||
||              Annotation : R data.frame                                     ||
||      Dir for temp files : C:/Users/biocbuild/bbs-3.13-bioc/tmpdir/Rtmp ... ||
||                 Threads : 1                                                ||
||                   Level : meta-feature level                               ||
||      Multimapping reads : counted                                          ||
|| Multi-overlapping reads : counted                                          ||
||   Min overlapping bases : 10                                               ||
||                                                                            ||
\\============================================================================//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid11396 ...         ||
||    Features : 87                                                           ||
||    Meta-features : 87                                                      ||
||    Chromosomes/contigs : 2                                                 ||
||                                                                            ||
|| Process BAM file sample3.bam...                                            ||
||    Strand specific : stranded                                              ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 1918                                                 ||
||    Successfully assigned alignments : 241 (12.6%)                          ||
||    Running time : 0.00 minutes                                             ||
||                                                                            ||
|| Write the final count table.                                               ||
|| Write the read assignment summary.                                         ||
||                                                                            ||
\\============================================================================//


        ==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
       Rsubread 2.6.4

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                                                                            ||
||                           sample1.bam                                      ||
||                                                                            ||
||              Paired-end : yes                                              ||
||        Count read pairs : yes                                              ||
||              Annotation : R data.frame                                     ||
||      Dir for temp files : C:/Users/biocbuild/bbs-3.13-bioc/tmpdir/Rtmp ... ||
||                 Threads : 1                                                ||
||                   Level : meta-feature level                               ||
||      Multimapping reads : counted                                          ||
|| Multi-overlapping reads : counted                                          ||
||   Min overlapping bases : 10                                               ||
||                                                                            ||
\\============================================================================//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid11396 ...         ||
||    Features : 77                                                           ||
||    Meta-features : 77                                                      ||
||    Chromosomes/contigs : 2                                                 ||
||                                                                            ||
|| Process BAM file sample1.bam...                                            ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 474                                                  ||
||    Successfully assigned alignments : 145 (30.6%)                          ||
||    Running time : 0.00 minutes                                             ||
||                                                                            ||
|| Write the final count table.                                               ||
|| Write the read assignment summary.                                         ||
||                                                                            ||
\\============================================================================//


        ==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
       Rsubread 2.6.4

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                                                                            ||
||                           sample2.bam                                      ||
||                                                                            ||
||              Paired-end : yes                                              ||
||        Count read pairs : yes                                              ||
||              Annotation : R data.frame                                     ||
||      Dir for temp files : C:/Users/biocbuild/bbs-3.13-bioc/tmpdir/Rtmp ... ||
||                 Threads : 1                                                ||
||                   Level : meta-feature level                               ||
||      Multimapping reads : counted                                          ||
|| Multi-overlapping reads : counted                                          ||
||   Min overlapping bases : 10                                               ||
||                                                                            ||
\\============================================================================//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid11396 ...         ||
||    Features : 77                                                           ||
||    Meta-features : 77                                                      ||
||    Chromosomes/contigs : 2                                                 ||
||                                                                            ||
|| Process BAM file sample2.bam...                                            ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 2455                                                 ||
||    Successfully assigned alignments : 826 (33.6%)                          ||
||    Running time : 0.00 minutes                                             ||
||                                                                            ||
|| Write the final count table.                                               ||
|| Write the read assignment summary.                                         ||
||                                                                            ||
\\============================================================================//


        ==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
       Rsubread 2.6.4

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                                                                            ||
||                           sample3.bam                                      ||
||                                                                            ||
||              Paired-end : yes                                              ||
||        Count read pairs : yes                                              ||
||              Annotation : R data.frame                                     ||
||      Dir for temp files : C:/Users/biocbuild/bbs-3.13-bioc/tmpdir/Rtmp ... ||
||                 Threads : 1                                                ||
||                   Level : meta-feature level                               ||
||      Multimapping reads : counted                                          ||
|| Multi-overlapping reads : counted                                          ||
||   Min overlapping bases : 10                                               ||
||                                                                            ||
\\============================================================================//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid11396 ...         ||
||    Features : 77                                                           ||
||    Meta-features : 77                                                      ||
||    Chromosomes/contigs : 2                                                 ||
||                                                                            ||
|| Process BAM file sample3.bam...                                            ||
||    Paired-end reads are included.                                          ||
||    Total alignments : 1918                                                 ||
||    Successfully assigned alignments : 703 (36.7%)                          ||
||    Running time : 0.00 minutes                                             ||
||                                                                            ||
|| Write the final count table.                                               ||
|| Write the read assignment summary.                                         ||
||                                                                            ||
\\============================================================================//

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 55 ]
> 
> proc.time()
   user  system elapsed 
 158.73    2.01  165.04 

Example timings

FRASER.Rcheck/examples_i386/FRASER-Ex.timings

nameusersystemelapsed
FRASER61.41 1.8363.67
FraserDataSet0.720.592.90
annotateRanges20.81 0.3027.45
calculatePSIValues1.700.001.71
countRNA0.710.010.72
counts38.23 0.3340.21
createTestFraserDataSet0.380.030.41
fds-methods1.340.021.36
filtering2.080.012.09
getter_setter_functions0.340.000.35
injectOutliers10.63 0.0210.64
loadFraserDataSet0.420.020.44
makeSimulatedFraserDataSet5.060.005.06
mergeExternalData 6.97 1.8113.06
optimHyperParams17.66 0.0817.74
plotFunctions125.53 0.07125.62
psiTypes000
results5.900.075.97
subset0.830.000.83

FRASER.Rcheck/examples_x64/FRASER-Ex.timings

nameusersystemelapsed
FRASER70.46 0.4971.59
FraserDataSet0.700.562.88
annotateRanges15.31 0.1119.72
calculatePSIValues1.990.001.98
countRNA1.150.061.22
counts39.86 0.1740.17
createTestFraserDataSet0.390.000.39
fds-methods1.460.001.46
filtering1.840.001.84
getter_setter_functions0.360.000.36
injectOutliers10.88 0.0210.89
loadFraserDataSet0.390.000.39
makeSimulatedFraserDataSet5.650.005.66
mergeExternalData 7.28 2.0514.51
optimHyperParams16.80 0.0416.85
plotFunctions136.22 0.16136.37
psiTypes000
results6.970.037.00
subset0.970.000.97