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CHECK report for ORFik on tokay1

This page was generated on 2019-04-13 11:29:19 -0400 (Sat, 13 Apr 2019).

Package 1101/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ORFik 1.2.1
Kornel Labun
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/ORFik
Branch: RELEASE_3_8
Last Commit: 2e3a8c6
Last Changed Date: 2019-01-04 13:42:32 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ORFik
Version: 1.2.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ORFik.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings ORFik_1.2.1.tar.gz
StartedAt: 2019-04-13 04:19:37 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 04:26:51 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 433.7 seconds
RetCode: 0
Status:  OK  
CheckDir: ORFik.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ORFik.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings ORFik_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/ORFik.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ORFik/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ORFik' version '1.2.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'ORFik' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
assignTSSByCage: no visible global function definition for 'is'
computeFeatures: no visible global function definition for 'is'
computeFeatures: no visible binding for global variable 'entropyRFP'
computeFeatures: no visible binding for global variable
  'disengagementScores'
computeFeatures: no visible binding for global variable 'RRS'
computeFeatures: no visible binding for global variable 'RSS'
computeFeatures: no visible binding for global variable
  'fractionLengths'
computeFeatures: no visible binding for global variable 'te'
computeFeatures: no visible binding for global variable 'fpkmRFP'
computeFeatures: no visible binding for global variable 'fpkmRNA'
computeFeatures: no visible binding for global variable 'ORFScores'
computeFeatures: no visible binding for global variable 'ioScore'
computeFeatures: no visible binding for global variable 'inFrameCDS'
computeFeatures: no visible binding for global variable
  'isOverlappingCds'
computeFeatures: no visible binding for global variable 'rankInTx'
computeFeaturesCage: no visible global function definition for 'is'
computeFeaturesCage: no visible binding for global variable
  'entropyRFP'
computeFeaturesCage: no visible binding for global variable
  'disengagementScores'
computeFeaturesCage: no visible binding for global variable 'RRS'
computeFeaturesCage: no visible binding for global variable 'RSS'
computeFeaturesCage: no visible binding for global variable
  'fractionLengths'
computeFeaturesCage: no visible binding for global variable 'te'
computeFeaturesCage: no visible binding for global variable 'fpkmRFP'
computeFeaturesCage: no visible binding for global variable 'fpkmRNA'
computeFeaturesCage: no visible binding for global variable 'ORFScores'
computeFeaturesCage: no visible binding for global variable 'ioScore'
computeFeaturesCage: no visible binding for global variable
  'inFrameCDS'
computeFeaturesCage: no visible binding for global variable
  'isOverlappingCds'
computeFeaturesCage: no visible binding for global variable 'rankInTx'
convertToOneBasedRanges: no visible global function definition for '.'
disengagementScore: no visible global function definition for 'is'
extendLeaders: no visible global function definition for 'is'
findFa: no visible global function definition for 'is'
findORFsFasta: no visible global function definition for 'is'
groupGRangesBy: no visible global function definition for 'is'
insideOutsideORF: no visible global function definition for 'is'
kozakSequenceScore: no visible global function definition for 'is'
longestORFs: no visible global function definition for 'is'
longestORFs: no visible global function definition for '.'
mapToGRanges: no visible global function definition for 'is'
readWidths: no visible global function definition for 'is'
reassignTSSbyCage: no visible global function definition for 'is'
reassignTxDbByCage: no visible global function definition for 'is'
remakeTxdbExonIds: no visible global function definition for '.'
remakeTxdbExonIds: no visible binding for global variable 'chr'
removeTxdbExons: no visible binding for global variable 'exon_rank'
removeTxdbExons: no visible binding for global variable 'ranks'
ribosomeReleaseScore: no visible global function definition for 'is'
strandBool: no visible global function definition for 'is'
txNamesWithLeaders: no visible global function definition for 'is'
txSeqsFromFa: no visible global function definition for 'is'
Undefined global functions or variables:
  . ORFScores RRS RSS chr disengagementScores entropyRFP exon_rank
  fpkmRFP fpkmRNA fractionLengths inFrameCDS ioScore is
  isOverlappingCds rankInTx ranks te
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 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-3.8-bioc/R/library/ORFik/libs/i386/ORFik.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
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
computeFeatures 5.62   0.31     5.9
* 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-3.8-bioc/meat/ORFik.Rcheck/00check.log'
for details.



Installation output

ORFik.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/ORFik_1.2.1.tar.gz && rm -rf ORFik.buildbin-libdir && mkdir ORFik.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ORFik.buildbin-libdir ORFik_1.2.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL ORFik_1.2.1.zip && rm ORFik_1.2.1.tar.gz ORFik_1.2.1.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  295k  100  295k    0     0  7418k      0 --:--:-- --:--:-- --:--:-- 8202k

install for i386

* installing *source* package 'ORFik' ...
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c findORFsHelpers.cpp -o findORFsHelpers.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c findOrfs.cpp -o findOrfs.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c findOrfsFasta.cpp -o findOrfsFasta.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o ORFik.dll tmp.def RcppExports.o findORFsHelpers.o findOrfs.o findOrfsFasta.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/ORFik.buildbin-libdir/ORFik/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ORFik'
    finding HTML links ... done
    ORFik-package                           html  
    addCdsOnLeaderEnds                      html  
    addNewTSSOnLeaders                      html  
    asTX                                    html  
    finding level-2 HTML links ... done

    assignAnnotations                       html  
    assignFirstExonsStartSite               html  
    assignLastExonsStopSite                 html  
    assignTSSByCage                         html  
    bedToGR                                 html  
    changePointAnalysis                     html  
    checkRFP                                html  
    checkRNA                                html  
    codonSumsPerGroup                       html  
    computeFeatures                         html  
    computeFeaturesCage                     html  
    convertToOneBasedRanges                 html  
    coverageByWindow                        html  
    coveragePerTiling                       html  
    defineIsoform                           html  
    defineTrailer                           html  
    detectRibosomeShifts                    html  
    disengagementScore                      html  
    distToCds                               html  
    distToTSS                               html  
    downstreamFromPerGroup                  html  
    downstreamN                             html  
    downstreamOfPerGroup                    html  
    entropy                                 html  
    extendLeaders                           html  
    extendsTSSexons                         html  
    filterCage                              html  
    findCageUTRFivelen                      html  
    findFa                                  html  
    findMapORFs                             html  
    findMaxPeaks                            html  
    findNewTSS                              html  
    findORFs                                html  
    findORFsFasta                           html  
    firstEndPerGroup                        html  
    firstExonPerGroup                       html  
    firstStartPerGroup                      html  
    floss                                   html  
    fpkm                                    html  
    fpkm_calc                               html  
    fractionLength                          html  
    fread.bed                               html  
    gSort                                   html  
    getStartStopWindows                     html  
    groupGRangesBy                          html  
    hasHits                                 html  
    initiationScore                         html  
    insideOutsideORF                        html  
    is.gr_or_grl                            html  
    is.grl                                  html  
    isInFrame                               html  
    isOverlapping                           html  
    isPeriodic                              html  
    kozakSequenceScore                      html  
    lastExonEndPerGroup                     html  
    lastExonPerGroup                        html  
    lastExonStartPerGroup                   html  
    longestORFs                             html  
    makeExonRanks                           html  
    makeORFNames                            html  
    mapToGRanges                            html  
    matchNaming                             html  
    metaWindow                              html  
    numExonsPerGroup                        html  
    orfID                                   html  
    orfScore                                html  
    overlapsToCoverage                      html  
    parseCigar                              html  
    pmapFromTranscriptF                     html  
    rankOrder                               html  
    readWidths                              html  
    reassignTSSbyCage                       html  
    reassignTxDbByCage                      html  
    reduceKeepAttr                          html  
    regroupRleList                          html  
    remakeTxdbExonIds                       html  
    removeMetaCols                          html  
    removeTxdbExons                         html  
    restrictTSSByUpstreamLeader             html  
    riboTISCoverageProportion               html  
    ribosomeReleaseScore                    html  
    ribosomeStallingScore                   html  
    seqnamesPerGroup                        html  
    shiftFootprints                         html  
    sortPerGroup                            html  
    startCodons                             html  
    startDefinition                         html  
    startRegionString                       html  
    startSites                              html  
    stopCodons                              html  
    stopDefinition                          html  
    stopSites                               html  
    strandBool                              html  
    strandPerGroup                          html  
    subsetCoverage                          html  
    subset_to_frame                         html  
    tile1                                   html  
    translationalEff                        html  
    txLen                                   html  
    txNames                                 html  
    txNamesWithLeaders                      html  
    txSeqsFromFa                            html  
    uORFSearchSpace                         html  
    uniqueGroups                            html  
    uniqueOrder                             html  
    unlistGrl                               html  
    updateTxdbRanks                         html  
    updateTxdbStartSites                    html  
    upstreamFromPerGroup                    html  
    upstreamOfPerGroup                      html  
    validGRL                                html  
    widthPerGroup                           html  
    windowPerGroup                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'ORFik' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c findORFsHelpers.cpp -o findORFsHelpers.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c findOrfs.cpp -o findOrfs.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c findOrfsFasta.cpp -o findOrfsFasta.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o ORFik.dll tmp.def RcppExports.o findORFsHelpers.o findOrfs.o findOrfsFasta.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/ORFik.buildbin-libdir/ORFik/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ORFik' as ORFik_1.2.1.zip
* DONE (ORFik)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'ORFik' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

ORFik.Rcheck/tests_i386/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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(ORFik)
Loading required package: IRanges
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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid


Attaching package: 'IRanges'

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

    windows

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
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")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply

Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    type

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

    strsplit

Loading required package: Rsamtools
> 
> test_check("ORFik")
== testthat results  ===========================================================
OK: 236 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  31.09    1.53   32.67 

ORFik.Rcheck/tests_x64/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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(ORFik)
Loading required package: IRanges
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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid


Attaching package: 'IRanges'

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

    windows

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
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")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply

Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    type

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

    strsplit

Loading required package: Rsamtools
> 
> test_check("ORFik")
== testthat results  ===========================================================
OK: 236 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  44.67    0.79   46.73 

Example timings

ORFik.Rcheck/examples_i386/ORFik-Ex.timings

nameusersystemelapsed
assignTSSByCage000
computeFeatures3.820.083.87
computeFeaturesCage000
coverageByWindow0.270.010.28
coveragePerTiling0.220.000.22
defineTrailer0.390.000.39
detectRibosomeShifts000
disengagementScore0.500.000.52
distToCds0.290.000.37
distToTSS0.300.000.38
entropy1.050.001.73
extendLeaders0.790.020.92
findMapORFs1.690.031.72
findORFs0.090.060.16
findORFsFasta0.070.020.11
firstEndPerGroup0.030.030.06
firstExonPerGroup0.070.040.10
firstStartPerGroup0.070.070.15
floss0.360.180.54
fpkm0.080.040.11
fractionLength0.080.000.08
fread.bed0.090.000.17
getStartStopWindows2.270.072.35
groupGRangesBy0.030.000.03
initiationScore1.060.001.06
insideOutsideORF0.610.000.61
isInFrame0.250.000.25
isOverlapping0.230.000.24
kozakSequenceScore0.420.000.42
lastExonEndPerGroup0.080.000.08
lastExonPerGroup0.080.000.08
lastExonStartPerGroup0.060.000.06
longestORFs0.160.000.16
makeORFNames0.120.000.13
metaWindow0.200.020.18
numExonsPerGroup0.080.000.08
orfScore0.470.020.49
overlapsToCoverage0.030.000.03
rankOrder0.060.000.06
reassignTSSbyCage0.520.000.52
reassignTxDbByCage000
reduceKeepAttr0.120.030.14
ribosomeReleaseScore0.110.000.11
ribosomeStallingScore0.220.000.21
seqnamesPerGroup0.070.000.07
shiftFootprints000
sortPerGroup0.250.000.25
startCodons0.340.000.34
startDefinition000
startSites0.230.000.23
stopCodons0.350.000.35
stopDefinition000
stopSites0.280.000.28
strandBool000
strandPerGroup0.060.000.06
tile10.190.000.19
translationalEff0.080.000.08
txNames0.020.000.02
txNamesWithLeaders0.900.000.91
uORFSearchSpace0.750.061.14
uniqueGroups0.190.000.18
uniqueOrder0.330.000.72
unlistGrl0.030.000.03
widthPerGroup0.060.000.07

ORFik.Rcheck/examples_x64/ORFik-Ex.timings

nameusersystemelapsed
assignTSSByCage000
computeFeatures5.620.315.90
computeFeaturesCage0.000.020.01
coverageByWindow0.470.020.49
coveragePerTiling0.170.000.17
defineTrailer0.110.000.11
detectRibosomeShifts000
disengagementScore0.420.000.44
distToCds0.320.000.32
distToTSS0.220.000.22
entropy0.860.000.86
extendLeaders0.670.000.62
findMapORFs0.750.000.75
findORFs0.070.000.06
findORFsFasta0.040.000.05
firstEndPerGroup0.070.000.06
firstExonPerGroup0.040.000.04
firstStartPerGroup0.050.000.05
floss0.160.000.16
fpkm0.040.000.04
fractionLength0.050.000.05
fread.bed0.050.000.05
getStartStopWindows3.110.003.11
groupGRangesBy0.060.000.06
initiationScore2.010.002.02
insideOutsideORF0.880.000.87
isInFrame0.190.000.19
isOverlapping0.170.000.17
kozakSequenceScore0.310.000.31
lastExonEndPerGroup0.050.000.05
lastExonPerGroup0.060.000.06
lastExonStartPerGroup0.050.000.05
longestORFs0.120.000.12
makeORFNames0.110.000.11
metaWindow0.130.000.13
numExonsPerGroup0.060.000.06
orfScore0.470.000.45
overlapsToCoverage0.030.000.04
rankOrder0.080.000.07
reassignTSSbyCage0.480.000.49
reassignTxDbByCage000
reduceKeepAttr0.20.00.2
ribosomeReleaseScore0.130.000.13
ribosomeStallingScore0.190.000.18
seqnamesPerGroup0.060.000.07
shiftFootprints000
sortPerGroup0.190.000.18
startCodons0.360.000.36
startDefinition000
startSites0.230.000.24
stopCodons0.360.000.36
stopDefinition000
stopSites0.20.00.2
strandBool0.020.000.02
strandPerGroup0.050.000.04
tile10.150.000.16
translationalEff0.100.000.09
txNames0.030.000.03
txNamesWithLeaders0.670.000.68
uORFSearchSpace0.450.030.45
uniqueGroups0.110.000.11
uniqueOrder0.190.000.19
unlistGrl0.030.000.03
widthPerGroup0.030.000.03