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CHECK report for ORFik on malbec2

This page was generated on 2020-10-17 11:55:19 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ORFik PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1246/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ORFik 1.8.6
Haakon Tjeldnes
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/ORFik
Branch: RELEASE_3_11
Last Commit: 3b6321e
Last Changed Date: 2020-10-05 05:11:01 -0400 (Mon, 05 Oct 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ORFik
Version: 1.8.6
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:ORFik.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings ORFik_1.8.6.tar.gz
StartedAt: 2020-10-17 03:52:06 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:00:58 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 532.6 seconds
RetCode: 0
Status:  OK 
CheckDir: ORFik.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:ORFik.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings ORFik_1.8.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/ORFik.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ORFik/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ORFik’ version ‘1.8.6’
* 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 for sufficient/correct file permissions ... 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
* 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:
  ‘GenomicFeatures:::.merge_seqinfo_and_infer_missing_seqlengths’
  ‘IRanges:::regroupBySupergroup’ ‘S4Vectors:::normarg_mcols’
  ‘biomartr:::getENSEMBL.Seq’ ‘biomartr:::getENSEMBL.gtf’
  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 ... NOTE
QC_count_tables: no visible binding for global variable ‘leaders’
QC_count_tables : <anonymous>: no visible binding for global variable
  ‘ratio_mrna_aligned’
QC_count_tables : <anonymous>: no visible binding for global variable
  ‘mRNA’
QC_count_tables : <anonymous>: no visible binding for global variable
  ‘ratio_cds_mrna’
QC_count_tables : <anonymous>: no visible binding for global variable
  ‘CDS’
QC_count_tables : <anonymous>: no visible binding for global variable
  ‘ratio_cds_leader’
QC_count_tables : <anonymous>: no visible binding for global variable
  ‘LEADERS’
QC_count_tables: no visible binding for global variable ‘tx’
QCplots: no visible binding for global variable ‘leaders’
QCplots: no visible binding for global variable ‘trailers’
QCstats.plot: no visible binding for global variable ‘sample_id’
QCstats.plot: no visible binding for global variable ‘value’
QCstats.plot: no visible binding for global variable ‘Sample’
STAR.align.folder: no visible global function definition for
  ‘detectCores’
STAR.align.single: no visible global function definition for
  ‘detectCores’
STAR.index: no visible global function definition for ‘detectCores’
STAR.multiQC: no visible binding for global variable ‘sample_id’
STAR.multiQC: no visible binding for global variable ‘value’
TOP.Motif.ecdf: no visible binding for global variable ‘seq1’
TOP.Motif.ecdf: no visible binding for global variable ‘TOP’
allFeaturesHelper: no visible binding for global variable ‘te’
allFeaturesHelper: no visible binding for global variable ‘fpkmRFP’
allFeaturesHelper: no visible binding for global variable ‘fpkmRNA’
allFeaturesHelper: no visible binding for global variable ‘countRFP’
allFeaturesHelper: no visible binding for global variable ‘entropyRFP’
allFeaturesHelper: no visible binding for global variable
  ‘disengagementScores’
allFeaturesHelper: no visible binding for global variable ‘RRS’
allFeaturesHelper: no visible binding for global variable ‘RSS’
allFeaturesHelper: no visible binding for global variable ‘ORFScores’
allFeaturesHelper: no visible binding for global variable ‘ioScore’
allFeaturesHelper: no visible binding for global variable
  ‘startCodonCoverage’
allFeaturesHelper: no visible binding for global variable
  ‘startRegionRelative’
allFeaturesHelper: no visible binding for global variable ‘kozak’
allFeaturesHelper: no visible binding for global variable ‘StartCodons’
allFeaturesHelper: no visible binding for global variable ‘StopCodons’
allFeaturesHelper: no visible binding for global variable
  ‘fractionLengths’
allFeaturesHelper: no visible binding for global variable ‘distORFCDS’
allFeaturesHelper: no visible binding for global variable ‘inFrameCDS’
allFeaturesHelper: no visible binding for global variable
  ‘isOverlappingCds’
allFeaturesHelper: no visible binding for global variable ‘rankInTx’
artificial.orfs: no visible binding for global variable ‘random’
artificial.orfs: no visible binding for global variable ‘pick’
artificial.orfs: no visible global function definition for ‘.’
collapse.by.scores: no visible global function definition for ‘.’
coverageHeatMap: no visible binding for global variable ‘position’
coverageHeatMap: no visible binding for global variable ‘fraction’
coveragePerTiling: no visible binding for global variable ‘ones’
coveragePerTiling: no visible binding for global variable ‘position’
coveragePerTiling: no visible binding for global variable ‘frame’
coverageScorings: no visible binding for global variable ‘count’
coverageScorings: no visible binding for global variable ‘zscore’
coverageScorings: no visible binding for global variable ‘windowMean’
coverageScorings: no visible binding for global variable ‘windowSD’
coverageScorings: no visible global function definition for ‘.’
coverageScorings: no visible binding for global variable ‘gene_sum’
detectRibosomeShifts: no visible global function definition for ‘.’
detectRibosomeShifts: no visible binding for global variable ‘size’
detectRibosomeShifts: no visible binding for global variable ‘pShifted’
detectRibosomeShifts: no visible binding for global variable
  ‘sum.count’
detectRibosomeShifts: no visible binding for global variable ‘count’
detectRibosomeShifts: no visible binding for global variable ‘fraction’
entropy: no visible binding for global variable ‘Hx’
entropy: no visible binding for global variable ‘codonSums’
entropy: no visible global function definition for ‘.’
filterExtremePeakGenes: no visible binding for global variable ‘count’
filterExtremePeakGenes: no visible binding for global variable
  ‘median_per_gene’
filterExtremePeakGenes: no visible global function definition for ‘.’
filterTranscripts: no visible binding for global variable ‘utr5_len’
filterTranscripts: no visible binding for global variable ‘utr3_len’
findNGSPairs: no visible global function definition for ‘.’
findNGSPairs: no visible binding for global variable ‘forward’
findPeaksPerGene: no visible binding for global variable ‘sum_per_gene’
findPeaksPerGene: no visible binding for global variable ‘count’
findPeaksPerGene: no visible binding for global variable
  ‘mean_per_gene’
findPeaksPerGene: no visible binding for global variable ‘sd_per_gene’
findPeaksPerGene: no visible binding for global variable ‘zscore’
findPeaksPerGene: no visible binding for global variable ‘gene_id’
floss: no visible binding for global variable ‘ORFGrouping’
floss: no visible binding for global variable ‘widths’
floss: no visible global function definition for ‘.’
floss: no visible binding for global variable ‘CDSGrouping’
floss: no visible binding for global variable ‘fraction.x’
floss: no visible binding for global variable ‘fraction.y’
gSort: no visible binding for global variable ‘grnames’
getNGenesCoverage: no visible global function definition for ‘.’
getNGenesCoverage: no visible binding for global variable ‘fraction’
heatMapL: no visible global function definition for ‘p’
initiationScore: no visible global function definition for ‘.’
initiationScore: no visible binding for global variable ‘dif’
initiationScore: no visible binding for global variable ‘fraction’
initiationScore: no visible binding for global variable ‘difPer’
kozakHeatmap: no visible global function definition for ‘.’
kozakHeatmap: no visible binding for global variable ‘variable’
kozakHeatmap: no visible binding for global variable ‘value’
kozakHeatmap: no visible binding for global variable
  ‘count_seq_pos_with_count’
kozakHeatmap: no visible binding for global variable ‘median_score’
list.experiments: no visible binding for global variable ‘name’
longestORFs: no visible global function definition for ‘.’
metaWindow: no visible binding for global variable ‘position’
metaWindow: no visible binding for global variable ‘frame’
orfScore: no visible binding for global variable ‘frame’
orfScore: no visible binding for global variable ‘frame_one_RP’
orfScore: no visible binding for global variable ‘frame_two_RP’
pSitePlot: no visible binding for global variable ‘count’
pSitePlot: no visible binding for global variable ‘frame’
pSitePlot: no visible binding for global variable ‘position’
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’
rnaNormalize: no visible binding for global variable ‘feature’
scaledWindowPositions: no visible binding for global variable
  ‘scalingFactor’
scaledWindowPositions: no visible binding for global variable
  ‘position’
scaledWindowPositions: no visible global function definition for ‘.’
scoreSummarizedExperiment: no visible global function definition for
  ‘rowSums2’
topMotif: no visible binding for global variable ‘seq1’
topMotif: no visible binding for global variable ‘seq2’
topMotif: no visible binding for global variable ‘seq3’
topMotif: no visible binding for global variable ‘seq4’
topMotif: no visible binding for global variable ‘seq5’
transcriptWindow: no visible binding for global variable ‘fractions’
transcriptWindow1: no visible binding for global variable ‘leaders’
windowCoveragePlot: no visible binding for global variable ‘feature’
windowCoveragePlot: no visible binding for global variable ‘fraction’
windowCoveragePlot: no visible binding for global variable
  ‘fraction_min’
windowCoveragePlot: no visible binding for global variable ‘position’
collapseDuplicatedReads,GAlignmentPairs: no visible global function
  definition for ‘.’
collapseDuplicatedReads,GAlignmentPairs: no visible binding for global
  variable ‘start1’
collapseDuplicatedReads,GAlignmentPairs: no visible binding for global
  variable ‘start2’
collapseDuplicatedReads,GAlignmentPairs: no visible binding for global
  variable ‘cigar1’
collapseDuplicatedReads,GAlignmentPairs: no visible binding for global
  variable ‘cigar2’
collapseDuplicatedReads,GAlignments: no visible global function
  definition for ‘.’
collapseDuplicatedReads,GRanges: no visible binding for global variable
  ‘size’
collapseDuplicatedReads,GRanges: no visible global function definition
  for ‘.’
Undefined global functions or variables:
  . CDS CDSGrouping Hx LEADERS ORFGrouping ORFScores RRS RSS Sample
  StartCodons StopCodons TOP chr cigar1 cigar2 codonSums count countRFP
  count_seq_pos_with_count detectCores dif difPer disengagementScores
  distORFCDS entropyRFP exon_rank feature forward fpkmRFP fpkmRNA
  fraction fraction.x fraction.y fractionLengths fraction_min fractions
  frame frame_one_RP frame_two_RP gene_id gene_sum grnames inFrameCDS
  ioScore isOverlappingCds kozak leaders mRNA mean_per_gene
  median_per_gene median_score name ones p pShifted pick position
  random rankInTx ranks ratio_cds_leader ratio_cds_mrna
  ratio_mrna_aligned rowSums2 sample_id scalingFactor sd_per_gene seq1
  seq2 seq3 seq4 seq5 size start1 start2 startCodonCoverage
  startRegionRelative sum.count sum_per_gene te trailers tx utr3_len
  utr5_len value variable widths windowMean windowSD zscore
Consider adding
  importFrom("graphics", "frame")
to your NAMESPACE file.
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
shiftFootprintsByExperiment 9.344  0.650   9.018
computeFeatures             9.320  0.104   9.428
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/ORFik.Rcheck/00check.log’
for details.



Installation output

ORFik.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL ORFik
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘ORFik’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c findORFsHelpers.cpp -o findORFsHelpers.o
findORFsHelpers.cpp: In function ‘void calc_z(const string&, vi&)’:
findORFsHelpers.cpp:57:7: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
       for (z[i] = r - i; r < len; ++r, ++z[i])
       ^~~
findORFsHelpers.cpp:60:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
         --r;
         ^~
findORFsHelpers.cpp: In function ‘Rcpp::IntegerMatrix orfs_as_matrix(std::__cxx11::string&, std::__cxx11::string, std::__cxx11::string, int)’:
findORFsHelpers.cpp:212:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i = 0; i < uorfSize/2; i++) {
                   ~~^~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c findOrfs.cpp -o findOrfs.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c findOrfsFasta.cpp -o findOrfsFasta.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pmapFromTranscripts.cpp -o pmapFromTranscripts.o
pmapFromTranscripts.cpp: In function ‘Rcpp::List pmapFromTranscriptsCPP(const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const char&, bool)’:
pmapFromTranscripts.cpp:151:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0;i < xSize; i++){
                  ~~^~~~~~~
pmapFromTranscripts.cpp:155:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < indexSize; i++){
                   ~~^~~~~~~~~~~
pmapFromTranscripts.cpp:161:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 1; i < indexSize; i++){
                   ~~^~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pmapToTranscripts.cpp -o pmapToTranscripts.o
pmapToTranscripts.cpp: In function ‘void pmapToPositive(vi&, const int&, int&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&)’:
pmapToTranscripts.cpp:22:7: warning: variable ‘currentWidth’ set but not used [-Wunused-but-set-variable]
   int currentWidth = 0;
       ^~~~~~~~~~~~
pmapToTranscripts.cpp: In function ‘void pmapToNegative(vi&, const int&, int&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&)’:
pmapToTranscripts.cpp:68:7: warning: variable ‘currentWidth’ set but not used [-Wunused-but-set-variable]
   int currentWidth = 0;
       ^~~~~~~~~~~~
pmapToTranscripts.cpp: In function ‘Rcpp::List pmapToTranscriptsCPP(const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const char&, const std::vector<int>&)’:
pmapToTranscripts.cpp:126:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0;i < xSize; i++){ // Width per exon in x
                  ~~^~~~~~~
pmapToTranscripts.cpp:130:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < indexSize; i++){ // Width per exon in tx
                   ~~^~~~~~~~~~~
pmapToTranscripts.cpp:136:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 1; i < indexSize; i++){
                   ~~^~~~~~~~~~~
pmapToTranscripts.cpp:147:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (auto i = 1; i < 2 * xSize; i = i + 2) {
                    ~~^~~~~~~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o ORFik.so RcppExports.o findORFsHelpers.o findOrfs.o findOrfsFasta.o pmapFromTranscripts.o pmapToTranscripts.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-ORFik/00new/ORFik/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ORFik)

Tests output

ORFik.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, 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, 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

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


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, rowsum

Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: Rsamtools
> 
> test_check("ORFik")
     widths     group.size   
 Min.   : 6   Min.   :1.000  
 1st Qu.: 9   1st Qu.:1.000  
 Median :12   Median :1.000  
 Mean   :12   Mean   :1.667  
 3rd Qu.:15   3rd Qu.:2.000  
 Max.   :18   Max.   :3.000  
[1] "ORFik_CAGE_heart"
[1] "ORFik_RFP_heart"
[1] "ORFik_RFP"
[1] "ORFik_RNA_heart"
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 323 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 87.346   1.882  89.609 

Example timings

ORFik.Rcheck/ORFik-Ex.timings

nameusersystemelapsed
ORFik.template.experiment0.5580.0440.601
ORFikQC0.4000.0560.456
QCreport0.3990.0000.399
QCstats0.4240.0000.423
QCstats.plot0.4040.0000.404
STAR.align.folder000
STAR.align.single0.0010.0000.001
STAR.index000
STAR.install000
STAR.remove.crashed.genome000
TOP.Motif.ecdf0.0000.0000.001
assignTSSByCage0.0030.0000.003
bamVarName0.5930.0720.665
collapse.by.scores0.2320.0080.236
collapseDuplicatedReads-GAlignmentPairs-method0.0680.0000.068
collapseDuplicatedReads-GAlignments-method0.030.000.03
collapseDuplicatedReads-GRanges-method0.0520.0000.052
collapseDuplicatedReads0.0340.0000.034
computeFeatures9.3200.1049.428
computeFeaturesCage0.0000.0000.001
convertLibs0.3730.0000.373
convertToOneBasedRanges0.1930.0000.194
countOverlapsW0.120.000.12
countTable0.4120.0000.411
coverageHeatMap1.8710.0001.872
coveragePerTiling0.5560.0000.556
coverageScorings0.0140.0000.011
create.experiment0.3610.0000.361
defineTrailer0.1490.0000.148
detectRibosomeShifts0.0000.0010.000
disengagementScore0.5120.0030.515
distToCds0.2270.0000.228
distToTSS0.1980.0000.199
entropy1.0290.0000.989
experiment-class0.2390.0040.243
export.bed120.0230.0000.022
export.ofst-GAlignmentPairs-method0.0690.0000.068
export.ofst-GAlignments-method0.0640.0000.063
export.ofst-GRanges-method0.0640.0000.063
export.ofst0.0640.0000.064
export.wiggle0.0450.0000.044
extendLeaders0.6460.0000.646
extendTrailers0.4830.0000.481
filepath0.3690.0000.369
filterTranscripts202
fimport0.2590.0120.287
findFa0.0090.0000.009
findMapORFs0.7980.0000.798
findORFs0.0810.0040.085
findORFsFasta0.0510.0000.048
findPeaksPerGene1.4070.0041.411
findUORFs0.0010.0000.001
firstEndPerGroup0.0770.0000.077
firstExonPerGroup0.0850.0000.085
firstStartPerGroup0.0720.0000.072
floss0.4540.0000.447
fpkm0.1950.0040.199
fractionLength0.0920.0000.092
fread.bed0.0610.0610.150
gcContent0.9280.0600.988
getGenomeAndAnnotation000
groupGRangesBy0.1100.0120.122
groupings0.0940.0040.098
heatMapRegion0.3110.0040.315
import.ofst0.0680.0040.072
initiationScore0.9970.0081.004
insideOutsideORF1.0180.0001.016
install.fastp0.0000.0000.001
isInFrame0.3470.0000.348
isOverlapping0.3270.0000.327
kozakHeatmap000
kozakSequenceScore0.8350.0000.835
lastExonEndPerGroup0.1230.0000.123
lastExonPerGroup0.1240.0000.124
lastExonStartPerGroup0.1140.0000.114
list.experiments0.0380.0000.037
loadRegion1.8700.0041.875
loadRegions1.2890.0001.288
loadTxdb0.1610.0000.162
longestORFs0.2720.0000.276
makeORFNames0.1620.0040.171
makeSummarizedExperimentFromBam0.3690.0000.370
metaWindow0.2820.0010.212
numExonsPerGroup0.0780.0000.078
orfScore1.3220.0071.249
organism.df0.3580.0040.362
outputLibs0.3360.0000.337
pSitePlot0.4540.0000.454
pmapFromTranscriptF0.1380.0000.138
pmapToTranscriptF0.1400.0000.139
rankOrder0.1540.0000.155
read.experiment0.3730.0000.373
readBam0.1440.0040.148
readWidths0.0200.0000.019
reassignTSSbyCage0.8760.0080.884
reassignTxDbByCage0.0000.0000.001
reduceKeepAttr0.1940.0000.195
remove.experiments0.3050.0000.305
ribosomeReleaseScore0.2520.0000.251
ribosomeStallingScore0.550.000.55
save.experiment0.3690.0000.369
scaledWindowPositions0.6470.0010.606
seqnamesPerGroup0.1170.0040.121
shiftFootprints0.0000.0000.001
shiftFootprintsByExperiment9.3440.6509.018
shiftPlots0.4140.0000.414
shifts.load0.4290.0000.429
simpleLibs0.3950.0000.395
sortPerGroup0.5420.0000.542
startCodons1.0810.0001.082
startDefinition0.0010.0000.000
startSites0.5930.0000.593
stopCodons1.0520.0001.052
stopDefinition0.0010.0000.001
stopSites0.6070.0000.608
strandBool0.0150.0000.015
strandPerGroup0.1300.0000.129
tile10.3990.0000.399
topMotif0.0000.0000.001
transcriptWindow1.7620.0001.761
translationalEff0.2470.0000.247
txNames0.0490.0010.049
txNamesToGeneNames0.8680.0020.870
uORFSearchSpace0.7990.0000.798
uniqueGroups0.2600.0000.261
uniqueOrder0.3050.0000.304
unlistGrl0.0380.0000.038
widthPerGroup0.0530.0000.053
windowCoveragePlot0.5610.0000.559
windowPerGroup0.3610.0000.362