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CHECK report for ORFik on malbec1

This page was generated on 2021-05-06 12:28:28 -0400 (Thu, 06 May 2021).

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 1278/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ORFik 1.10.13  (landing page)
Haakon Tjeldnes
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/ORFik
Branch: RELEASE_3_12
Last Commit: 3f2976e
Last Changed Date: 2021-03-26 10:15:54 -0400 (Fri, 26 Mar 2021)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: ORFik
Version: 1.10.13
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:ORFik.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings ORFik_1.10.13.tar.gz
StartedAt: 2021-05-06 04:13:59 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 04:23:16 -0400 (Thu, 06 May 2021)
EllapsedTime: 557.0 seconds
RetCode: 0
Status:   OK  
CheckDir: ORFik.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:ORFik.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings ORFik_1.10.13.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/ORFik.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.10.13’
* 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 ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   2.8Mb
* 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.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘findFa’ ‘find_url_ebi’ ‘hasHits’ ‘trimming.table’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DTEG.plot: no visible binding for global variable ‘rna’
DTEG.plot: no visible binding for global variable ‘rfp’
DTEG.plot: no visible binding for global variable ‘Regulation’
QC_count_tables: no visible binding for global variable ‘leaders’
QC_count_tables : <anonymous>: no visible binding for global variable
  ‘percentage_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 ‘variable’
QCstats.plot: no visible binding for global variable ‘sample_total’
QCstats.plot: no visible binding for global variable ‘value’
QCstats.plot: no visible global function definition for ‘.’
QCstats.plot: no visible binding for global variable ‘sample_id’
QCstats.plot: no visible binding for global variable ‘percentage’
QCstats.plot: no visible binding for global variable
  ‘perc_of_counts_per_sample’
QCstats.plot: no visible binding for global variable ‘read length’
RiboQC.plot: no visible binding for global variable ‘variable’
RiboQC.plot: no visible binding for global variable ‘sample_total’
RiboQC.plot: no visible binding for global variable ‘value’
RiboQC.plot: no visible global function definition for ‘.’
RiboQC.plot: no visible binding for global variable ‘sample_id’
RiboQC.plot: no visible binding for global variable ‘percentage’
RiboQC.plot : <anonymous>: no visible binding for global variable
  ‘fraction’
RiboQC.plot: no visible binding for global variable ‘percent’
RiboQC.plot: no visible binding for global variable ‘fraction’
RiboQC.plot: no visible binding for global variable ‘frame’
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’
download.SRA.metadata: no visible binding for global variable ‘spots’
download.SRA.metadata: no visible binding for global variable ‘Run’
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’
filterTranscripts: no visible binding for global variable ‘tx_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’
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’
kozak_IR_ranking: no visible global function definition for ‘.’
kozak_IR_ranking: no visible binding for global variable ‘IR’
kozak_IR_ranking: no visible binding for global variable
  ‘upstream_kozak_strength’
kozak_IR_ranking: no visible binding for global variable ‘count’
kozak_IR_ranking: no visible binding for global variable ‘mean_IR’
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’
readLengthTable: no visible binding for global variable
  ‘counts_per_sample’
readLengthTable: no visible binding for global variable
  ‘perc_of_counts_per_sample’
regionPerReadLength : <anonymous>: no visible binding for global
  variable ‘fraction’
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’
te.plot: no visible global function definition for ‘rowMin’
te.plot: no visible binding for global variable ‘variable’
te.plot: no visible binding for global variable ‘LFC_TE’
te.plot: no visible binding for global variable ‘rfp_log2’
te.plot: no visible binding for global variable ‘rna_log2’
te.plot: no visible binding for global variable ‘rna_log10’
te.table: no visible global function definition for ‘rowMin’
te.table: no visible binding for global variable ‘variable’
te.table: no visible binding for global variable ‘TE_log2’
te.table: no visible binding for global variable ‘rfp_log2’
te.table: no visible binding for global variable ‘rna_log2’
te_rna.plot: no visible binding for global variable ‘df.rfp’
te_rna.plot: no visible binding for global variable ‘df.rna’
te_rna.plot: no visible binding for global variable ‘subtitle’
te_rna.plot: no visible binding for global variable ‘rna_log10’
te_rna.plot: no visible binding for global variable ‘TE_log2’
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 IR LEADERS LFC_TE ORFGrouping ORFScores RRS RSS
  Regulation Run StartCodons StopCodons TE_log2 TOP chr cigar1 cigar2
  codonSums count countRFP count_seq_pos_with_count counts_per_sample
  detectCores df.rfp df.rna 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_IR mean_per_gene
  median_per_gene median_score name ones pShifted
  perc_of_counts_per_sample percent percentage percentage_mrna_aligned
  pick position random rankInTx ranks ratio_cds_leader ratio_cds_mrna
  read length rfp rfp_log2 rna rna_log10 rna_log2 rowMin rowSums2
  sample_id sample_total scalingFactor sd_per_gene seq1 seq2 seq3 seq4
  seq5 size spots start1 start2 startCodonCoverage startRegionRelative
  subtitle sum.count sum_per_gene te trailers tx tx_len
  upstream_kozak_strength utr3_len utr5_len value variable widths
  windowMean windowSD zscore
Consider adding
  importFrom("base", "length")
  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 5.836  0.064   5.919
computeFeatures             5.288  0.012   5.310
* 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/ORFik.Rcheck/00check.log’
for details.



Installation output

ORFik.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL ORFik
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘ORFik’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c findORFsHelpers.cpp -o findORFsHelpers.o
findORFsHelpers.cpp: In function ‘Rcpp::IntegerMatrix orfs_as_matrix(std::__cxx11::string&, std::__cxx11::string, std::__cxx11::string, int)’:
findORFsHelpers.cpp:214:21: 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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-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-3.12-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-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.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: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
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    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':

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Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

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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] "CAGE_heart"
[1] "RFP_heart"
[1] "RFP"
[1] "RNA_heart"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 331 ]
> 
> proc.time()
   user  system elapsed 
101.648   2.612 104.625 

Example timings

ORFik.Rcheck/ORFik-Ex.timings

nameusersystemelapsed
DTEG.analysis000
DTEG.plot000
ORFik.template.experiment0.5760.0400.617
ORFikQC0.3560.0160.374
QCreport0.2960.0200.318
QCstats1.4560.0961.559
QCstats.plot0.4280.0040.432
RiboQC.plot0.4280.0000.429
STAR.align.folder000
STAR.align.single000
STAR.index000
STAR.install000
STAR.remove.crashed.genome000
TOP.Motif.ecdf000
assignTSSByCage0.0000.0040.003
bamVarName0.7080.0000.710
collapse.by.scores0.2400.0000.239
collapse.fastq000
collapseDuplicatedReads-GAlignmentPairs-method0.0800.0040.085
collapseDuplicatedReads-GAlignments-method0.0440.0000.046
collapseDuplicatedReads-GRanges-method0.0280.0000.028
collapseDuplicatedReads0.0280.0040.030
computeFeatures5.2880.0125.310
computeFeaturesCage000
config.exper000
convertLibs0.2440.0000.240
convertToOneBasedRanges0.1280.0000.129
countOverlapsW0.0880.0040.090
countTable0.2400.0000.239
coverageHeatMap1.1760.0001.177
coveragePerTiling0.7400.0040.746
coverageScorings0.0120.0000.008
create.experiment0.2440.0000.242
defineTrailer0.2080.0000.208
detectRibosomeShifts0.0040.0000.002
disengagementScore0.8160.0000.819
distToCds0.2400.0000.241
distToTSS0.2040.0040.208
download.SRA000
download.SRA.metadata000
entropy1.3960.0001.400
experiment-class0.4680.0000.470
export.bed120.0400.0000.039
export.ofst-GAlignmentPairs-method0.1240.0000.123
export.ofst-GAlignments-method0.1160.0000.114
export.ofst-GRanges-method0.1160.0000.117
export.ofst0.0960.0000.096
export.wiggle0.0440.0040.051
extendLeaders1.5920.0161.660
extendTrailers0.8560.0000.857
filepath0.2360.0000.237
filterTranscripts1.4040.0001.407
fimport0.4640.0120.491
findFa0.0080.0000.006
findMapORFs0.7560.0000.754
findORFs0.2000.0000.201
findORFsFasta0.0960.0040.142
findPeaksPerGene1.7640.0001.766
findUORFs0.0000.0000.001
firstEndPerGroup0.0840.0000.083
firstExonPerGroup0.0880.0000.087
firstStartPerGroup0.0680.0040.071
floss0.2920.0000.284
fpkm0.1160.0000.116
fractionLength0.0560.0000.056
fread.bed0.0600.0520.126
gcContent0.4960.0320.528
getGenomeAndAnnotation000
get_genome_fasta000
get_genome_gtf000
get_noncoding_rna000
get_phix_genome0.0000.0000.001
get_silva_rRNA000
groupGRangesBy0.10.00.1
groupings0.0880.0000.091
heatMapRegion0.3120.0040.316
import.ofst0.0720.0000.074
initiationScore0.8840.0000.884
insideOutsideORF0.9280.0000.929
install.fastp000
install.sratoolkit0.0000.0000.001
isInFrame0.2280.0000.228
isOverlapping0.2520.0000.252
kozakHeatmap000
kozakSequenceScore0.5600.0000.563
lastExonEndPerGroup0.1200.0000.124
lastExonPerGroup0.1400.0040.144
lastExonStartPerGroup0.0760.0000.076
list.experiments0.0280.0000.027
loadRegion2.0120.0042.023
loadRegions1.0880.0001.094
loadTxdb0.1520.0000.151
longestORFs0.1520.0000.153
makeORFNames0.10.00.1
makeSummarizedExperimentFromBam0.2680.0000.268
mergeFastq000
metaWindow0.3080.0000.309
numExonsPerGroup0.10.00.1
orfScore0.9680.0040.968
organism.df0.3280.0000.329
outputLibs0.2560.0040.258
pSitePlot0.5120.0000.513
pmapFromTranscriptF0.1120.0000.111
pmapToTranscriptF0.1200.0000.121
rankOrder0.1560.0000.156
read.experiment0.3400.0000.344
readBam0.1840.0000.187
readWidths0.0160.0000.016
reassignTSSbyCage0.6400.0000.641
reassignTxDbByCage000
reduceKeepAttr0.1520.0000.151
regionPerReadLength2.7160.4963.230
remove.experiments0.2680.0000.266
ribosomeReleaseScore0.2040.0000.207
ribosomeStallingScore0.3560.0120.367
save.experiment0.2720.0080.279
scaledWindowPositions0.4200.0000.416
seqnamesPerGroup0.0760.0000.077
shiftFootprints0.0040.0000.001
shiftFootprintsByExperiment5.8360.0645.919
shiftPlots0.4080.0000.411
shifts.load0.3440.0000.346
simpleLibs0.2360.0000.234
sortPerGroup0.3840.0000.383
startCodons1.0360.0041.045
startDefinition000
startRegion0.6040.0000.606
startSites0.3600.0000.363
stopCodons0.6720.0000.674
stopDefinition000
stopRegion0.6400.0000.641
stopSites0.4840.0000.482
strandBool0.0080.0000.009
strandPerGroup0.0680.0040.070
te.plot0.0000.0000.001
te.table000
te_rna.plot000
tile10.240.000.24
topMotif000
transcriptWindow1.2680.0001.270
translationalEff0.1880.0000.186
txNames0.0960.0000.095
txNamesToGeneNames1.2000.0001.206
uORFSearchSpace0.6320.0000.630
uniqueGroups0.1640.0000.166
uniqueOrder0.2040.0000.207
unlistGrl0.040.000.04
widthPerGroup0.0520.0000.054
windowCoveragePlot0.5640.0000.562
windowPerGroup0.3640.0000.367
windowPerReadLength1.1400.0001.138