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CHECK report for ORFik on malbec2

This page was generated on 2019-04-07 11:46:36 -0400 (Sun, 07 Apr 2019).

Package 1127/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ORFik 1.3.13
Kornel Labun
Snapshot Date: 2019-04-06 17:01:31 -0400 (Sat, 06 Apr 2019)
URL: https://git.bioconductor.org/packages/ORFik
Branch: master
Last Commit: c92f736
Last Changed Date: 2019-04-01 05:18:42 -0400 (Mon, 01 Apr 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: ORFik
Version: 1.3.13
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ORFik.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ORFik_1.3.13.tar.gz
StartedAt: 2019-04-07 02:57:37 -0400 (Sun, 07 Apr 2019)
EndedAt: 2019-04-07 03:03:21 -0400 (Sun, 07 Apr 2019)
EllapsedTime: 344.3 seconds
RetCode: 0
Status:  OK 
CheckDir: ORFik.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ORFik.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ORFik_1.3.13.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/ORFik.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.3.13’
* 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 ... 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
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
  ‘fractionLengths’
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 ‘ORFScores’
allFeaturesHelper: no visible binding for global variable ‘ioScore’
allFeaturesHelper: no visible binding for global variable ‘inFrameCDS’
allFeaturesHelper: no visible binding for global variable
  ‘isOverlappingCds’
allFeaturesHelper: no visible binding for global variable ‘rankInTx’
convertToOneBasedRanges: 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 ‘fraction’
entropy: no visible binding for global variable ‘Hx’
entropy: no visible binding for global variable ‘codonSums’
entropy: no visible global function definition for ‘.’
gSort: no visible binding for global variable ‘grnames’
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’
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 ‘position’
pSitePlot: no visible binding for global variable ‘frame’
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’
scaledWindowPositions: no visible binding for global variable
  ‘scalingFactor’
scaledWindowPositions: no visible binding for global variable
  ‘position’
scaledWindowPositions: no visible global function definition for ‘.’
windowCoveragePlot: no visible binding for global variable ‘feature’
windowCoveragePlot: no visible binding for global variable ‘fraction’
windowCoveragePlot: no visible binding for global variable ‘position’
windowCoveragePlot: no visible binding for global variable
  ‘fraction_min’
Undefined global functions or variables:
  . Hx ORFScores RRS RSS chr codonSums count dif difPer
  disengagementScores entropyRFP exon_rank feature fpkmRFP fpkmRNA
  fraction fractionLengths fraction_min frame frame_one_RP frame_two_RP
  gene_sum grnames inFrameCDS ioScore isOverlappingCds ones position
  rankInTx ranks scalingFactor te 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 compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
computeFeatures 19.334  0.178   7.310
orfScore         6.975  0.057   3.876
entropy          6.339  0.037   3.664
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/ORFik.Rcheck/00check.log’
for details.



Installation output

ORFik.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL ORFik
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘ORFik’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-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 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o ORFik.so RcppExports.o findORFsHelpers.o findOrfs.o findOrfsFasta.o pmapFromTranscripts.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-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 Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 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, colMeans, colSums, 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, 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

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, rowsum

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: 255 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
141.513   0.989  62.680 

Example timings

ORFik.Rcheck/ORFik-Ex.timings

nameusersystemelapsed
assignTSSByCage000
computeFeatures19.334 0.178 7.310
computeFeaturesCage0.0010.0000.000
coverageHeatMap2.4470.0091.979
coveragePerTiling0.4230.0000.920
coverageScorings1.3450.0070.773
defineTrailer0.1670.0000.217
detectRibosomeShifts000
disengagementScore0.4810.0000.488
distToCds0.2490.0000.284
distToTSS0.2760.0000.312
entropy6.3390.0373.664
extendLeaders2.8410.0200.937
filterTranscripts3.0260.0001.200
findMapORFs3.0620.0110.824
findORFs1.2960.0010.218
findORFsFasta0.6500.0000.171
firstEndPerGroup0.0840.0000.084
firstExonPerGroup0.0790.0000.079
firstStartPerGroup0.0750.0000.075
floss0.1520.0000.152
fpkm0.0360.0000.037
fractionLength0.0450.0000.045
fread.bed0.0180.0540.087
gcContent2.0540.0290.829
groupGRangesBy0.0660.0030.069
groupings0.0480.0080.056
initiationScore2.7720.0431.390
insideOutsideORF2.7850.0011.104
isInFrame0.2350.0000.235
isOverlapping0.2230.0000.223
kozakSequenceScore1.7120.0041.088
lastExonEndPerGroup0.0790.0000.201
lastExonPerGroup0.0820.0000.164
lastExonStartPerGroup0.0800.0000.177
loadTxdb0.1650.0040.380
longestORFs0.5670.0000.532
makeORFNames0.090.000.15
metaWindow1.7050.0051.040
numExonsPerGroup0.0510.0000.051
orfScore6.9750.0573.876
overlapsToCoverage0.0720.0000.058
pSitePlot0.4880.0000.546
pmapFromTranscriptF0.1270.0000.159
rankOrder0.0790.0030.134
reassignTSSbyCage2.3870.0040.950
reassignTxDbByCage000
reduceKeepAttr0.9100.0080.356
ribosomeReleaseScore0.1070.0080.115
ribosomeStallingScore0.2580.0000.258
scaledWindowPositions2.4410.0160.834
seqnamesPerGroup0.0950.0000.084
shiftFootprints0.0010.0000.000
sortPerGroup1.5200.0210.462
startCodons1.8490.0080.667
startDefinition000
startSites1.6550.0080.493
stopCodons2.0050.0040.686
stopDefinition000
stopSites1.7110.0200.451
strandBool0.0080.0000.008
strandPerGroup0.0760.0000.076
tile10.1530.0020.156
translationalEff0.0840.0000.084
txNames0.0320.0000.032
uORFSearchSpace2.2420.0040.632
uniqueGroups0.1040.0000.104
uniqueOrder1.5600.0841.236
unlistGrl0.0370.0000.038
widthPerGroup0.050.000.05
windowCoveragePlot1.2340.0040.519
windowPerGroup0.2900.0040.295