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CHECK report for genomation on merida1

This page was generated on 2019-04-16 11:58:11 -0400 (Tue, 16 Apr 2019).

Package 618/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genomation 1.14.0
Altuna Akalin , Vedran Franke
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/genomation
Branch: RELEASE_3_8
Last Commit: 6b67490
Last Changed Date: 2018-10-30 11:41:56 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  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: genomation
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:genomation.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings genomation_1.14.0.tar.gz
StartedAt: 2019-04-16 00:11:19 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 00:16:59 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 340.3 seconds
RetCode: 0
Status:  OK 
CheckDir: genomation.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:genomation.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings genomation_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/genomation.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genomation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genomation’ version ‘1.14.0’
* package encoding: latin1
* 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 ‘genomation’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       3.6Mb
    extdata   1.2Mb
* 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
Namespace in Imports field not imported from: ‘RUnit’
  All declared Imports should be used.
Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’
  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
ScoreMatrixBin,RleList-GRangesList: no visible binding for global
  variable ‘id’
ScoreMatrixBin,RleList-GRangesList: no visible global function
  definition for ‘:=’
Undefined global functions or variables:
  := id
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
The following directory looks like a leftover from 'knitr':
  ‘cache’
Please remove from your package.
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                                     user system elapsed
enrichmentMatrix-ScoreMatrixList-method             8.336  4.574   8.246
enrichmentMatrix-ScoreMatrix-method                 5.050  0.340   5.580
enrichmentMatrix-ScoreMatrixList-ScoreMatrix-method 4.241  0.388   7.536
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘genomation_unit_tests.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: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/genomation.Rcheck/00check.log’
for details.



Installation output

genomation.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL genomation
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘genomation’ ...
** libs
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c binSum.cpp -o binSum.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o genomation.so RcppExports.o binSum.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/genomation/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘GenomationManual.Rmd’ using ‘UTF-8’ 
** testing if installed package can be loaded
* DONE (genomation)

Tests output

genomation.Rcheck/tests/genomation_unit_tests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.

> (require("genomation") & require("GenomicRanges") & require("GenomicAlignments") & require("rtracklayer") & require("readr") & require("Biostrings")) || stop("unable to load genomation package")
Loading required package: genomation
Loading required package: grid
Loading required package: GenomicRanges
Loading required package: stats4
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

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
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
Loading required package: rtracklayer
Loading required package: readr
[1] TRUE
> genomation:::.test()
Normalizing to rpm ...
Normalizing to rpm ...
Normalizing to rpm ...
testing:min
testing:max
testing:median
Normalizing to rpm ...
Normalizing to rpm ...
Normalizing to rpm ...
Normalizing to rpm ...
Normalizing to rpm ...
Normalizing to rpm ...
Normalizing to rpm ...
Parsed with column specification:
cols(
  X1 = col_character(),
  X2 = col_double(),
  X3 = col_double(),
  X4 = col_character(),
  X5 = col_double(),
  X6 = col_character(),
  X7 = col_double(),
  X8 = col_double(),
  X9 = col_number()
)
Parsed with column specification:
cols(
  X1 = col_character(),
  X2 = col_double(),
  X3 = col_double(),
  X4 = col_character(),
  X5 = col_double(),
  X6 = col_character(),
  X7 = col_double(),
  X8 = col_double(),
  X9 = col_number()
)


RUNIT TEST PROTOCOL -- Tue Apr 16 00:16:52 2019 
*********************************************** 
Number of test functions: 24 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
genomation RUnit Tests - 24 test functions, 0 errors, 0 failures
Number of test functions: 24 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In .local(target, windows, strand.aware) :
  1 windows fall off the target
2: In .local(target, windows, strand.aware) :
  2 windows fall off the target
3: In .local(target, windows, strand.aware) :
  2 windows fall off the target
4: In .local(target, windows, strand.aware) :
  2 windows fall off the target
5: In .local(target, windows, strand.aware) :
  2 windows fall off the target
6: In .local(target, windows, strand.aware) :
  2 windows fall off the target
7: In .local(target, windows, bin.num, bin.op, strand.aware) :
  2 windows fall off the target
8: In .local(target, windows, bin.num, bin.op, strand.aware) :
  2 windows fall off the target
> 
> proc.time()
   user  system elapsed 
 38.691   2.109  40.375 

Example timings

genomation.Rcheck/genomation-Ex.timings

nameusersystemelapsed
AnnotationByGeneParts-methods0.7400.0180.764
ScoreMatrix-methods3.4990.1813.698
ScoreMatrixBin-methods3.4380.6432.622
ScoreMatrixList-methods0.6530.0530.720
annotateWithFeature-methods0.0520.0020.054
annotateWithFeatureFlank-methods0.3440.0020.348
annotateWithFeatures-methods2.0381.0701.525
annotateWithGeneParts-methods1.2230.6860.885
binMatrix-methods0.2500.0150.270
convertBed2Exons-methods0.1520.0070.159
convertBed2Introns-methods0.1000.0020.104
enrichmentMatrix-ScoreMatrix-method5.050.345.58
enrichmentMatrix-ScoreMatrixList-ScoreMatrix-method4.2410.3887.536
enrichmentMatrix-ScoreMatrixList-method8.3364.5748.246
findFeatureComb-methods1.4311.2460.628
getFeatsWithTargetsStats-methods0.5320.0600.605
getFlanks-methods0.2460.0280.286
getRandomEnrichment-methods0.0040.0030.007
getTargetAnnotationStats-methods0.4510.0490.507
gffToGRanges0.1280.0150.174
heatMatrix0.4260.1440.579
heatMeta0.6150.1160.743
heatTargetAnnotation-methods2.7100.5130.875
intersectScoreMatrixList-methods0.7090.6710.337
multiHeatMatrix0.5930.0650.672
orderBy-methods0.6510.0460.705
patternMatrix-methods0.1560.0050.163
plotMeta0.5120.0300.554
plotTargetAnnotation-methods0.3720.0070.386
readBed0.0530.0140.069
readBroadPeak0.0270.0050.033
readFeatureFlank-methods0.1730.0050.181
readGeneric0.0400.0080.050
readNarrowPeak0.0350.0080.050
readTranscriptFeatures-methods0.2680.0090.278
scaleScoreMatrix-methods0.2550.0050.265
scaleScoreMatrixList0.6760.0330.719