Package: systemPipeR

Version: 1.18.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:systemPipeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings systemPipeR_1.18.2.tar.gz

StartedAt: 2019-10-16 07:18:08 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 07:28:44 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 635.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: systemPipeR.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:systemPipeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings systemPipeR_1.18.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/systemPipeR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘systemPipeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘systemPipeR’ version ‘1.18.2’
* 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 ... NOTE
Found the following hidden files and directories:
  inst/extdata/.batchtools.conf.R
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘systemPipeR’ 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 ... WARNING
Invalid citation information in ‘inst/CITATION’:
  Error in (function (bibtype, textVersion = NULL, header = NULL, footer = NULL,     key = NULL, ..., other = list(), mheader = NULL, mfooter = NULL) {    BibTeX_names <- names(BibLaTeX_entry_field_db)    args <- c(list(...), other)    if (!length(args))         return(structure(list(), class = "bibentry"))    if (any(vapply(names(args), .is_not_nonempty_text, FALSE)))         stop("all fields have to be named")    args <- c(list(bibtype = bibtype, textVersion = textVersion,         header = header, footer = footer, key = key), list(...))    args <- lapply(args, .listify)    other <- lapply(other, .listify)    max_length <- max(vapply(c(args, other), length, 0L))    args_length <- vapply(args, length, 0L)    if (!all(args_length_ok <- args_length %in% c(1L, max_length)))         warning(gettextf("Not all arguments are of the same length, %s: %s",             "the following need to be recycled", paste(names(args)[!args_length_ok],                 collapse = ", ")), domain = NA)    args <- lapply(args, function(x) rep(x, length.out = max_length))    other_length <- vapply(other, length, 0L)    if (!all(other_length_ok <- other_length %in% c(1L, max_length)))         warning(gettextf("Not all arguments are of the same length, %s: %s",             "the following need to be recycled", paste(names(other)[!other_length_ok],                 collapse = ", ")), domain = NA)    other <- lapply(other, function(x) rep(x, length.out = max_length))    bibentry1 <- function(bibtype, textVersion, header = NULL,         footer = NULL, key = NULL, ..., other = list()) {        bibtype <- as.character(bibtype)        stopifnot(length(bibtype) == 1L)        pos <- match(tolower(bibtype), tolower(BibTeX_names))        if (is.na(pos))             stop(gettextf("%s has to be one of %s", sQuote("bibtype"),                 paste(BibTeX_names, collapse = ", ")), domain = NA)        bibtype <- BibTeX_names[pos]        rval <- c(list(...), other)        rval <- rval[!vapply(rval, .is_not_nonempty_text, FALSE)]        fields <- tolower(names(rval))        names(rval) <- fields        attr(rval, "bibtype") <- bibtype        .BibEntryCheckBibEntry1(rval)        pos <- fields %in% .BibEntryNameList        if (any(pos)) {            for (i in which(pos)) if (!inherits(rval[[i]], "person"))                 rval[[i]] <- ArrangeAuthors(rval[[i]])        }        pos <- fields %in% c("dateobj") | pos        if (any(!pos)) {            for (i in which(!pos)) rval[[i]] <- as.character(rval[[i]])        }        attr(rval, "key") <- if (is.null(key))             NULL        else as.character(key)        if (is.null(rval[["dateobj"]])) {            tdate <- try(ProcessDates(rval), TRUE)            if (!inherits(tdate, "try-error"))                 attr(rval, "dateobj") <- tdate        }        else {            attr(rval, "dateobj") <- rval[["dateobj"]]            rval[["dateobj"]] <- NULL        }        if (!is.null(textVersion))             attr(rval, "textVersion") <- as.character(textVersion)        if (!.is_not_nonempty_text(header))             attr(rval, "header") <- paste(header, collapse = "\n")        if (!.is_not_nonempty_text(footer))             attr(rval, "footer") <- paste(footer, collapse = "\n")        return(rval)    }    rval <- lapply(seq_along(args$bibtype), function(i) do.call("bibentry1",         c(lapply(args, "[[", i), list(other = lapply(other, "[[",             i)))))    if (!.is_not_nonempty_text(mheader))         attr(rval, "mheader") <- paste(mheader, collapse = "\n")    if (!.is_not_nonempty_text(mfooter))         attr(rval, "mfooter") <- paste(mfooter, collapse = "\n")    class(rval) <- c("BibEntry", "bibentry")    rval})(year = "2019", key = "_2019"): argument "bibtype" is missing, with no default
* 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: ‘BiocGenerics’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.AffyID2GeneID: no visible global function definition for ‘read.delim’
.readGOorg: no visible global function definition for ‘read.delim’
.readGOorg: no visible global function definition for ‘na.omit’
.resizeFeature: no visible global function definition for ‘DataFrame’
.sampleDFgene2GO: no visible global function definition for ‘na.omit’
.subsetReadsByMappingRegion: no visible global function definition for
  ‘IRanges’
.subsetReadsByMappingRegion: no visible global function definition for
  ‘seqlengths’
.subsetReadsByMappingRegion: no visible global function definition for
  ‘readGAlignments’
GOHyperGAll: no visible global function definition for ‘phyper’
GOHyperGAll_Simplify: no visible global function definition for
  ‘na.omit’
GOHyperGAll_Subset: no visible binding for global variable
  ‘test_sample’
assembleCommandlineList: no visible binding for global variable ‘WF’
combineVarReports: no visible global function definition for
  ‘read.delim’
countRangeset: no visible global function definition for ‘read.delim’
countRangeset: no visible global function definition for ‘import.bed’
countRangeset: no visible global function definition for
  ‘summarizeOverlaps’
countRangeset: no visible global function definition for ‘write.table’
featureCoverage: no visible global function definition for
  ‘readGAlignments’
featureCoverage: no visible global function definition for ‘qwidth’
featureCoverage: no visible global function definition for
  ‘subsetByOverlaps’
featureCoverage: no visible global function definition for ‘Rle’
featureCoverage: no visible global function definition for ‘na.omit’
featureCoverage: no visible global function definition for
  ‘write.table’
featuretypeCounts: no visible global function definition for
  ‘readGAlignments’
featuretypeCounts: no visible global function definition for
  ‘readGAlignmentPairs’
featuretypeCounts: no visible global function definition for
  ‘subsetByOverlaps’
featuretypeCounts: no visible global function definition for ‘qwidth’
featuretypeCounts: no visible global function definition for ‘last’
featuretypeCounts: no visible global function definition for ‘first’
filterDEGs: no visible binding for global variable ‘Comparisons’
filterDEGs: no visible binding for global variable ‘Counts’
filterDEGs: no visible binding for global variable ‘Type’
findBestMatch: no visible global function definition for ‘setNames’
genFeatures: no visible global function definition for ‘DataFrame’
genFeatures: no visible global function definition for ‘seqlengths<-’
getQsubargs: no visible binding for global variable ‘tophatargs’
goBarplot: no visible binding for global variable ‘SampleMatch’
goBarplot: no visible binding for global variable ‘Sample’
loadWorkflow: no visible global function definition for ‘read.delim’
olBarplot: no visible binding for global variable ‘Intersect_Sets’
olBarplot: no visible binding for global variable ‘Counts’
olBarplot: no visible binding for global variable ‘Level’
overLapper : : no visible global function definition for
  ‘combn’
plotfeatureCoverage: no visible global function definition for
  ‘aggregate’
plotfeatureCoverage: no visible binding for global variable ‘Coverage’
plotfeatureCoverage: no visible binding for global variable ‘Strand’
plotfeaturetypeCounts: no visible binding for global variable ‘Feature’
plotfeaturetypeCounts: no visible binding for global variable ‘Counts’
plotfeaturetypeCounts: no visible binding for global variable ‘Strand’
plotfeaturetypeCounts: no visible global function definition for
  ‘dev.off’
plotfeaturetypeCounts: no visible binding for global variable ‘Length’
predORF : .predORF: no visible global function definition for ‘na.omit’
predORF : .predORF: no visible global function definition for ‘IRanges’
readComp: no visible global function definition for ‘read.delim’
readComp: no visible global function definition for ‘combn’
renderInputs: no visible binding for global variable ‘WF’
renderOutputs: no visible binding for global variable ‘WF’
runDiff: no visible global function definition for ‘read.delim’
runDiff: no visible global function definition for ‘write.table’
runDiff: no visible global function definition for ‘pdf’
runDiff: no visible global function definition for ‘dev.off’
run_edgeR: no visible global function definition for ‘model.matrix’
run_edgeR: no visible global function definition for ‘pdf’
run_edgeR: no visible global function definition for ‘dev.off’
scaleRanges : .scaleRanges: no visible global function definition for
  ‘IRanges’
scaleRanges: no visible global function definition for ‘DataFrame’
seeFastq : seeFastqSingle: no visible global function definition for
  ‘boxplot’
seeFastqPlot : fastqPlot: no visible binding for global variable
  ‘Cycle’
seeFastqPlot : fastqPlot: no visible binding for global variable ‘low’
seeFastqPlot : fastqPlot: no visible binding for global variable ‘mid’
seeFastqPlot : fastqPlot: no visible binding for global variable ‘top’
seeFastqPlot : fastqPlot: no visible binding for global variable
  ‘Frequency’
seeFastqPlot : fastqPlot: no visible binding for global variable ‘Base’
seeFastqPlot : fastqPlot: no visible binding for global variable
  ‘Quality’
seeFastqPlot : fastqPlot: no visible binding for global variable
  ‘RelDiv’
seeFastqPlot : fastqPlot: no visible binding for global variable
  ‘Method’
seeFastqPlot : fastqPlot: no visible binding for global variable
  ‘minQuality’
seeFastqPlot : fastqPlot: no visible binding for global variable
  ‘Percent’
seeFastqPlot : fastqPlot: no visible binding for global variable
  ‘Outliers’
systemArgs: no visible global function definition for ‘read.delim’
varSummary: no visible global function definition for ‘read.delim’
variantReport: no visible global function definition for ‘write.table’
vennPlot: no visible global function definition for ‘symbols’
vennPlot: no visible global function definition for ‘text’
vennPlot : plotellipse: no visible global function definition for
  ‘plot’
vennPlot : ellipseVenn: no visible global function definition for
  ‘split.screen’
vennPlot : ellipseVenn: no visible global function definition for
  ‘screen’
vennPlot : ellipseVenn: no visible global function definition for
  ‘text’
vennPlot : ellipseVenn: no visible global function definition for
  ‘close.screen’
writeTargetsRef: no visible global function definition for ‘read.delim’
modules,SYSargs2: no visible global function definition for ‘setNames’
Undefined global functions or variables:
  Base Comparisons Counts Coverage Cycle DataFrame Feature Frequency
  IRanges Intersect_Sets Length Level Method Outliers Percent Quality
  RelDiv Rle Sample SampleMatch Strand Type WF aggregate boxplot
  close.screen combn dev.off first import.bed last low mid minQuality
  model.matrix na.omit pdf phyper plot qwidth read.delim
  readGAlignmentPairs readGAlignments screen seqlengths seqlengths<-
  setNames split.screen subsetByOverlaps summarizeOverlaps symbols
  test_sample text top tophatargs write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "boxplot", "close.screen", "plot", "screen",
             "split.screen", "symbols", "text")
  importFrom("stats", "aggregate", "model.matrix", "na.omit", "phyper",
             "setNames")
  importFrom("utils", "combn", "read.delim", "write.table")
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 Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
genFeatures          33.300  0.915  34.218
run_DESeq2           10.361  0.112  10.473
run_track             6.956  0.035   6.990
output_update         6.166  0.143   6.309
SYSargs2Pipe-methods  6.083  0.022   6.107
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/systemPipeR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL systemPipeR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘systemPipeR’ ...
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (systemPipeR)

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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.

> BiocGenerics:::testPackage("systemPipeR")

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


Attaching package: 'S4Vectors'

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

    expand.grid


Attaching package: 'Biostrings'

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

    strsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


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 object is masked from 'package:Biostrings':

    type

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

    aperm, apply, rowsum




RUNIT TEST PROTOCOL -- Wed Oct 16 07:28:34 2019 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
systemPipeR RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In normalizePath(infile1) :
  path[1]="SRR446027_1.fastq": No such file or directory
2: In normalizePath(infile1) :
  path[2]="SRR446028_1.fastq": No such file or directory
3: In normalizePath(infile1) :
  path[3]="SRR446029_1.fastq": No such file or directory
4: In normalizePath(infile1) :
  path[4]="SRR446030_1.fastq": No such file or directory
> 
> proc.time()
   user  system elapsed 
 24.236   1.896  26.102 

name	user	system	elapsed
GOHyperGAll	0.001	0.001	0.002
INTERSECTset-class	1.099	0.014	1.112
SYSargs-class	0.069	0.014	0.086
SYSargs2-class	3.630	0.462	4.093
SYSargs2Pipe-class	2.965	0.010	2.976
SYSargs2Pipe-methods	6.083	0.022	6.107
SYSargs2list-methods	2.698	0.011	2.708
VENNset-class	0.016	0.008	0.024
alignStats	2.962	0.012	2.974
catDB-class	0.001	0.001	0.001
catmap	0.000	0.001	0.001
clusterRun	3.111	0.134	3.247
countRangeset	0.095	0.003	0.099
featureCoverage	0.011	0.001	0.013
featuretypeCounts	0.014	0.002	0.016
filterDEGs	1.344	0.060	1.405
filterVars	0.018	0.004	0.023
genFeatures	33.300	0.915	34.218
getQsubargs	0.020	0.005	0.026
loadWorkflow	4.474	0.491	4.965
mergeBamByFactor	0.016	0.003	0.020
module	0.000	0.001	0.001
moduleload	0.000	0.000	0.001
olBarplot	0.884	0.058	0.944
output_update	6.166	0.143	6.309
overLapper	0.691	0.045	0.738
plotfeatureCoverage	0.019	0.003	0.022
plotfeaturetypeCounts	0.018	0.003	0.021
predORF	0.299	0.002	0.301
preprocessReads	0.034	0.006	0.043
qsubRun	0.015	0.002	0.018
readComp	0.020	0.003	0.023
renderWF	3.385	0.110	3.494
returnRPKM	0	0	0
runCommandline	2.873	0.021	2.894
runDiff	0.063	0.003	0.066
run_DESeq2	10.361	0.112	10.473
run_edgeR	1.112	0.033	1.144
run_track	6.956	0.035	6.990
scaleRanges	0.168	0.003	0.170
seeFastq	0.000	0.001	0.001
subsetWF	3.949	0.007	3.957
symLink2bam	0.018	0.003	0.021
sysargs	0.018	0.003	0.022
systemArgs	0.027	0.005	0.033
targets.as.df	3.230	0.008	3.238
variantReport	0.016	0.003	0.019
vennPlot	0.664	0.040	0.706
writeTargetsRef	0.002	0.001	0.001
writeTargetsout	3.383	0.016	3.400