CHECK report for systemPipeR on malbec2
This page was generated on 2019-10-16 12:05:18 -0400 (Wed, 16 Oct 2019).
systemPipeR 1.18.2
Thomas Girke
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/systemPipeR |
| Branch: RELEASE_3_9 |
| Last Commit: da3e435 |
| Last Changed Date: 2019-06-21 20:48:40 -0400 (Fri, 21 Jun 2019) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
Summary
Command output
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:systemPipeR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings systemPipeR_1.18.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/systemPipeR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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 23.442 0.227 23.873
run_DESeq2 5.961 0.032 5.996
* 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
‘/home/biocbuild/bbs-3.9-bioc/meat/systemPipeR.Rcheck/00check.log’
for details.
Installation output
systemPipeR.Rcheck/00install.out
Tests output
systemPipeR.Rcheck/tests/runTests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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.
> 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 05:30:23 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
19.360 0.649 20.014
Example timings
systemPipeR.Rcheck/systemPipeR-Ex.timings