Thomas Girke
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/systemPipeR |
| Branch: RELEASE_3_8 |
| Last Commit: 6f1a478 |
| Last Changed Date: 2019-01-04 13:07:22 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:50:49 -0400 (Tue, 16 Apr 2019).
| Package 1541/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| systemPipeR 1.16.1 Thomas Girke
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: systemPipeR |
| Version: 1.16.1 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:systemPipeR.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings systemPipeR_1.16.1.tar.gz |
| StartedAt: 2019-04-16 03:21:55 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 03:27:30 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 335.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: systemPipeR.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:systemPipeR.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings systemPipeR_1.16.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/systemPipeR.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.16.1’
* 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/.BatchJobs.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 ... 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
Namespaces in Imports field not imported from:
‘BiocGenerics’ ‘VariantAnnotation’
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’
clusterRun: no visible global function definition for ‘chunk’
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’
filterVars: no visible global function definition for ‘readVcf’
filterVars: no visible global function definition for ‘totalDepth<-’
filterVars: no visible global function definition for ‘refDepth<-’
filterVars: no visible global function definition for ‘altDepth<-’
filterVars: no visible global function definition for ‘asVCF’
filterVars: no visible global function definition for ‘writeVcf’
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’
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 : <anonymous>: 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’
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 ‘readVcf’
variantReport: no visible global function definition for
‘locateVariants’
variantReport: no visible global function definition for ‘AllVariants’
variantReport: no visible global function definition for
‘predictCoding’
variantReport: no visible global function definition for ‘ref’
variantReport: no visible global function definition for ‘alt’
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’
show,INTERSECTset: no visible binding for global variable ‘vennset’
Undefined global functions or variables:
AllVariants Base Comparisons Counts Coverage Cycle DataFrame Feature
Frequency IRanges Intersect_Sets Length Level Method Outliers Percent
Quality RelDiv Rle Sample SampleMatch Strand Type aggregate alt
altDepth<- asVCF boxplot chunk close.screen combn dev.off first
import.bed last locateVariants low mid minQuality model.matrix
na.omit pdf phyper plot predictCoding qwidth read.delim
readGAlignmentPairs readGAlignments readVcf ref refDepth<- screen
seqlengths seqlengths<- split.screen subsetByOverlaps
summarizeOverlaps symbols test_sample text top tophatargs
totalDepth<- vennset write.table writeVcf
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")
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 21.904 0.336 22.282
run_DESeq2 5.276 0.020 5.303
* 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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.8-bioc/meat/systemPipeR.Rcheck/00check.log’
for details.
systemPipeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL systemPipeR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’ * installing *source* package ‘systemPipeR’ ... ** 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 * DONE (systemPipeR)
systemPipeR.Rcheck/tests/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
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, 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
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
RUNIT TEST PROTOCOL -- Tue Apr 16 03:27:26 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
15.716 0.448 16.219
systemPipeR.Rcheck/systemPipeR-Ex.timings
| name | user | system | elapsed | |
| GOHyperGAll | 0 | 0 | 0 | |
| INTERSECTset-class | 0.016 | 0.000 | 0.014 | |
| SYSargs-class | 0.048 | 0.000 | 0.060 | |
| VENNset-class | 0.012 | 0.000 | 0.010 | |
| alignStats | 0.016 | 0.000 | 0.017 | |
| catDB-class | 0.000 | 0.000 | 0.001 | |
| catmap | 0 | 0 | 0 | |
| clusterRun | 0.016 | 0.000 | 0.016 | |
| countRangeset | 0.076 | 0.000 | 0.074 | |
| featureCoverage | 0.004 | 0.004 | 0.008 | |
| featuretypeCounts | 0.008 | 0.000 | 0.008 | |
| filterDEGs | 1.196 | 0.028 | 1.225 | |
| filterVars | 0.016 | 0.000 | 0.014 | |
| genFeatures | 21.904 | 0.336 | 22.282 | |
| getQsubargs | 0.012 | 0.004 | 0.017 | |
| mergeBamByFactor | 0.012 | 0.000 | 0.028 | |
| moduleload | 0 | 0 | 0 | |
| olBarplot | 0.696 | 0.012 | 0.711 | |
| overLapper | 0.632 | 0.008 | 0.643 | |
| plotfeatureCoverage | 0.016 | 0.000 | 0.014 | |
| plotfeaturetypeCounts | 0.016 | 0.000 | 0.013 | |
| predORF | 0.288 | 0.000 | 0.288 | |
| preprocessReads | 0.032 | 0.000 | 0.119 | |
| qsubRun | 0.016 | 0.000 | 0.017 | |
| readComp | 0.016 | 0.008 | 0.024 | |
| returnRPKM | 0 | 0 | 0 | |
| runCommandline | 0.016 | 0.000 | 0.017 | |
| runDiff | 0.056 | 0.000 | 0.056 | |
| run_DESeq2 | 5.276 | 0.020 | 5.303 | |
| run_edgeR | 1.016 | 0.004 | 1.023 | |
| scaleRanges | 0.212 | 0.000 | 0.215 | |
| seeFastq | 0.000 | 0.000 | 0.001 | |
| symLink2bam | 0.012 | 0.000 | 0.014 | |
| sysargs | 0.016 | 0.000 | 0.017 | |
| systemArgs | 0.016 | 0.000 | 0.017 | |
| variantReport | 0.016 | 0.000 | 0.016 | |
| vennPlot | 0.600 | 0.008 | 0.610 | |
| writeTargetsRef | 0.004 | 0.000 | 0.001 | |
| writeTargetsout | 0.012 | 0.000 | 0.014 | |