Thomas Girke
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/systemPipeR |
| Branch: master |
| Last Commit: dd281c5 |
| Last Changed Date: 2019-02-16 18:20:06 -0400 (Sat, 16 Feb 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 11:39:50 -0400 (Tue, 09 Apr 2019).
| Package 1591/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| systemPipeR 1.17.6 Thomas Girke
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: systemPipeR |
| Version: 1.17.6 |
| Command: /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_1.17.6.tar.gz |
| StartedAt: 2019-04-09 03:59:16 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 04:05:18 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 362.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: systemPipeR.Rcheck |
| Warnings: 0 |
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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_1.17.6.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/systemPipeR.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 ‘systemPipeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘systemPipeR’ version ‘1.17.6’
* 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 ... NOTE
installed size is 5.4Mb
sub-directories of 1Mb or more:
extdata 4.1Mb
* 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’
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’
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 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<- 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 24.177 0.375 24.941
run_DESeq2 10.947 0.008 10.968
* 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: 4 NOTEs
See
‘/home/biocbuild/bbs-3.9-bioc/meat/systemPipeR.Rcheck/00check.log’
for details.
systemPipeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL systemPipeR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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)
systemPipeR.Rcheck/tests/runTests.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.
> 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, 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, rowsum
RUNIT TEST PROTOCOL -- Tue Apr 9 04:05:14 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
11.858 0.424 12.282
systemPipeR.Rcheck/systemPipeR-Ex.timings
| name | user | system | elapsed | |
| GOHyperGAll | 0 | 0 | 0 | |
| INTERSECTset-class | 0.009 | 0.004 | 0.014 | |
| SYSargs-class | 0.040 | 0.004 | 0.209 | |
| VENNset-class | 0.009 | 0.000 | 0.009 | |
| alignStats | 0.016 | 0.000 | 0.019 | |
| catDB-class | 0.000 | 0.000 | 0.001 | |
| catmap | 0.000 | 0.001 | 0.000 | |
| clusterRun | 0.012 | 0.005 | 0.016 | |
| countRangeset | 0.103 | 0.004 | 0.131 | |
| featureCoverage | 0.013 | 0.000 | 0.013 | |
| featuretypeCounts | 0.012 | 0.000 | 0.013 | |
| filterDEGs | 1.207 | 0.000 | 1.328 | |
| filterVars | 0.011 | 0.000 | 0.011 | |
| genFeatures | 24.177 | 0.375 | 24.941 | |
| getQsubargs | 0.008 | 0.002 | 0.010 | |
| mergeBamByFactor | 0.007 | 0.001 | 0.020 | |
| module | 0 | 0 | 0 | |
| moduleload | 0.001 | 0.000 | 0.000 | |
| olBarplot | 0.652 | 0.000 | 0.652 | |
| overLapper | 0.614 | 0.016 | 0.630 | |
| plotfeatureCoverage | 0.014 | 0.000 | 0.013 | |
| plotfeaturetypeCounts | 0.014 | 0.000 | 0.014 | |
| predORF | 0.278 | 0.000 | 0.279 | |
| preprocessReads | 0.029 | 0.000 | 0.044 | |
| qsubRun | 0.015 | 0.000 | 0.016 | |
| readComp | 0.018 | 0.004 | 0.022 | |
| returnRPKM | 0 | 0 | 0 | |
| runCommandline | 0.016 | 0.000 | 0.025 | |
| runDiff | 0.049 | 0.004 | 0.054 | |
| run_DESeq2 | 10.947 | 0.008 | 10.968 | |
| run_edgeR | 1.001 | 0.000 | 1.001 | |
| scaleRanges | 0.166 | 0.000 | 0.165 | |
| seeFastq | 0 | 0 | 0 | |
| symLink2bam | 0.009 | 0.002 | 0.012 | |
| sysargs | 0.016 | 0.000 | 0.016 | |
| systemArgs | 0.016 | 0.000 | 0.016 | |
| variantReport | 0.013 | 0.000 | 0.013 | |
| vennPlot | 0.43 | 0.00 | 0.43 | |
| writeTargetsRef | 0 | 0 | 0 | |
| writeTargetsout | 0.008 | 0.000 | 0.008 | |