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BioC 3.4: CHECK report for systemPipeR on morelia

This page was generated on 2016-09-21 03:53:39 -0700 (Wed, 21 Sep 2016).

Package 1189/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
systemPipeR 1.7.3
Thomas Girke
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/systemPipeR
Last Changed Rev: 120039 / Revision: 121152
Last Changed Date: 2016-08-10 17:47:29 -0700 (Wed, 10 Aug 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: systemPipeR
Version: 1.7.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings systemPipeR_1.7.3.tar.gz
StartedAt: 2016-09-20 13:44:54 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 13:49:02 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 248.2 seconds
RetCode: 0
Status:  OK 
CheckDir: systemPipeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings systemPipeR_1.7.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/systemPipeR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.7.3’
* 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 ... NOTE
Found the following non-portable file paths:
  systemPipeR/vignettes/systemPipeR_cache/html/align_stats_parallel_cluster_0f051c2b1f70364c102c25e53a23f12e.RData
  systemPipeR/vignettes/systemPipeR_cache/html/align_stats_parallel_cluster_0f051c2b1f70364c102c25e53a23f12e.rdb
  systemPipeR/vignettes/systemPipeR_cache/html/align_stats_parallel_cluster_0f051c2b1f70364c102c25e53a23f12e.rdx
  systemPipeR/vignettes/systemPipeR_cache/html/align_stats_parallel_e41a74f26d017f5fc177af2655e45d55.RData
  systemPipeR/vignettes/systemPipeR_cache/html/align_stats_parallel_e41a74f26d017f5fc177af2655e45d55.rdb
  systemPipeR/vignettes/systemPipeR_cache/html/align_stats_parallel_e41a74f26d017f5fc177af2655e45d55.rdx
  systemPipeR/vignettes/systemPipeR_cache/html/construct_sysargs_a8854172136869af90c5343d9951536e.RData
  systemPipeR/vignettes/systemPipeR_cache/html/custom_preprocessing_e41edaa3ba2719fdfc02ff89b468a9e1.RData
  systemPipeR/vignettes/systemPipeR_cache/html/custom_preprocessing_e41edaa3ba2719fdfc02ff89b468a9e1.rdb
  systemPipeR/vignettes/systemPipeR_cache/html/custom_preprocessing_e41edaa3ba2719fdfc02ff89b468a9e1.rdx
  systemPipeR/vignettes/systemPipeR_cache/html/deseq2_deg_counts_89654aad3b028aaa60cf3b27b7166c34.RData
  systemPipeR/vignettes/systemPipeR_cache/html/fastq_quality_parallel_cluster_981fb1c217635fd948ed528cf5d9f37c.RData
  systemPipeR/vignettes/systemPipeR_cache/html/fastq_quality_parallel_cluster_981fb1c217635fd948ed528cf5d9f37c.rdb
  systemPipeR/vignettes/systemPipeR_cache/html/fastq_quality_parallel_cluster_981fb1c217635fd948ed528cf5d9f37c.rdx
  systemPipeR/vignettes/systemPipeR_cache/html/fastq_quality_parallel_single_87e6e7dcfdfbf7bc314100638c26c52d.RData
  systemPipeR/vignettes/systemPipeR_cache/html/fastq_quality_parallel_single_87e6e7dcfdfbf7bc314100638c26c52d.rdb
  systemPipeR/vignettes/systemPipeR_cache/html/fastq_quality_parallel_single_87e6e7dcfdfbf7bc314100638c26c52d.rdx
  systemPipeR/vignettes/systemPipeR_cache/html/genChip_workflow_single_6eee2576b65a48f51e1dd54432ac8ea0.RData
  systemPipeR/vignettes/systemPipeR_cache/html/genChip_workflow_single_6eee2576b65a48f51e1dd54432ac8ea0.rdb
  systemPipeR/vignettes/systemPipeR_cache/html/genChip_workflow_single_6eee2576b65a48f51e1dd54432ac8ea0.rdx
  systemPipeR/vignettes/systemPipeR_cache/html/genRibo_workflow_single_a7ee40491d0f82a7209ce7f20aa1bce9.RData
  systemPipeR/vignettes/systemPipeR_cache/html/genRibo_workflow_single_a7ee40491d0f82a7209ce7f20aa1bce9.rdb
  systemPipeR/vignettes/systemPipeR_cache/html/genRibo_workflow_single_a7ee40491d0f82a7209ce7f20aa1bce9.rdx
  systemPipeR/vignettes/systemPipeR_cache/html/genRna_workflow_single_865fbdca4c56e8ae4f6295e250ab220b.RData
  systemPipeR/vignettes/systemPipeR_cache/html/genRna_workflow_single_865fbdca4c56e8ae4f6295e250ab220b.rdb
  systemPipeR/vignettes/systemPipeR_cache/html/genRna_workflow_single_865fbdca4c56e8ae4f6295e250ab220b.rdx
  systemPipeR/vignettes/systemPipeR_cache/html/genVar_workflow_single_85369033487573758c368e1b18c2e939.RData
  systemPipeR/vignettes/systemPipeR_cache/html/genVar_workflow_single_85369033487573758c368e1b18c2e939.rdb
  systemPipeR/vignettes/systemPipeR_cache/html/genVar_workflow_single_85369033487573758c368e1b18c2e939.rdx
  systemPipeR/vignettes/systemPipeR_cache/html/hierarchical_clustering_26f264bb871fd0c2f342b0c079aee49e.RData
  systemPipeR/vignettes/systemPipeR_cache/html/hierarchical_clustering_26f264bb871fd0c2f342b0c079aee49e.rdb
  systemPipeR/vignettes/systemPipeR_cache/html/hierarchical_clustering_26f264bb871fd0c2f342b0c079aee49e.rdx
  systemPipeR/vignettes/systemPipeR_cache/html/plot_go_enrichment_a4a220bf9eb7f1125e3a802cedd67c24.RData
  systemPipeR/vignettes/systemPipeR_cache/html/process_monitoring_0e49b11e73810c66c83bdcd6bcd3e394.RData
  systemPipeR/vignettes/systemPipeR_cache/html/read_counting_mirna_4195067fd0942be85d1decde3da75c3e.RData
  systemPipeR/vignettes/systemPipeR_cache/html/read_counting_mirna_4195067fd0942be85d1decde3da75c3e.rdb
  systemPipeR/vignettes/systemPipeR_cache/html/read_counting_mirna_4195067fd0942be85d1decde3da75c3e.rdx
  systemPipeR/vignettes/systemPipeR_cache/html/read_counting_multicore_8f4bae011588aec1419eb6f86f683f9b.RData
  systemPipeR/vignettes/systemPipeR_cache/html/read_counting_multicore_8f4bae011588aec1419eb6f86f683f9b.rdb
  systemPipeR/vignettes/systemPipeR_cache/html/read_counting_multicore_8f4bae011588aec1419eb6f86f683f9b.rdx
  systemPipeR/vignettes/systemPipeR_cache/html/read_counting_multinode_83ec3b9d8967b28eed8957801d322dda.RData
  systemPipeR/vignettes/systemPipeR_cache/html/read_counting_multinode_83ec3b9d8967b28eed8957801d322dda.rdb
  systemPipeR/vignettes/systemPipeR_cache/html/read_counting_multinode_83ec3b9d8967b28eed8957801d322dda.rdx
  systemPipeR/vignettes/systemPipeR_cache/html/run_bowtie_parallel_5bfc0855d4e02f149c5d7aedcfa6ac7b.RData
  systemPipeR/vignettes/systemPipeR_cache/html/run_bowtie_parallel_5bfc0855d4e02f149c5d7aedcfa6ac7b.rdb
  systemPipeR/vignettes/systemPipeR_cache/html/run_bowtie_parallel_5bfc0855d4e02f149c5d7aedcfa6ac7b.rdx
  systemPipeR/vignettes/systemPipeR_cache/html/run_bowtie_single_c498a76143c61cef609d9c01a7de3243.RData

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* 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:
    doc       3.0Mb
    extdata   1.7Mb
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
genFeatures 8.998  0.278  20.313
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘GenomicAlignments’
* 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: 6 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/systemPipeR.Rcheck/00check.log’
for details.


systemPipeR.Rcheck/00install.out:

* installing *source* package ‘systemPipeR’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (systemPipeR)

systemPipeR.Rcheck/systemPipeR-Ex.timings:

nameusersystemelapsed
GOHyperGAll0.0010.0000.001
INTERSECTset-class0.0080.0030.011
SYSargs-class0.0320.0030.034
VENNset-class0.0060.0020.008
alignStats0.0130.0010.015
catDB-class0.0010.0010.001
catmap0.0010.0000.001
clusterRun0.0140.0020.016
countRangeset0.0470.0020.048
featureCoverage0.0110.0010.011
featuretypeCounts0.0100.0010.010
filterDEGs2.0060.0362.043
filterVars0.0160.0020.018
genFeatures 8.998 0.27820.313
getQsubargs0.0160.0020.018
mergeBamByFactor0.0110.0010.012
moduleload0.0010.0000.000
olBarplot0.5150.0130.529
overLapper0.5770.0140.594
plotfeatureCoverage0.0160.0010.016
plotfeaturetypeCounts0.0160.0010.017
predORF0.2120.0020.237
preprocessReads0.0210.0010.022
qsubRun0.0130.0010.014
readComp0.0160.0010.017
returnRPKM0.0000.0000.001
runCommandline0.0130.0010.014
runDiff0.0370.0010.038
run_DESeq22.7740.0322.807
run_edgeR2.3380.0442.384
scaleRanges0.1600.0010.161
seeFastq0.0010.0000.001
symLink2bam0.0130.0010.014
sysargs0.0190.0020.021
systemArgs0.0170.0010.019
variantReport0.0120.0010.012
vennPlot0.4730.0110.573
writeTargetsRef0.0010.0000.002
writeTargetsout0.0140.0010.015