BioC 3.2: CHECK report for systemPipeR on oaxaca

Package: systemPipeR

Version: 1.4.8

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings systemPipeR_1.4.8.tar.gz

StartedAt: 2016-04-23 04:52:30 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 04:58:55 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 385.2 seconds

RetCode: 0

Status:  OK

CheckDir: systemPipeR.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings systemPipeR_1.4.8.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/systemPipeR.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘1.4.8’
* 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 ... [33s/34s] OK
* checking installed package size ... NOTE
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc       2.9Mb
    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
countRangeset: warning in read.delim(infile1(args)[i], comment = "#"):
  partial argument match of 'comment' to 'comment.char'
vennPlot : ellipseVenn: warning in close.screen(all = TRUE): partial
  argument match of 'all' to 'all.screens'
writeTargetsRef: warning in read.delim(infile, comment = "#"): partial
  argument match of 'comment' to 'comment.char'
.resizeFeature: no visible global function definition for ‘DataFrame’
.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_Subset: no visible binding for global variable
  ‘test_sample’
clusterRun: no visible global function definition for ‘chunk’
countRangeset: no visible global function definition for ‘import.bed’
countRangeset: no visible global function definition for
  ‘summarizeOverlaps’
featureCoverage: no visible global function definition for
  ‘readGAlignments’
featureCoverage: no visible global function definition for ‘qwidth’
featureCoverage: no visible global function definition for ‘Rle’
featuretypeCounts: no visible global function definition for
  ‘readGAlignments’
featuretypeCounts: no visible global function definition for
  ‘readGAlignmentPairs’
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’
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 binding for global variable ‘Length’
predORF : .predORF: no visible global function definition for ‘IRanges’
scaleRanges : .scaleRanges: no visible global function definition for
  ‘IRanges’
scaleRanges: no visible global function definition for ‘DataFrame’
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’
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’
show,INTERSECTset: no visible binding for global variable ‘vennset’
* 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 ... [42s/53s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
genFeatures 13.091  0.404  23.055
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [16s/16s]
 [16s/16s] 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: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/systemPipeR.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
GOHyperGAll	0.002	0.000	0.002
INTERSECTset-class	0.009	0.003	0.012
SYSargs-class	0.035	0.003	0.039
VENNset-class	0.009	0.003	0.011
alignStats	0.020	0.002	0.021
catDB-class	0.001	0.000	0.002
catmap	0.001	0.001	0.001
clusterRun	0.014	0.001	0.015
countRangeset	0.055	0.008	0.062
featureCoverage	0.013	0.002	0.014
featuretypeCounts	0.018	0.002	0.019
filterDEGs	3.197	0.057	3.255
filterVars	0.012	0.001	0.014
genFeatures	13.091	0.404	23.055
getQsubargs	0.181	0.003	0.184
mergeBamByFactor	0.019	0.001	0.020
moduleload	0.001	0.000	0.001
olBarplot	0.473	0.012	0.488
overLapper	0.563	0.017	0.581
plotfeatureCoverage	0.014	0.001	0.015
plotfeaturetypeCounts	0.014	0.001	0.015
predORF	0.567	0.006	0.612
preprocessReads	0.031	0.002	0.032
qsubRun	0.017	0.001	0.018
readComp	0.024	0.002	0.026
returnRPKM	0.000	0.000	0.001
runCommandline	0.013	0.001	0.015
runDiff	0.050	0.001	0.051
run_DESeq2	3.972	0.023	3.998
run_edgeR	3.800	0.084	3.886
scaleRanges	0.206	0.001	0.208
seeFastq	0.000	0.001	0.000
symLink2bam	0.010	0.001	0.011
sysargs	0.015	0.001	0.019
systemArgs	0.020	0.002	0.022
variantReport	0.020	0.002	0.022
vennPlot	0.519	0.034	1.584
writeTargetsRef	0.001	0.001	0.002
writeTargetsout	0.010	0.001	0.011