systemPipeR 1.4.4
Thomas Girke
| Snapshot Date: 2015-11-09 16:24:09 -0800 (Mon, 09 Nov 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/systemPipeR | | Last Changed Rev: 110016 / Revision: 110496 | | Last Changed Date: 2015-10-27 17:48:57 -0700 (Tue, 27 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ OK ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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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_1.4.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/systemPipeR.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.4.4’
* 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 ... [35s/36s] OK
* checking installed package size ... NOTE
installed size is 5.4Mb
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’
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’
GOHyperGAll_Subset: no visible binding for global variable
‘test_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 ‘extendmax’
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 ... [49s/61s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
genFeatures 15.013 0.806 28.154
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [18s/18s]
[18s/18s] 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.