systemPipeR 1.8.1
Thomas Girke
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/systemPipeR | | Last Changed Rev: 122897 / Revision: 128728 | | Last Changed Date: 2016-10-20 20:22:17 -0400 (Thu, 20 Oct 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### rm -rf systemPipeR.buildbin-libdir systemPipeR.Rcheck && mkdir systemPipeR.buildbin-libdir systemPipeR.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=systemPipeR.buildbin-libdir systemPipeR_1.8.1.tar.gz >systemPipeR.Rcheck\00install.out 2>&1 && cp systemPipeR.Rcheck\00install.out systemPipeR-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=systemPipeR.buildbin-libdir --install="check:systemPipeR-install.out" --force-multiarch --no-vignettes --timings systemPipeR_1.8.1.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/systemPipeR.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'systemPipeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'systemPipeR' version '1.8.1'
* 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 ... 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 whether package 'systemPipeR' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.5Mb
sub-directories of 1Mb or more:
doc 3.1Mb
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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
genFeatures 12.32 0.96 13.48
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
genFeatures 11.16 0.45 11.61
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
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
'C:/Users/biocbuild/bbs-3.4-bioc/meat/systemPipeR.Rcheck/00check.log'
for details.
install for i386
* 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
install for x64
* installing *source* package 'systemPipeR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'systemPipeR' as systemPipeR_1.8.1.zip
* DONE (systemPipeR)