BioC 3.5: CHECK report for hiReadsProcessor on oaxaca
This page was generated on 2017-03-04 16:48:01 -0500 (Sat, 04 Mar 2017).
hiReadsProcessor 1.11.0 Nirav V Malani
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/hiReadsProcessor | Last Changed Rev: 122712 / Revision: 127142 | Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | |
tokay2 | Windows Server 2012 R2 Standard / x64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... |
toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
Summary
Package: hiReadsProcessor |
Version: 1.11.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings hiReadsProcessor_1.11.0.tar.gz |
StartedAt: 2017-03-04 04:21:46 -0800 (Sat, 04 Mar 2017) |
EndedAt: 2017-03-04 04:26:35 -0800 (Sat, 04 Mar 2017) |
EllapsedTime: 289.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: hiReadsProcessor.Rcheck |
Warnings: 0 |
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings hiReadsProcessor_1.11.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/hiReadsProcessor.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hiReadsProcessor/DESCRIPTION’ ... OK
* this is package ‘hiReadsProcessor’ version ‘1.11.0’
* 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:
.BBSoptions
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 ‘hiReadsProcessor’ can be installed ... OK
* checking installed package size ... OK
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
chunkize: no visible global function definition for ‘breakInChunks’
chunkize: no visible global function definition for ‘detectCores’
clusterSites : <anonymous>: no visible binding for global variable
‘queryHits’
clusterSites: no visible binding for global variable ‘clusteredValue’
clusterSites: no visible binding for global variable
‘clusteredValue.freq’
crossOverCheck: no visible binding for global variable ‘queryHits’
decodeByBarcode: no visible global function definition for ‘metadata<-’
decodeByBarcode: no visible global function definition for ‘metadata’
extractSeqs : <anonymous>: no visible global function definition for
‘metadata’
extractSeqs : <anonymous> : <anonymous> : <anonymous>: no visible
global function definition for ‘IRanges’
extractSeqs : <anonymous> : <anonymous>: no visible global function
definition for ‘IRanges’
findBarcodes: no visible global function definition for ‘metadata<-’
findBarcodes: no visible global function definition for ‘metadata’
findIntegrations: no visible global function definition for
‘fasta.info’
findIntegrations : <anonymous>: no visible global function definition
for ‘IRanges’
findVector : <anonymous>: no visible global function definition for
‘IRanges’
pairUpAlignments : <anonymous>: no visible binding for global variable
‘queryHits’
pairwiseAlignSeqs: no visible global function definition for
‘IRangesList’
pairwiseAlignSeqs: no visible global function definition for ‘IRanges’
primerIDAlignSeqs: no visible global function definition for ‘IRanges’
primerIDAlignSeqs: no visible global function definition for
‘IRangesList’
pslToRangedObject: no visible global function definition for ‘IRanges’
read.BAMasPSL: no visible global function definition for ‘ScanBamParam’
read.BAMasPSL: no visible global function definition for ‘scanBamFlag’
read.BAMasPSL: no visible global function definition for ‘DataFrame’
read.SeqFolder: no visible global function definition for ‘SimpleList’
read.psl: no visible global function definition for ‘mclapply’
read.psl : <anonymous>: no visible binding for global variable
‘matches’
read.psl : <anonymous>: no visible binding for global variable
‘misMatches’
read.psl : <anonymous>: no visible binding for global variable
‘qBaseInsert’
read.psl : <anonymous>: no visible binding for global variable
‘tBaseInsert’
read.psl: no visible binding for global variable ‘matches’
read.psl: no visible binding for global variable ‘misMatches’
read.psl: no visible binding for global variable ‘qBaseInsert’
read.psl: no visible binding for global variable ‘tBaseInsert’
read.sampleInfo: no visible global function definition for ‘SimpleList’
splitSeqsToFiles: no visible global function definition for
‘fasta.info’
vpairwiseAlignSeqs: no visible global function definition for ‘Rle’
vpairwiseAlignSeqs: no visible global function definition for
‘runLength’
vpairwiseAlignSeqs: no visible global function definition for ‘IRanges’
vpairwiseAlignSeqs: no visible global function definition for
‘runValue’
Undefined global functions or variables:
DataFrame IRanges IRangesList Rle ScanBamParam SimpleList
breakInChunks clusteredValue clusteredValue.freq detectCores
fasta.info matches mclapply metadata metadata<- misMatches
qBaseInsert queryHits runLength runValue scanBamFlag tBaseInsert
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
pairwiseAlignSeqs 2.042 0.459 7.835
vpairwiseAlignSeqs 1.432 0.393 7.188
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/hiReadsProcessor.Rcheck/00check.log’
for details.
hiReadsProcessor.Rcheck/00install.out:
* installing *source* package ‘hiReadsProcessor’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (hiReadsProcessor)
hiReadsProcessor.Rcheck/hiReadsProcessor-Ex.timings:
name | user | system | elapsed
|
addFeature | 0.268 | 0.011 | 0.280 |
|
addListNameToReads | 1.062 | 0.014 | 1.076 |
|
annotateSites | 0 | 0 | 0 |
|
blatSeqs | 0 | 0 | 0 |
|
chunkize | 0.074 | 0.001 | 0.074 |
|
clusterSites | 0.969 | 0.006 | 0.998 |
|
crossOverCheck | 0.134 | 0.000 | 0.135 |
|
dereplicateReads | 0.067 | 0.001 | 0.068 |
|
doRCtest | 0.109 | 0.044 | 2.688 |
|
extractFeature | 0.277 | 0.078 | 0.356 |
|
extractSeqs | 0.479 | 0.031 | 0.511 |
|
findAndTrimSeq | 1.679 | 0.098 | 1.777 |
|
findBarcodes | 0.465 | 0.001 | 0.466 |
|
findIntegrations | 0.000 | 0.000 | 0.001 |
|
findLTRs | 0.000 | 0.000 | 0.001 |
|
findLinkers | 0.000 | 0.000 | 0.001 |
|
findPrimers | 0.001 | 0.000 | 0.001 |
|
findVector | 0.001 | 0.000 | 0.001 |
|
getIntegrationSites | 1.099 | 0.008 | 1.108 |
|
getSectorsForSamples | 0.122 | 0.005 | 0.126 |
|
getSonicAbund | 0.361 | 0.066 | 0.445 |
|
isuSites | 2.551 | 0.044 | 2.594 |
|
otuSites | 2.626 | 0.013 | 2.641 |
|
pairUpAlignments | 0.001 | 0.000 | 0.001 |
|
pairwiseAlignSeqs | 2.042 | 0.459 | 7.835 |
|
primerIDAlignSeqs | 1.885 | 0.233 | 4.680 |
|
pslCols | 0.001 | 0.000 | 0.001 |
|
pslToRangedObject | 0.139 | 0.004 | 0.143 |
|
read.BAMasPSL | 0 | 0 | 0 |
|
read.SeqFolder | 0.101 | 0.002 | 0.125 |
|
read.blast8 | 0.000 | 0.001 | 0.000 |
|
read.psl | 0 | 0 | 0 |
|
read.sampleInfo | 0.352 | 0.004 | 0.356 |
|
read.seqsFromSector | 0.001 | 0.000 | 0.000 |
|
removeReadsWithNs | 0.021 | 0.000 | 0.022 |
|
replicateReads | 0.071 | 0.001 | 0.073 |
|
sampleSummary | 0.533 | 0.014 | 0.547 |
|
splitByBarcode | 0.081 | 0.001 | 0.081 |
|
splitSeqsToFiles | 0.229 | 0.007 | 0.235 |
|
startgfServer | 0.001 | 0.000 | 0.001 |
|
trimSeqs | 0.029 | 0.001 | 0.030 |
|
vpairwiseAlignSeqs | 1.432 | 0.393 | 7.188 |
|
write.listedDNAStringSet | 0.000 | 0.000 | 0.001 |
|
write.psl | 0.029 | 0.006 | 0.036 |
|