BioC 3.5: CHECK report for hiReadsProcessor on toluca2
This page was generated on 2017-04-23 14:38:53 -0400 (Sun, 23 Apr 2017).
hiReadsProcessor 1.11.0
Nirav V Malani
| Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/hiReadsProcessor | | Last Changed Rev: 128796 / Revision: 129046 | | Last Changed Date: 2017-04-17 15:33:48 -0400 (Mon, 17 Apr 2017) |
| 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 | |
| veracruz2 | OS X 10.11.6 El Capitan / 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: 2017-04-23 05:17:16 -0400 (Sun, 23 Apr 2017) |
| EndedAt: 2017-04-23 05:22:37 -0400 (Sun, 23 Apr 2017) |
| EllapsedTime: 321.0 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 r72187)
* 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 2.050 0.479 8.554
primerIDAlignSeqs 2.096 0.247 5.272
vpairwiseAlignSeqs 1.382 0.377 7.135
* 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 | 0.266 | 0.008 | 0.277 |
|
| addListNameToReads | 1.103 | 0.011 | 1.132 |
|
| annotateSites | 0 | 0 | 0 |
|
| blatSeqs | 0 | 0 | 0 |
|
| chunkize | 0.059 | 0.000 | 0.059 |
|
| clusterSites | 0.985 | 0.006 | 0.999 |
|
| crossOverCheck | 0.109 | 0.000 | 0.110 |
|
| dereplicateReads | 0.076 | 0.000 | 0.077 |
|
| doRCtest | 0.101 | 0.039 | 2.708 |
|
| extractFeature | 0.235 | 0.083 | 0.321 |
|
| extractSeqs | 0.990 | 0.099 | 1.093 |
|
| findAndTrimSeq | 1.167 | 0.039 | 1.230 |
|
| findBarcodes | 0.479 | 0.001 | 0.499 |
|
| findIntegrations | 0.000 | 0.000 | 0.001 |
|
| findLTRs | 0.000 | 0.000 | 0.001 |
|
| findLinkers | 0.001 | 0.000 | 0.001 |
|
| findPrimers | 0.000 | 0.000 | 0.001 |
|
| findVector | 0.000 | 0.001 | 0.000 |
|
| getIntegrationSites | 1.068 | 0.006 | 1.076 |
|
| getSectorsForSamples | 0.113 | 0.003 | 0.117 |
|
| getSonicAbund | 0.356 | 0.054 | 0.411 |
|
| isuSites | 2.983 | 0.043 | 3.039 |
|
| otuSites | 3.098 | 0.014 | 3.202 |
|
| pairUpAlignments | 0.000 | 0.000 | 0.001 |
|
| pairwiseAlignSeqs | 2.050 | 0.479 | 8.554 |
|
| primerIDAlignSeqs | 2.096 | 0.247 | 5.272 |
|
| pslCols | 0.001 | 0.000 | 0.001 |
|
| pslToRangedObject | 0.144 | 0.005 | 0.156 |
|
| read.BAMasPSL | 0.001 | 0.000 | 0.000 |
|
| read.SeqFolder | 0.167 | 0.003 | 0.192 |
|
| read.blast8 | 0 | 0 | 0 |
|
| read.psl | 0.000 | 0.001 | 0.001 |
|
| read.sampleInfo | 0.473 | 0.011 | 0.542 |
|
| read.seqsFromSector | 0 | 0 | 0 |
|
| removeReadsWithNs | 0.020 | 0.000 | 0.021 |
|
| replicateReads | 0.064 | 0.000 | 0.066 |
|
| sampleSummary | 0.701 | 0.012 | 0.780 |
|
| splitByBarcode | 0.077 | 0.001 | 0.079 |
|
| splitSeqsToFiles | 0.209 | 0.004 | 0.233 |
|
| startgfServer | 0 | 0 | 0 |
|
| trimSeqs | 0.030 | 0.000 | 0.033 |
|
| vpairwiseAlignSeqs | 1.382 | 0.377 | 7.135 |
|
| write.listedDNAStringSet | 0.001 | 0.001 | 0.000 |
|
| write.psl | 0.026 | 0.005 | 0.031 |
|