BioC 3.3: CHECK report for hiReadsProcessor on morelia

Package: hiReadsProcessor

Version: 1.7.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings hiReadsProcessor_1.7.1.tar.gz

StartedAt: 2016-04-21 03:53:54 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 03:59:13 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 318.8 seconds

RetCode: 0

Status:  OK

CheckDir: hiReadsProcessor.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 hiReadsProcessor_1.7.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/hiReadsProcessor.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘1.7.1’
* 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:
  .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 ... [27s/29s] 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
blatSeqs: no visible global function definition for ‘runif’
chunkize: no visible global function definition for ‘breakInChunks’
chunkize: no visible global function definition for ‘detectCores’
clusterSites: no visible binding for global variable ‘n’
clusterSites: no visible global function definition for ‘desc’
clusterSites : <anonymous>: no visible binding for global variable
  ‘queryHits’
clusterSites: no visible global function definition for ‘contains’
clusterSites: no visible binding for global variable ‘clusteredValue’
clusterSites: no visible binding for global variable
  ‘clusteredValue.freq’
crossOverCheck: no visible binding for global variable ‘n’
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 : <anonymous>: no visible global function definition
  for ‘IRanges’
findVector : <anonymous>: no visible global function definition for
  ‘IRanges’
getIntegrationSites: no visible global function definition for ‘ave’
getSonicAbund: no visible binding for global variable ‘n’
pairUpAlignments : <anonymous>: no visible global function definition
  for ‘aggregate’
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’
pslToRangedObject: no visible global function definition for ‘na.omit’
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.blast8 : <anonymous>: no visible global function definition for
  ‘count.fields’
read.blast8 : <anonymous>: no visible global function definition for
  ‘read.delim’
read.psl: no visible global function definition for ‘mclapply’
read.psl : <anonymous>: no visible global function definition for
  ‘count.fields’
read.psl : <anonymous>: no visible global function definition for
  ‘read.delim’
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 : <anonymous>: no visible global function definition for
  ‘filter’
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.psl: no visible global function definition for ‘filter’
read.sampleInfo: no visible global function definition for ‘read.delim’
read.sampleInfo: no visible global function definition for ‘SimpleList’
splitSeqsToFiles: no visible global function definition for ‘runif’
troubleshootLinkers : <anonymous>: no visible global function
  definition for ‘try_default’
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’
write.listedDNAStringSet : <anonymous>: no visible global function
  definition for ‘na.omit’
write.psl: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  DataFrame IRanges IRangesList Rle ScanBamParam SimpleList aggregate
  ave breakInChunks clusteredValue clusteredValue.freq contains
  count.fields desc detectCores filter matches mclapply metadata
  metadata<- misMatches n na.omit qBaseInsert queryHits read.delim
  runLength runValue runif scanBamFlag tBaseInsert try_default
  write.table
Consider adding
  importFrom("stats", "aggregate", "ave", "filter", "na.omit", "runif")
  importFrom("utils", "count.fields", "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 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 ... [58s/48s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
pairwiseAlignSeqs  1.239  0.360   5.873
vpairwiseAlignSeqs 0.910  0.297   5.654
* 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-3.3-bioc/meat/hiReadsProcessor.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
addFeature	0.147	0.019	0.180
addListNameToReads	0.492	0.028	0.515
annotateSites	0	0	0
blatSeqs	0.000	0.000	0.001
chunkize	0.063	0.002	0.065
clusterSites	0.000	0.000	0.001
crossOverCheck	0.210	0.006	0.238
dereplicateReads	0.067	0.001	0.069
doRCtest	0.071	0.024	2.204
extractFeature	0.210	0.071	0.281
extractSeqs	0.913	0.053	0.970
findAndTrimSeq	1.312	0.086	1.402
findBarcodes	0.381	0.001	0.383
findIntegrations	0.001	0.000	0.001
findLTRs	0.001	0.000	0.000
findLinkers	0.001	0.000	0.000
findPrimers	0.001	0.000	0.001
findVector	0.001	0.000	0.001
getIntegrationSites	0.832	0.018	0.862
getSectorsForSamples	0.140	0.014	0.154
getSonicAbund	0.387	0.091	0.510
isuSites	1.962	0.036	2.016
otuSites	1.997	0.017	2.063
pairUpAlignments	0	0	0
pairwiseAlignSeqs	1.239	0.360	5.873
primerIDAlignSeqs	1.649	0.224	4.013
pslCols	0.001	0.000	0.001
pslToRangedObject	0.087	0.007	0.093
read.BAMasPSL	0.001	0.000	0.001
read.SeqFolder	2.969	0.047	3.269
read.blast8	0.001	0.000	0.000
read.psl	0.001	0.000	0.001
read.sampleInfo	2.933	0.034	2.968
read.seqsFromSector	0.000	0.000	0.001
removeReadsWithNs	0.039	0.001	0.039
replicateReads	0.076	0.001	0.077
sampleSummary	0.876	0.012	0.893
splitByBarcode	0.058	0.000	0.059
splitSeqsToFiles	0.000	0.000	0.001
startgfServer	0	0	0
trimSeqs	0.048	0.001	0.049
vpairwiseAlignSeqs	0.910	0.297	5.654
write.listedDNAStringSet	0	0	0
write.psl	0.038	0.007	0.045