BioC 3.3: CHECK report for hiReadsProcessor on oaxaca

Package: hiReadsProcessor

Version: 1.8.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings hiReadsProcessor_1.8.2.tar.gz

StartedAt: 2016-10-13 02:43:44 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 02:48:16 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 271.8 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_1.8.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/hiReadsProcessor.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.8.2’
* 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 ... NOTE
Namespace in Imports field not imported from: ‘readxl’
  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
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 : <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’
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’
Undefined global functions or variables:
  DataFrame IRanges IRangesList Rle ScanBamParam SimpleList
  breakInChunks clusteredValue clusteredValue.freq detectCores matches
  mclapply metadata metadata<- misMatches qBaseInsert queryHits
  runLength runValue scanBamFlag tBaseInsert try_default
* 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
vpairwiseAlignSeqs 14.462  4.515   4.809
* 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: 3 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	0.124	0.009	0.134
addListNameToReads	0.410	0.026	0.436
annotateSites	0.001	0.000	0.001
blatSeqs	0	0	0
chunkize	0.054	0.001	0.055
clusterSites	0.000	0.000	0.001
crossOverCheck	0.178	0.003	0.201
dereplicateReads	0.067	0.001	0.068
doRCtest	0.058	0.023	1.862
extractFeature	0.180	0.042	0.222
extractSeqs	0.744	0.039	0.786
findAndTrimSeq	1.130	0.080	1.212
findBarcodes	0.348	0.001	0.349
findIntegrations	0.001	0.000	0.000
findLTRs	0.001	0.000	0.001
findLinkers	0.001	0.000	0.000
findPrimers	0	0	0
findVector	0	0	0
getIntegrationSites	0.712	0.008	0.722
getSectorsForSamples	0.111	0.005	0.117
getSonicAbund	0.326	0.053	0.400
isuSites	1.517	0.017	1.536
otuSites	1.700	0.012	1.712
pairUpAlignments	0.001	0.000	0.000
pairwiseAlignSeqs	1.074	0.319	4.800
primerIDAlignSeqs	1.364	0.175	3.250
pslCols	0.001	0.001	0.001
pslToRangedObject	0.079	0.009	0.089
read.BAMasPSL	0.000	0.001	0.001
read.SeqFolder	2.657	0.056	3.257
read.blast8	0.001	0.000	0.001
read.psl	0	0	0
read.sampleInfo	2.320	0.007	2.307
read.seqsFromSector	0.001	0.000	0.001
removeReadsWithNs	0.036	0.001	0.037
replicateReads	0.067	0.000	0.068
sampleSummary	0.638	0.014	0.651
splitByBarcode	0.046	0.000	0.046
splitSeqsToFiles	0.000	0.000	0.001
startgfServer	0	0	0
trimSeqs	0.033	0.000	0.033
vpairwiseAlignSeqs	14.462	4.515	4.809
write.listedDNAStringSet	0	0	0
write.psl	0.031	0.009	0.040