Package: hiReadsProcessor

Version: 1.20.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:hiReadsProcessor.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings hiReadsProcessor_1.20.1.tar.gz

StartedAt: 2019-10-16 03:39:29 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 03:46:03 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 393.5 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 --install=check:hiReadsProcessor.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings hiReadsProcessor_1.20.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/hiReadsProcessor.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hiReadsProcessor/DESCRIPTION’ ... OK
* this is package ‘hiReadsProcessor’ version ‘1.20.1’
* 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 ... 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 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 : : 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 : : no visible global function definition for
  ‘metadata’
extractSeqs :  :  : : no visible
  global function definition for ‘IRanges’
extractSeqs :  : : 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 : : no visible global function definition
  for ‘IRanges’
findVector : : no visible global function definition for
  ‘IRanges’
pairUpAlignments : : 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 : : 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
pairwiseAlignSeqs  4.380  1.654   5.661
vpairwiseAlignSeqs 4.237  1.696   5.570
primerIDAlignSeqs  4.245  0.849   4.922
* 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-3.9-bioc/meat/hiReadsProcessor.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL hiReadsProcessor
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘hiReadsProcessor’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (hiReadsProcessor)

name	user	system	elapsed
addFeature	0.418	0.023	0.441
addListNameToReads	0.469	0.027	0.495
annotateSites	0.000	0.000	0.001
blatSeqs	0.000	0.001	0.000
chunkize	0.037	0.002	0.039
clusterSites	0.306	0.019	0.325
crossOverCheck	0.249	0.029	0.277
dereplicateReads	0.058	0.009	0.067
doRCtest	2.635	0.198	2.777
extractFeature	0.172	0.058	0.229
extractSeqs	0.939	0.159	1.098
findAndTrimSeq	1.427	0.499	1.926
findBarcodes	0.871	0.003	0.873
findIntegrations	0	0	0
findLTRs	0.001	0.000	0.000
findLinkers	0.000	0.001	0.000
findPrimers	0.001	0.000	0.001
findVector	0.000	0.000	0.001
getIntegrationSites	1.877	0.023	1.901
getSectorsForSamples	0.088	0.009	0.097
getSonicAbund	0.347	0.178	0.527
isuSites	3.604	0.057	3.662
otuSites	4.310	0.014	4.323
pairUpAlignments	0	0	0
pairwiseAlignSeqs	4.380	1.654	5.661
primerIDAlignSeqs	4.245	0.849	4.922
pslCols	0.001	0.001	0.001
pslToRangedObject	0.288	0.012	0.300
read.BAMasPSL	0	0	0
read.SeqFolder	2.019	0.195	2.221
read.blast8	0.000	0.000	0.001
read.psl	0.001	0.000	0.001
read.sampleInfo	1.741	0.013	1.759
read.seqsFromSector	0	0	0
removeReadsWithNs	0.027	0.001	0.028
replicateReads	0.054	0.002	0.055
sampleSummary	0.836	0.036	0.872
splitByBarcode	0.048	0.001	0.049
splitSeqsToFiles	0.208	0.011	0.219
startgfServer	0	0	0
trimSeqs	0.034	0.001	0.035
vpairwiseAlignSeqs	4.237	1.696	5.570
write.listedDNAStringSet	0.001	0.000	0.001
write.psl	0.040	0.015	0.056