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CHECK report for dada2 on malbec1

This page was generated on 2019-04-16 11:51:53 -0400 (Tue, 16 Apr 2019).

Package 365/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dada2 1.10.1
Benjamin Callahan
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/dada2
Branch: RELEASE_3_8
Last Commit: 322b76d
Last Changed Date: 2019-01-04 13:28:01 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ ERROR ]
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  ERROR  OK 

Summary

Package: dada2
Version: 1.10.1
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:dada2.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings dada2_1.10.1.tar.gz
StartedAt: 2019-04-15 23:17:32 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:21:54 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 261.5 seconds
RetCode: 1
Status:  ERROR 
CheckDir: dada2.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:dada2.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings dada2_1.10.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/dada2.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dada2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dada2’ version ‘1.10.1’
* 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:
  .travis.yml
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 ‘dada2’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.9Mb
  sub-directories of 1Mb or more:
    extdata   1.1Mb
    libs      6.0Mb
* 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 ... WARNING
'::' or ':::' import not declared from: ‘BiocManager’
'loadNamespace' or 'requireNamespace' call not declared from: ‘BiocManager’
Unexported object imported by a ':::' call: ‘ShortRead:::.set_omp_threads’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Call(ShortRead:::.set_omp_threads, ...)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
bcinstall: no visible global function definition for ‘install.packages’
mergePairsByID: no visible global function definition for ‘:=’
mergePairsByID: no visible binding for global variable ‘seqF’
mergePairsByID: no visible binding for global variable ‘seqR’
mergePairsByID: no visible binding for global variable ‘abundance’
mergePairsByID: no visible binding for global variable ‘accept’
mergePairsByID: no visible binding for global variable ‘als1’
mergePairsByID: no visible binding for global variable ‘als2’
mergePairsByID: no visible binding for global variable ‘prefer’
mergePairsByID: no visible binding for global variable ‘n0R’
mergePairsByID: no visible binding for global variable ‘n0F’
mergePairsByID: no visible binding for global variable ‘allMismatch’
mergePairsByID: no visible binding for global variable ‘mismatch’
mergePairsByID: no visible binding for global variable ‘indel’
plotErrors: no visible binding for global variable ‘Qual’
plotErrors: no visible binding for global variable ‘Observed’
plotErrors: no visible binding for global variable ‘Input’
plotErrors: no visible binding for global variable ‘Estimated’
plotErrors: no visible binding for global variable ‘Nominal’
plotQualityProfile: no visible binding for global variable ‘Cycle’
plotQualityProfile: no visible binding for global variable ‘Score’
plotQualityProfile: no visible binding for global variable ‘Count’
plotQualityProfile: no visible binding for global variable ‘Mean’
plotQualityProfile: no visible binding for global variable ‘Q25’
plotQualityProfile: no visible binding for global variable ‘Q50’
plotQualityProfile: no visible binding for global variable ‘Q75’
plotQualityProfile: no visible binding for global variable ‘Cum’
samdf_to_qiime2: no visible global function definition for
  ‘write.table’
seqtab_to_mothur: no visible global function definition for
  ‘write.table’
seqtab_to_mothur: no visible binding for global variable ‘four’
seqtab_to_qiime: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  := Count Cum Cycle Estimated Input Mean Nominal Observed Q25 Q50 Q75
  Qual Score abundance accept allMismatch als1 als2 four indel
  install.packages mismatch n0F n0R prefer seqF seqR write.table
Consider adding
  importFrom("utils", "install.packages", "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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘dada2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mergePairsByID
> ### Title: Merge forward and reverse reads after DADA denoising, even if
> ###   reads were not originally ordered together.
> ### Aliases: mergePairsByID
> 
> ### ** Examples
> 
> # For the following example files, there are two ways to merge denoised directions.
> # Because the read sequences are in order, `mergePairs()` works.
> # `mergePairsByID` always works,
> # because it uses the read IDs to match denoised pairs.
> exFileF = system.file("extdata", "sam1F.fastq.gz", package="dada2")
> exFileR = system.file("extdata", "sam1R.fastq.gz", package="dada2")
> srF = ShortRead::readFastq(exFileF)
> srR = ShortRead::readFastq(exFileR)
> derepF = derepFastq(exFileF)
> derepR = derepFastq(exFileR)
> dadaF <- dada(derepF, err=tperr1, errorEstimationFunction=loessErrfun, selfConsist=TRUE)
selfConsist step 1 .
   selfConsist step 2
   selfConsist step 3
   selfConsist step 4
Convergence after  4  rounds.
> dadaR <- dada(derepR, err=tperr1, errorEstimationFunction=loessErrfun, selfConsist=TRUE)
selfConsist step 1 .
   selfConsist step 2
   selfConsist step 3
   selfConsist step 4
Convergence after  4  rounds.
> # Run and compare
> ex1time = system.time({
+ ex1 <- mergePairs(dadaF, derepF, dadaR, derepR, verbose = TRUE)
+     ex1 <- data.table::data.table(ex1)
+  })
1213 paired-reads (in 5 unique pairings) successfully merged out of 1315 (in 13 pairings) input.
> ex1time
   user  system elapsed 
  0.044   0.000   0.046 
> # The new function, based on read IDs.
> ex2time = system.time({
+   ex2 = dada2:::mergePairsByID(dadaF = dadaF, derepF = derepF, srF = srF,
+                        dadaR = dadaR, derepR = derepR, srR = srR, verbose = TRUE)
+ })
1434 unique forward read IDs.
1343 unique reverse read IDs.
1315 paired reads, corresponding to 13 unique pairs that must be assessed for overlap merge
1213 paired-reads (in 5 unique pairings) successfully merged
from 1315 read pairs.
> ex2time
   user  system elapsed 
  6.256   0.020   1.846 
> # Compare results (should be identical)
> ex2[(accept)]
                                                                                                                                                                                                                                                         seqF
1: TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGTATCAAAC
2: TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGACTATTAAGTCAGCTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGTCGTCTTGAGTGCAGTAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGACTGTAACTGACGCTGATGCTCGAAAGTGTGGGTATCAAAC
3: TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGCAACTGACACTGATGCTCGAAAGTGTGGGTATCAAAC
4: TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTTACTGACACTGATGCTCGAAAGTGTGGGTATCAAAC
5: TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGATGTAAGTCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGAAACTATGTTGCTAGAGTGCAGGAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAAC
                                                                                                                                                                                                                                                         seqR
1: GGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGTATCAAACAGG
2: GGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGACTATTAAGTCAGCTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGTCGTCTTGAGTGCAGTAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGACTGTAACTGACGCTGATGCTCGAAAGTGTGGGTATCAAACAGG
3: GGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGCAACTGACACTGATGCTCGAAAGTGTGGGTATCAAACAGG
4: GGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTTACTGACACTGATGCTCGAAAGTGTGGGTATCAAACAGG
5: GTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGATGTAAGTCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGAAACTATGTTGCTAGAGTGCAGGAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG
   n0F n0R abundance
1: 164  27       424
2:  27   6        61
3:  57  11       156
4: 206  31       526
5:  17   2        46
                                                                                                                                                                                                                                                            als1
1: TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGTATCAAAC---
2: TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGACTATTAAGTCAGCTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGTCGTCTTGAGTGCAGTAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGACTGTAACTGACGCTGATGCTCGAAAGTGTGGGTATCAAAC---
3: TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGCAACTGACACTGATGCTCGAAAGTGTGGGTATCAAAC---
4: TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTTACTGACACTGATGCTCGAAAGTGTGGGTATCAAAC---
5: TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGATGTAAGTCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGAAACTATGTTGCTAGAGTGCAGGAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAAC---
                                                                                                                                                                                                                                                            als2
1: ---GGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGTATCAAACAGG
2: ---GGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGACTATTAAGTCAGCTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGTCGTCTTGAGTGCAGTAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGACTGTAACTGACGCTGATGCTCGAAAGTGTGGGTATCAAACAGG
3: ---GGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGCAACTGACACTGATGCTCGAAAGTGTGGGTATCAAACAGG
4: ---GGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTTACTGACACTGATGCTCGAAAGTGTGGGTATCAAACAGG
5: ---GTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGATGTAAGTCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGAAACTATGTTGCTAGAGTGCAGGAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG
   match mismatch indel prefer allMismatch accept
1:   247        0     0      1           0   TRUE
2:   247        0     0      1           0   TRUE
3:   247        0     0      1           0   TRUE
4:   247        0     0      1           0   TRUE
5:   247        0     0      1           0   TRUE
                                                                                                                                                                                                                                                        sequence
1: TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGTATCAAACAGG
2: TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGACTATTAAGTCAGCTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGTCGTCTTGAGTGCAGTAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGACTGTAACTGACGCTGATGCTCGAAAGTGTGGGTATCAAACAGG
3: TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGCAACTGACACTGATGCTCGAAAGTGTGGGTATCAAACAGG
4: TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTTACTGACACTGATGCTCGAAAGTGTGGGTATCAAACAGG
5: TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGATGTAAGTCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGAAACTATGTTGCTAGAGTGCAGGAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG
> data.table::setkey(ex2, sequence)
> ex2[(accept), list(abundance = sum(abundance)), by = sequence]
                                                                                                                                                                                                                                                        sequence
1: TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGTATCAAACAGG
2: TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGACTATTAAGTCAGCTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGTCGTCTTGAGTGCAGTAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGACTGTAACTGACGCTGATGCTCGAAAGTGTGGGTATCAAACAGG
3: TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGCAACTGACACTGATGCTCGAAAGTGTGGGTATCAAACAGG
4: TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTTACTGACACTGATGCTCGAAAGTGTGGGTATCAAACAGG
5: TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGATGTAAGTCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGAAACTATGTTGCTAGAGTGCAGGAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG
   abundance
1:       424
2:        61
3:       156
4:       526
5:        46
> # Same sequence set (exactly)
> setequal(x = ex1$sequence,
+          y = ex2[(accept)]$sequence)
[1] TRUE
> # Test concatenation functionality
> ex1cattime = system.time({
+ ex1cat <- mergePairs(dadaF, derepF, dadaR, derepR, justConcatenate = TRUE, verbose = TRUE)
+ sapply(ex1cat, class)
+   # need to convert to a character
+   ex1cat$sequence <- unlist(ex1cat$sequence)
+   ex1cat <- data.table::data.table(ex1cat)
+ })
1315 paired-reads (in 13 unique pairings) successfully merged out of 1315 (in 13 pairings) input.
> ex1cattime
   user  system elapsed 
  0.040   0.000   0.038 
> ex2cattime = system.time({
+   ex2cat <- dada2:::mergePairsByID(dadaF = dadaF, derepF = derepF, srF = srF,
+                            dadaR = dadaR, derepR = derepR, srR = srR,
+                            justConcatenate = TRUE, verbose = TRUE)
+ })
1434 unique forward read IDs.
1343 unique reverse read IDs.
1315 paired reads, corresponding to 13 unique pairs that must be assessed for overlap merge
Error in `[.data.table`(upiddt, , `:=`(sequence, paste0(seqF, rep("N",  : 
  Supplied 10 items to be assigned to group 1 of size 1 in column 'sequence'. The RHS length must either be 1 (single values are ok) or match the LHS length exactly. If you wish to 'recycle' the RHS please use rep() explicitly to make this intent clear to readers of your code.
Calls: system.time -> <Anonymous> -> [ -> [.data.table
Timing stopped at: 4.788 0.02 1.374
Execution halted
* 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: 1 ERROR, 1 WARNING, 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/dada2.Rcheck/00check.log’
for details.

Installation output

dada2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL dada2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘dada2’ ...
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
In file included from ../inst/include/dada2.h:7:0,
                 from RcppExports.cpp:4:
../inst/include/dada2_RcppExports.h:14:14: warning: ‘void dada2::{anonymous}::validateSignature(const char*)’ defined but not used [-Wunused-function]
         void validateSignature(const char* sig) {
              ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c Rmain.cpp -o Rmain.o
Rmain.cpp: In function ‘Rcpp::List dada_uniques(std::vector<std::__cxx11::basic_string<char> >, std::vector<int>, std::vector<bool>, Rcpp::NumericMatrix, Rcpp::NumericMatrix, int, int, int, bool, double, int, double, double, double, int, double, int, int, bool, bool, bool, int, bool, bool, int, bool, bool)’:
Rmain.cpp:68:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(quals.nrow() != maxlen) {
                     ^
Rmain.cpp:81:8: warning: variable ‘HW_SSE3’ set but not used [-Wunused-but-set-variable]
   bool HW_SSE3 = false;
        ^
Rmain.cpp: In function ‘B* run_dada(Raw**, int, Rcpp::NumericMatrix, int, int, int, int, bool, double, int, double, double, int, double, int, int, bool, bool, bool, bool, bool, int, bool, bool)’:
Rmain.cpp:307:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   while( (bb->nclust < max_clust) && (newi = b_bud(bb, min_fold, min_hamming, min_abund, verbose)) ) {
                      ^
Rmain.cpp: In function ‘Rcpp::List dada_uniques(std::vector<std::__cxx11::basic_string<char> >, std::vector<int>, std::vector<bool>, Rcpp::NumericMatrix, Rcpp::NumericMatrix, int, int, int, bool, double, int, double, double, double, int, double, int, int, bool, bool, bool, int, bool, bool, int, bool, bool)’:
Rmain.cpp:282:15: warning: ‘kord’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     free(kord);
               ^
Rmain.cpp:281:14: warning: ‘k16’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     free(k16);
              ^
Rmain.cpp:280:13: warning: ‘k8’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     free(k8);
             ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c chimera.cpp -o chimera.o
chimera.cpp: In function ‘bool C_is_bimera(std::__cxx11::string, std::vector<std::__cxx11::basic_string<char> >, bool, int, int, int, int, int)’:
chimera.cpp:25:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i<pars.size() && rval==false;i++) {
            ^
chimera.cpp:29:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if((left+right) >= sq.size()) { // Toss id/pure-shift/internal-indel "parents"
                     ^
chimera.cpp:44:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if((max_right+max_left)>=sq.size()) {
                            ^
chimera.cpp:48:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if((oo_max_left+oo_max_right_oo)>=sq.size() || (oo_max_left_oo+oo_max_right)>=sq.size()) {
                                       ^
chimera.cpp:48:83: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if((oo_max_left+oo_max_right_oo)>=sq.size() || (oo_max_left_oo+oo_max_right)>=sq.size()) {
                                                                                   ^
chimera.cpp: In function ‘void get_lr(char**, int&, int&, int&, int&, bool, int)’:
chimera.cpp:231:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   while(al[0][pos] == '-' && pos<len) {
                                 ^
chimera.cpp:237:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   while(pos<len && al[0][pos] == al[1][pos]) {
            ^
chimera.cpp:244:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(pos<len && al[0][pos] != '-') { left_oo++; }
           ^
chimera.cpp:245:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     while(pos<len && al[0][pos] == al[1][pos]) {
              ^
chimera.cpp:254:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   while(al[1][pos] == '-' && pos>+(len-max_shift)) {
                                 ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c cluster.cpp -o cluster.o
cluster.cpp: In function ‘void b_compare(B*, unsigned int, Rcpp::NumericMatrix, int, int, int, int, bool, double, int, bool, int, bool, bool, bool)’:
cluster.cpp:17:23: warning: variable ‘cind’ set but not used [-Wunused-but-set-variable]
   unsigned int index, cind, center_reads;
                       ^
cluster.cpp: In function ‘void b_compare_parallel(B*, unsigned int, Rcpp::NumericMatrix, int, int, int, int, bool, double, int, bool, int, bool, bool, bool)’:
cluster.cpp:166:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(row=0;row<errMat.nrow();row++) {
                ^
cluster.cpp:167:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(col=0;col<errMat.ncol();col++) {
                  ^
cluster.cpp:156:23: warning: variable ‘cind’ set but not used [-Wunused-but-set-variable]
   unsigned int index, cind, row, col, ncol;
                       ^
cluster.cpp: In function ‘int b_bud(B*, double, int, int, bool)’:
cluster.cpp:317:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i<b->nclust;i++) {
            ^
cluster.cpp:318:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(r=1; r<b->bi[i]->nraw; r++) { // r=0 is the center
               ^
cluster.cpp:321:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if(raw->reads < min_abund) { continue; }
                     ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c containers.cpp -o containers.o
containers.cpp: In function ‘void b_free(B*)’:
containers.cpp:140:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<b->nclust;i++) { bi_free(b->bi[i]); }
                ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c error.cpp -o error.o
error.cpp: In function ‘Rcpp::DataFrame b_make_positional_substitution_df(B*, Sub**, unsigned int, Rcpp::NumericMatrix, bool)’:
error.cpp:170:51: warning: variable ‘ncol’ set but not used [-Wunused-but-set-variable]
   unsigned int i, pos, pos1, qind, j, r, s, nti0, ncol;
                                                   ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c evaluate.cpp -o evaluate.o
evaluate.cpp: In function ‘Rcpp::IntegerVector C_eval_pair(std::__cxx11::string, std::__cxx11::string)’:
evaluate.cpp:88:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   } while((s1gap || s2gap) && start<s1.size());
                                    ^
evaluate.cpp: In function ‘Rcpp::CharacterVector C_pair_consensus(std::__cxx11::string, std::__cxx11::string, int, bool)’:
evaluate.cpp:133:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i<s1.size();i++) {
            ^
evaluate.cpp:152:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(i=0;i<s1.size();i++) {
              ^
evaluate.cpp:163:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i<s1.size();i++) {
            ^
evaluate.cpp: In function ‘Rcpp::NumericVector kmer_dist(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, int)’:
evaluate.cpp:219:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<nseqs;i++) {
                ^
evaluate.cpp: In function ‘Rcpp::NumericVector kord_dist(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, int, int)’:
evaluate.cpp:243:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<nseqs;i++) {
                ^
evaluate.cpp:255:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<nseqs;i++) {
                ^
evaluate.cpp: In function ‘Rcpp::IntegerVector kmer_matches(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, int)’:
evaluate.cpp:286:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<nseqs;i++) {
                ^
evaluate.cpp:298:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i<nseqs;i++) {
            ^
evaluate.cpp:310:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(j=0;j<klen_min;j++) {
              ^
evaluate.cpp: In function ‘Rcpp::IntegerVector kdist_matches(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, int)’:
evaluate.cpp:339:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i<nseqs;i++) {
            ^
evaluate.cpp:348:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(j=0;j<n_kmers;j++) {
              ^
evaluate.cpp:327:10: warning: variable ‘len1’ set but not used [-Wunused-but-set-variable]
   size_t len1 = 0, len2 = 0;
          ^
evaluate.cpp:327:20: warning: variable ‘len2’ set but not used [-Wunused-but-set-variable]
   size_t len1 = 0, len2 = 0;
                    ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c filter.cpp -o filter.o
filter.cpp: In function ‘Rcpp::IntegerVector C_matchRef(std::vector<std::__cxx11::basic_string<char> >, std::__cxx11::string, unsigned int, bool)’:
filter.cpp:16:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i<len;i++) {
            ^
filter.cpp:20:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i<seqs.size();i++) {
            ^
filter.cpp:24:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(j=0;j<=(len-word_size);j++) {
              ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c kmers.cpp -o kmers.o
kmers.cpp: In function ‘double kmer_dist_SSEi_8(uint8_t*, int, uint8_t*, int, int)’:
kmers.cpp:81:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i<STEP;i++) {
            ^
kmers.cpp: In function ‘double kord_dist(uint16_t*, int, uint16_t*, int, int)’:
kmers.cpp:101:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i<klen;i++) {
            ^
kmers.cpp: In function ‘double kord_dist_SSEi(uint16_t*, int, uint16_t*, int, int)’:
kmers.cpp:131:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i<STEP;i++) {
            ^
kmers.cpp:134:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=n_vec;i<klen;i++,kord1++,kord2++) { // kord starts pointing to where it was left
                ^
kmers.cpp: In function ‘void assign_kmer8(uint8_t*, const char*, int)’:
kmers.cpp:146:8: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(k >= len || k < 3 || k > 8) { Rcpp::stop("Invalid kmer-size."); }
        ^
kmers.cpp:158:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0; i<klen; i++) {
             ^
kmers.cpp: In function ‘void assign_kmer(uint16_t*, const char*, int)’:
kmers.cpp:195:8: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(k >= len || k < 3 || k > 8) { Rcpp::stop("Invalid kmer-size."); }
        ^
kmers.cpp:205:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0; i<klen; i++) {
             ^
kmers.cpp: In function ‘void assign_kmer_order(uint16_t*, char*, int)’:
kmers.cpp:234:8: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(k >= len || k < 1 || k > 8) { Rcpp::stop("Invalid kmer-size."); }
        ^
kmers.cpp:239:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i<klen;i++) { kord[i] = 0; }
            ^
kmers.cpp:241:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0; i<klen; i++) {
             ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c misc.cpp -o misc.o
misc.cpp: In function ‘void align_print(char**)’:
misc.cpp:24:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<strlen(al0);i++) {
                ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c nwalign_endsfree.cpp -o nwalign_endsfree.o
nwalign_endsfree.cpp: In function ‘char** nwalign_endsfree(const char*, size_t, const char*, size_t, int (*)[4], int, int)’:
nwalign_endsfree.cpp:89:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i <= len1; i++) {
                 ^
nwalign_endsfree.cpp:95:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (j = 0; j <= len2; j++) {
                 ^
nwalign_endsfree.cpp:114:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(band>=0 && (band<len1 || band<len2)) {
                      ^
nwalign_endsfree.cpp:114:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(band>=0 && (band<len1 || band<len2)) {
                                   ^
nwalign_endsfree.cpp:115:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(i=0;i<=len1;i++) {
              ^
nwalign_endsfree.cpp:117:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if(i+rband+1 <= len2) { d[i*ncol + i+rband+1] = -9999; }
                    ^
nwalign_endsfree.cpp:122:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 1; i <= len1; i++) {
                 ^
nwalign_endsfree.cpp:125:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       r = i+rband; if(r>len2) { r = len2; }
                        ^
nwalign_endsfree.cpp:130:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (i == len1) {
             ^
nwalign_endsfree.cpp:137:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (j == len2) {
             ^
nwalign_endsfree.cpp:201:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i=0;i<len_al;i++) {
             ^
nwalign_endsfree.cpp: In function ‘char** nwalign_endsfree_homo(const char*, size_t, const char*, size_t, int (*)[4], int, int, int)’:
nwalign_endsfree.cpp:230:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i=0,j=0;j<len1;j++) {
                 ^
nwalign_endsfree.cpp:231:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (j==len1-1 || s1[j]!=s1[j+1]) {
          ^
nwalign_endsfree.cpp:244:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i=0,j=0;j<len2;j++) {
                 ^
nwalign_endsfree.cpp:245:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (j==len2-1 || s2[j]!=s2[j+1]) {
          ^
nwalign_endsfree.cpp:264:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i <= len1; i++) {
                 ^
nwalign_endsfree.cpp:270:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (j = 0; j <= len2; j++) {
                 ^
nwalign_endsfree.cpp:289:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(band>=0 && (band<len1 || band<len2)) {
                      ^
nwalign_endsfree.cpp:289:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(band>=0 && (band<len1 || band<len2)) {
                                   ^
nwalign_endsfree.cpp:290:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(i=0;i<=len1;i++) {
              ^
nwalign_endsfree.cpp:292:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if(i+rband+1 <= len2) { d[i*ncol + i+rband+1] = -9999; }
                    ^
nwalign_endsfree.cpp:297:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 1; i <= len1; i++) {
                 ^
nwalign_endsfree.cpp:300:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       r = i+rband; if(r>len2) { r = len2; }
                        ^
nwalign_endsfree.cpp:305:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (i == len1) {
             ^
nwalign_endsfree.cpp:314:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (j == len2) {
             ^
nwalign_endsfree.cpp:379:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i=0;i<len_al;i++) {
             ^
nwalign_endsfree.cpp: In function ‘char** nwalign(const char*, size_t, const char*, size_t, int (*)[4], int, int)’:
nwalign_endsfree.cpp:419:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 1; i <= len1; i++) {
                 ^
nwalign_endsfree.cpp:425:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (j = 1; j <= len2; j++) {
                 ^
nwalign_endsfree.cpp:444:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(band>=0 && (band<len1 || band<len2)) {
                      ^
nwalign_endsfree.cpp:444:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(band>=0 && (band<len1 || band<len2)) {
                                   ^
nwalign_endsfree.cpp:445:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(i=0;i<=len1;i++) {
              ^
nwalign_endsfree.cpp:447:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if(i+rband+1 <= len2) { d[i*ncol + i+rband+1] = -9999; }
                    ^
nwalign_endsfree.cpp:452:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 1; i <= len1; i++) {
                 ^
nwalign_endsfree.cpp:455:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       r = i+rband; if(r>len2) { r = len2; }
                        ^
nwalign_endsfree.cpp:522:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i=0;i<len_al;i++) {
             ^
nwalign_endsfree.cpp: In function ‘char** nwalign_gapless(const char*, size_t, const char*, size_t)’:
nwalign_endsfree.cpp:548:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i=0;i<len_al;i++) {
                 ^
nwalign_endsfree.cpp:549:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     al[0][i] = i < len1 ? s1[i] : '-';
                  ^
nwalign_endsfree.cpp:550:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     al[1][i] = i < len2 ? s2[i] : '-';
                  ^
nwalign_endsfree.cpp: In function ‘Sub* sub_new(Raw*, Raw*, int, int, int, int, bool, double, int, bool, int, bool)’:
nwalign_endsfree.cpp:658:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(s=0;s<sub->nsubs;s++) {
                ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c nwalign_vectorized.cpp -o nwalign_vectorized.o
nwalign_vectorized.cpp: In function ‘char** nwalign_vectorized2(const char*, size_t, const char*, size_t, int16_t, int16_t, int16_t, int16_t, int)’:
nwalign_vectorized.cpp:96:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   start_col = 1 + (1+(band<len1 ? band : len1))/2;
                           ^
nwalign_vectorized.cpp:125:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   while(row < (1 + (band < len1 ? band : len1))) {
                          ^
nwalign_vectorized.cpp:178:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(row==(band<len1 ? band : len1)) { 
                  ^
nwalign_vectorized.cpp:218:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(row < band && row < len1) { // upper tri for seq1
            ^
nwalign_vectorized.cpp:75:21: warning: variable ‘end_col’ set but not used [-Wunused-but-set-variable]
   size_t start_col, end_col;
                     ^
nwalign_vectorized.cpp: In function ‘Rcpp::CharacterVector C_nwvec(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, int16_t, int16_t, int16_t, int, bool)’:
nwalign_vectorized.cpp:330:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i<s1.size();i++) {
            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c pval.cpp -o pval.o
pval.cpp: In function ‘double compute_lambda(Raw*, Sub*, Rcpp::NumericMatrix, bool, unsigned int)’:
pval.cpp:121:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(s=0;s<sub->nsubs;s++) {
            ^
pval.cpp:123:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(pos0 < 0 || pos0 >= sub->len0) { Rcpp::stop("CL: Bad pos0: %i (len0=%i).", pos0, sub->len0); }
                         ^
pval.cpp: In function ‘double compute_lambda_ts(Raw*, Sub*, unsigned int, double*, bool)’:
pval.cpp:177:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(s=0;s<sub->nsubs;s++) {
            ^
pval.cpp:179:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(pos0 < 0 || pos0 >= sub->len0) { Rcpp::stop("CL: Bad pos0: %i (len0=%i).", pos0, sub->len0); }
                         ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c taxonomy.cpp -o taxonomy.o
taxonomy.cpp: In function ‘void tax_kvec(const char*, unsigned int, unsigned char*)’:
taxonomy.cpp:42:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(kmer>=0 && kmer<n_kmers) {
                       ^
taxonomy.cpp: In function ‘int get_best_genus(int*, double*, unsigned int, unsigned int, unsigned int*, unsigned int, double*, double*)’:
taxonomy.cpp:72:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(g=0;g<ngenus;g++) {
            ^
taxonomy.cpp: In function ‘Rcpp::List C_assign_taxonomy(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::vector<int>, Rcpp::IntegerMatrix, bool, bool)’:
taxonomy.cpp:120:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(ref_to_genus[i]<0 || ref_to_genus[i] >= ngenus) {
                                             ^
taxonomy.cpp:149:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(kmer=0;kmer<n_kmers;kmer++) {
                    ^
taxonomy.cpp:158:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(kmer=0;kmer<n_kmers;kmer++) {
                  ^
taxonomy.cpp:223:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(i=0;i<(genusmat.ncol());i++) {
                ^
taxonomy.cpp: In member function ‘virtual void AssignParallel::operator()(std::size_t, std::size_t)’:
taxonomy.cpp:277:15: warning: variable ‘seqlen’ set but not used [-Wunused-but-set-variable]
     size_t i, seqlen;
               ^
taxonomy.cpp:278:31: warning: variable ‘boot_match’ set but not used [-Wunused-but-set-variable]
     unsigned int boot, booti, boot_match, arraylen, arraylen_rc;
                               ^
taxonomy.cpp: In function ‘Rcpp::List C_assign_taxonomy2(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::vector<int>, Rcpp::IntegerMatrix, bool, bool)’:
taxonomy.cpp:345:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(ref_to_genus[i]<0 || ref_to_genus[i] >= ngenus) {
                                             ^
taxonomy.cpp:374:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(kmer=0;kmer<n_kmers;kmer++) {
                    ^
taxonomy.cpp:383:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(kmer=0;kmer<n_kmers;kmer++) {
                  ^
taxonomy.cpp:407:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i<unifs.size();i++) { C_unifs[i] = unifs(i); }
            ^
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o dada2.so RcppExports.o Rmain.o chimera.o cluster.o containers.o error.o evaluate.o filter.o kmers.o misc.o nwalign_endsfree.o nwalign_vectorized.o pval.o taxonomy.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/dada2/libs
** R
** data
*** moving datasets to lazyload DB
** 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
* DONE (dada2)

Tests output

Example timings

dada2.Rcheck/dada2-Ex.timings

nameusersystemelapsed
PacBioErrfun10.544 0.02410.597
addSpecies1.4640.0241.512
assignSpecies0.6880.0000.688
assignTaxonomy0.2360.0120.238
collapseNoMismatch1.160.001.18
dada4.2080.0084.219
dada_to_seq_table2.8880.0201.921
derepFastq0.7640.0520.815
fastqFilter0.6920.0080.726
fastqPairedFilter1.4360.0081.450
filterAndTrim1.3960.0001.396
getDadaOpt0.0000.0000.001
getErrors1.5560.0001.559
getSequences0.5960.0120.607
getUniques0.7080.0120.723
inflateErr000
isBimera0.0680.0000.068
isBimeraDenovo3.1320.0043.235
isBimeraDenovoTable4.2400.0044.345
isPhiX0.3320.0040.335
isShiftDenovo1.8680.0001.877
learnErrors8.4320.0847.185
loessErrfun0.6400.0000.643
makeSequenceTable1.7680.0041.774
mergePairs4.2000.0044.225