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CHECK report for dada2 on tokay1

This page was generated on 2019-04-13 11:26:23 -0400 (Sat, 13 Apr 2019).

Package 365/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dada2 1.10.1
Benjamin Callahan
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 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 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ ERROR ] OK 
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  ERROR  OK 

Summary

Package: dada2
Version: 1.10.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:dada2.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings dada2_1.10.1.tar.gz
StartedAt: 2019-04-13 01:37:14 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 01:43:59 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 404.6 seconds
RetCode: 1
Status:  ERROR  
CheckDir: dada2.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:dada2.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings dada2_1.10.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/dada2.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 whether package 'dada2' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIpK7y0/R.INSTALLd3c18c5295/dada2/man/derepFastq.Rd:30: file link 'FastqStreamer' in package 'ShortRead' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIpK7y0/R.INSTALLd3c18c5295/dada2/man/derepFastq.Rd:12: file link 'FastqStreamer' in package 'ShortRead' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIpK7y0/R.INSTALLd3c18c5295/dada2/man/derepFastq.Rd:19: file link 'FastqStreamer' in package 'ShortRead' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIpK7y0/R.INSTALLd3c18c5295/dada2/man/fastqFilter.Rd:68: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIpK7y0/R.INSTALLd3c18c5295/dada2/man/fastqFilter.Rd:97: file link 'FastqStreamer' in package 'ShortRead' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIpK7y0/R.INSTALLd3c18c5295/dada2/man/fastqPairedFilter.Rd:98: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIpK7y0/R.INSTALLd3c18c5295/dada2/man/fastqPairedFilter.Rd:132: file link 'FastqStreamer' in package 'ShortRead' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIpK7y0/R.INSTALLd3c18c5295/dada2/man/filterAndTrim.Rd:101: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIpK7y0/R.INSTALLd3c18c5295/dada2/man/filterAndTrim.Rd:102: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIpK7y0/R.INSTALLd3c18c5295/dada2/man/filterAndTrim.Rd:151: file link 'FastqStreamer' in package 'ShortRead' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIpK7y0/R.INSTALLd3c18c5295/dada2/man/learnErrors.Rd:14: file link 'FastqStreamer' in package 'ShortRead' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIpK7y0/R.INSTALLd3c18c5295/dada2/man/mergePairsByID.Rd:54: file link 'id' in package 'ShortRead' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIpK7y0/R.INSTALLd3c18c5295/dada2/man/seqComplexity.Rd:52: file link 'oligonucleotideFrequency' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIpK7y0/R.INSTALLd3c18c5295/dada2/man/uniquesToFasta.Rd:22: file link 'writeFasta' in package 'ShortRead' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIpK7y0/R.INSTALLd3c18c5295/dada2/man/uniquesToFasta.Rd:27: file link 'writeFasta' in package 'ShortRead' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIpK7y0/R.INSTALLd3c18c5295/dada2/man/uniquesToFasta.Rd:29: file link 'writeFasta' in package 'ShortRead' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIpK7y0/R.INSTALLd3c18c5295/dada2/man/writeFasta.Rd:21: file link 'writeXStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIpK7y0/R.INSTALLd3c18c5295/dada2/man/writeFasta.Rd:31: file link 'writeXStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/dada2.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/dada2/libs/i386/dada2.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... 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)
+  })
1214 paired-reads (in 5 unique pairings) successfully merged out of 1315 (in 13 pairings) input.
> ex1time
   user  system elapsed 
   0.04    0.00    0.03 
> # 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
1214 paired-reads (in 5 unique pairings) successfully merged
from 1315 read pairs.
> ex2time
   user  system elapsed 
   0.07    0.01    0.11 
> # 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       157
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:       157
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 
   0.01    0.00    0.02 
> 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: 0.08 0 0.08
Execution halted
** running examples for arch 'x64' ... 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 
   0.06    0.00    0.06 
> # 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 
   0.15    0.03    0.11 
> # 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 
   0.05    0.00    0.05 
> 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: 0.07 0.01 0.07
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: 2 ERRORs, 2 WARNINGs, 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/dada2.Rcheck/00check.log'
for details.

Installation output

dada2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/dada2_1.10.1.tar.gz && rm -rf dada2.buildbin-libdir && mkdir dada2.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=dada2.buildbin-libdir dada2_1.10.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL dada2_1.10.1.zip && rm dada2_1.10.1.tar.gz dada2_1.10.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1309k  100 1309k    0     0  12.1M      0 --:--:-- --:--:-- --:--:-- 12.5M

install for i386

* installing *source* package 'dada2' ...
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -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) {
              ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -c Rmain.cpp -o Rmain.o
Rmain.cpp: In function 'Rcpp::List dada_uniques(std::vector<std::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::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);
             ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -c chimera.cpp -o chimera.o
chimera.cpp: In function 'bool C_is_bimera(std::string, std::vector<std::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)) {
                                 ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -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; }
                     ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -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]); }
                ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -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;
                                                   ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -c evaluate.cpp -o evaluate.o
evaluate.cpp: In function 'Rcpp::IntegerVector C_eval_pair(std::string, std::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::string, std::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::basic_string<char> >, std::vector<std::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::basic_string<char> >, std::vector<std::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::basic_string<char> >, std::vector<std::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::basic_string<char> >, std::vector<std::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;
                    ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -c filter.cpp -o filter.o
filter.cpp: In function 'Rcpp::IntegerVector C_matchRef(std::vector<std::basic_string<char> >, std::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++) {
              ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -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++) {
             ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -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++) {
                ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -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++) {
                ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -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::basic_string<char> >, std::vector<std::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++) {
            ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -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); }
                         ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -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::basic_string<char> >, std::vector<std::basic_string<char> >, std::vector<std::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::basic_string<char> >, std::vector<std::basic_string<char> >, std::vector<std::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); }
            ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o dada2.dll tmp.def 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 -LC:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/lib/i386 -ltbb -ltbbmalloc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/dada2.buildbin-libdir/dada2/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'dada2'
    finding HTML links ... done
    PacBioErrfun                            html  
    addSpecies                              html  
    finding level-2 HTML links ... done

    assignSpecies                           html  
    assignTaxonomy                          html  
    c-dada-method                           html  
    c-derep-method                          html  
    collapseNoMismatch                      html  
    dada-class                              html  
    dada                                    html  
    dada2-package                           html  
    dada_to_seq_table                       html  
    derep-class                             html  
    derepFasta                              html  
    derepFastq                              html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIpK7y0/R.INSTALLd3c18c5295/dada2/man/derepFastq.Rd:30: file link 'FastqStreamer' in package 'ShortRead' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIpK7y0/R.INSTALLd3c18c5295/dada2/man/derepFastq.Rd:12: file link 'FastqStreamer' in package 'ShortRead' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIpK7y0/R.INSTALLd3c18c5295/dada2/man/derepFastq.Rd:19: file link 'FastqStreamer' in package 'ShortRead' does not exist and so has been treated as a topic
    errBalancedF                            html  
    errBalancedR                            html  
    errExtremeF                             html  
    errExtremeR                             html  
    errHmpF                                 html  
    errHmpR                                 html  
    fastqFilter                             html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIpK7y0/R.INSTALLd3c18c5295/dada2/man/fastqFilter.Rd:68: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIpK7y0/R.INSTALLd3c18c5295/dada2/man/fastqFilter.Rd:97: file link 'FastqStreamer' in package 'ShortRead' does not exist and so has been treated as a topic
    fastqPairedFilter                       html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIpK7y0/R.INSTALLd3c18c5295/dada2/man/fastqPairedFilter.Rd:98: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIpK7y0/R.INSTALLd3c18c5295/dada2/man/fastqPairedFilter.Rd:132: file link 'FastqStreamer' in package 'ShortRead' does not exist and so has been treated as a topic
    filterAndTrim                           html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIpK7y0/R.INSTALLd3c18c5295/dada2/man/filterAndTrim.Rd:101: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIpK7y0/R.INSTALLd3c18c5295/dada2/man/filterAndTrim.Rd:102: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIpK7y0/R.INSTALLd3c18c5295/dada2/man/filterAndTrim.Rd:151: file link 'FastqStreamer' in package 'ShortRead' does not exist and so has been treated as a topic
    getDadaOpt                              html  
    getErrors                               html  
    getSequences                            html  
    getUniques                              html  
    inflateErr                              html  
    isBimera                                html  
    isBimeraDenovo                          html  
    isBimeraDenovoTable                     html  
    isPhiX                                  html  
    isShiftDenovo                           html  
    learnErrors                             html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIpK7y0/R.INSTALLd3c18c5295/dada2/man/learnErrors.Rd:14: file link 'FastqStreamer' in package 'ShortRead' does not exist and so has been treated as a topic
    loessErrfun                             html  
    makeSequenceTable                       html  
    makeSpeciesFasta_RDP                    html  
    makeSpeciesFasta_Silva                  html  
    makeTaxonomyFasta_RDP                   html  
    makeTaxonomyFasta_Silva                 html  
    mergePairs                              html  
    mergePairsByID                          html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIpK7y0/R.INSTALLd3c18c5295/dada2/man/mergePairsByID.Rd:54: file link 'id' in package 'ShortRead' does not exist and so has been treated as a topic
    mergeSequenceTables                     html  
    names-set-dada-ANY-method               html  
    names-set-derep-ANY-method              html  
    noqualErrfun                            html  
    nwalign                                 html  
    nwhamming                               html  
    plotErrors                              html  
    plotQualityProfile                      html  
    qtables2                                html  
    removeBimeraDenovo                      html  
    seqComplexity                           html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIpK7y0/R.INSTALLd3c18c5295/dada2/man/seqComplexity.Rd:52: file link 'oligonucleotideFrequency' in package 'Biostrings' does not exist and so has been treated as a topic
    setDadaOpt                              html  
    show-methods                            html  
    tperr1                                  html  
    uniques-vector                          html  
    uniquesToFasta                          html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIpK7y0/R.INSTALLd3c18c5295/dada2/man/uniquesToFasta.Rd:22: file link 'writeFasta' in package 'ShortRead' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIpK7y0/R.INSTALLd3c18c5295/dada2/man/uniquesToFasta.Rd:27: file link 'writeFasta' in package 'ShortRead' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIpK7y0/R.INSTALLd3c18c5295/dada2/man/uniquesToFasta.Rd:29: file link 'writeFasta' in package 'ShortRead' does not exist and so has been treated as a topic
    writeFasta                              html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIpK7y0/R.INSTALLd3c18c5295/dada2/man/writeFasta.Rd:21: file link 'writeXStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIpK7y0/R.INSTALLd3c18c5295/dada2/man/writeFasta.Rd:31: file link 'writeXStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'dada2' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -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) {
              ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -c Rmain.cpp -o Rmain.o
Rmain.cpp: In function 'Rcpp::List dada_uniques(std::vector<std::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::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);
             ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -c chimera.cpp -o chimera.o
chimera.cpp: In function 'bool C_is_bimera(std::string, std::vector<std::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)) {
                                 ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -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; }
                     ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -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]); }
                ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -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;
                                                   ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -c evaluate.cpp -o evaluate.o
evaluate.cpp: In function 'Rcpp::IntegerVector C_eval_pair(std::string, std::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::string, std::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::basic_string<char> >, std::vector<std::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::basic_string<char> >, std::vector<std::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::basic_string<char> >, std::vector<std::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::basic_string<char> >, std::vector<std::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;
                    ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -c filter.cpp -o filter.o
filter.cpp: In function 'Rcpp::IntegerVector C_matchRef(std::vector<std::basic_string<char> >, std::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++) {
              ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -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++) {
             ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -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++) {
                ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -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++) {
                ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -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::basic_string<char> >, std::vector<std::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++) {
            ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -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); }
                         ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -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::basic_string<char> >, std::vector<std::basic_string<char> >, std::vector<std::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::basic_string<char> >, std::vector<std::basic_string<char> >, std::vector<std::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); }
            ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o dada2.dll tmp.def 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 -LC:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/dada2.buildbin-libdir/dada2/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'dada2' as dada2_1.10.1.zip
* DONE (dada2)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'dada2' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

Example timings

dada2.Rcheck/examples_i386/dada2-Ex.timings

nameusersystemelapsed
PacBioErrfun9.300.339.70
addSpecies1.660.011.88
assignSpecies0.530.000.53
assignTaxonomy0.160.020.18
collapseNoMismatch0.810.061.01
dada3.800.013.81
dada_to_seq_table1.610.381.99
derepFastq0.530.220.75
fastqFilter0.810.010.94
fastqPairedFilter1.640.051.95
filterAndTrim1.130.021.14
getDadaOpt000
getErrors1.440.001.44
getSequences0.50.00.5
getUniques0.520.030.55
inflateErr000
isBimera0.060.010.08
isBimeraDenovo2.390.102.48
isBimeraDenovoTable3.700.083.78
isPhiX0.390.010.41
isShiftDenovo1.710.051.75
learnErrors8.260.196.05
loessErrfun0.440.030.46
makeSequenceTable0.830.000.83
mergePairs2.920.062.99

dada2.Rcheck/examples_x64/dada2-Ex.timings

nameusersystemelapsed
PacBioErrfun8.110.038.16
addSpecies1.400.051.45
assignSpecies0.690.000.69
assignTaxonomy0.170.020.17
collapseNoMismatch0.690.010.70
dada2.780.032.82
dada_to_seq_table1.330.411.73
derepFastq0.640.090.73
fastqFilter0.590.000.60
fastqPairedFilter1.020.041.04
filterAndTrim1.020.011.04
getDadaOpt000
getErrors1.120.061.18
getSequences0.390.070.46
getUniques0.420.000.42
inflateErr000
isBimera0.100.000.09
isBimeraDenovo2.610.042.66
isBimeraDenovoTable3.000.133.12
isPhiX0.390.000.39
isShiftDenovo1.870.041.93
learnErrors6.410.354.62
loessErrfun0.360.010.38
makeSequenceTable1.220.041.25
mergePairs2.310.032.34