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CHECK report for dada2 on merida2

This page was generated on 2018-10-17 08:56:03 -0400 (Wed, 17 Oct 2018).

Package 341/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dada2 1.8.0
Benjamin Callahan
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/dada2
Branch: RELEASE_3_7
Last Commit: 630ef9a
Last Changed Date: 2018-04-30 10:35:40 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: dada2
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:dada2.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings dada2_1.8.0.tar.gz
StartedAt: 2018-10-16 20:47:13 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 20:51:26 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 252.5 seconds
RetCode: 0
Status:  OK 
CheckDir: dada2.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:dada2.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings dada2_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/dada2.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dada2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dada2’ version ‘1.8.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘dada2’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
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 ‘biocLite’
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 biocLite four indel
  mismatch n0F n0R prefer seqF seqR write.table
Consider adding
  importFrom("utils", "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
mergePairsByID 6.036  1.092   4.731
learnErrors    5.225  0.464   4.497
* 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: 6 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/dada2.Rcheck/00check.log’
for details.



Installation output

dada2.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL dada2
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘dada2’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppParallel/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/dada2.h:7:
./../inst/include/dada2_RcppExports.h:14:14: warning: unused function 'validateSignature' [-Wunused-function]
        void validateSignature(const char* sig) {
             ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppParallel/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c Rmain.cpp -o Rmain.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppParallel/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c chimera.cpp -o chimera.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppParallel/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c cluster.cpp -o cluster.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppParallel/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c containers.cpp -o containers.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppParallel/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c error.cpp -o error.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppParallel/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c evaluate.cpp -o evaluate.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppParallel/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c filter.cpp -o filter.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppParallel/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c kmers.cpp -o kmers.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppParallel/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c misc.cpp -o misc.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppParallel/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c nwalign_endsfree.cpp -o nwalign_endsfree.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppParallel/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c nwalign_vectorized.cpp -o nwalign_vectorized.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppParallel/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c pval.cpp -o pval.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppParallel/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c taxonomy.cpp -o taxonomy.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o dada2.so RcppExports.o Rmain.o chimera.o cluster.o containers.o error.o evaluate.o filter.o kmers.o misc.o nwalign_endsfree.o nwalign_vectorized.o pval.o taxonomy.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/dada2/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (dada2)

Tests output


Example timings

dada2.Rcheck/dada2-Ex.timings

nameusersystemelapsed
addSpecies3.0660.0333.136
assignSpecies1.1790.0031.197
assignTaxonomy0.2190.0030.212
collapseNoMismatch1.3510.0251.395
dada2.3990.0502.464
dada_to_seq_table1.1620.0321.113
derepFastq1.8910.1101.176
fastqFilter0.5770.0210.603
fastqPairedFilter1.1250.0491.198
filterAndTrim0.9080.0370.953
getDadaOpt0.0020.0000.003
getErrors1.0960.0281.132
getSequences0.4620.0280.496
getUniques0.5020.0320.536
inflateErr0.0020.0000.002
isBimera0.0820.0120.094
isBimeraDenovo2.1180.0312.167
isBimeraDenovoTable2.3260.0412.380
isPhiX0.2220.0260.250
isShiftDenovo1.0910.0181.114
learnErrors5.2250.4644.497
loessErrfun0.4340.0130.452
makeSequenceTable0.6250.0190.651
mergePairs2.1430.0532.208
mergePairsByID6.0361.0924.731
mergeSequenceTables0.0120.0040.002
noqualErrfun1.2810.3670.669
nwalign0.0030.0000.003
nwhamming0.0030.0000.003
plotErrors3.3760.1143.535
plotQualityProfile0.9710.0481.027
removeBimeraDenovo2.3140.0482.382
seqComplexity0.0670.0010.068
setDadaOpt0.0050.0000.005
uniquesToFasta0.0880.0090.099