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BioC 3.5: CHECK report for dada2 on toluca2

This page was generated on 2017-04-23 14:41:17 -0400 (Sun, 23 Apr 2017).

Package 310/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dada2 1.3.5
Benjamin Callahan
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/dada2
Last Changed Rev: 128506 / Revision: 129046
Last Changed Date: 2017-04-10 20:50:39 -0400 (Mon, 10 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: dada2
Version: 1.3.5
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings dada2_1.3.5.tar.gz
StartedAt: 2017-04-23 02:38:39 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 02:44:07 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 327.7 seconds
RetCode: 0
Status:  OK 
CheckDir: dada2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings dada2_1.3.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/dada2.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.3.5’
* 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 ... OK
* 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 loading without being on the library search path ... 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
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’
plotComplementarySubstitutions: no visible binding for global variable
  ‘Sub1’
plotComplementarySubstitutions: no visible binding for global variable
  ‘Substitution’
plotComplementarySubstitutions: no visible binding for global variable
  ‘Sub2’
plotComplementarySubstitutions: no visible binding for global variable
  ‘SubGrp’
plotComplementarySubstitutions: no visible binding for global variable
  ‘Direction’
plotComplementarySubstitutions: no visible binding for global variable
  ‘Count’
plotComplementarySubstitutions: no visible binding for global variable
  ‘Forward’
plotComplementarySubstitutions: no visible binding for global variable
  ‘Reverse’
plotComplementarySubstitutions: no visible binding for global variable
  ‘Quality’
plotErrors: no visible binding for global variable ‘Qual’
plotErrors: no visible binding for global variable ‘Observed’
plotErrors: no visible binding for global variable ‘Estimated’
plotErrors: no visible binding for global variable ‘Input’
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 ‘minScore’
plotQualityProfile: no visible binding for global variable ‘label’
Undefined global functions or variables:
  Count Cycle Direction Estimated Forward Input Mean Nominal Observed
  Q25 Q50 Q75 Qual Quality Reverse Score Sub1 Sub2 SubGrp Substitution
  abundance accept allMismatch als1 als2 indel label minScore mismatch
  n0F n0R prefer seqF seqR
* 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
learnErrors 8.199  0.169   7.629
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/dada2.Rcheck/00check.log’
for details.


dada2.Rcheck/00install.out:

* installing *source* package ‘dada2’ ...
** libs
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppParallel/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -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/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppParallel/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -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/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppParallel/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2 -c chimera.cpp -o chimera.o
chimera.cpp:180:7: warning: unused variable 'nrow' [-Wunused-variable]
  int nrow = mat.nrow();
      ^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppParallel/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -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/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppParallel/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -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/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppParallel/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -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/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppParallel/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -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/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppParallel/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -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/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppParallel/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -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/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppParallel/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -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/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppParallel/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -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/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppParallel/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2 -c strmap.cpp -o strmap.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppParallel/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -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 error.o evaluate.o filter.o misc.o nwalign_endsfree.o nwalign_vectorized.o pval.o strmap.o taxonomy.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/dada2.Rcheck/dada2/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (dada2)

dada2.Rcheck/dada2-Ex.timings:

nameusersystemelapsed
addSpecies0.0010.0000.001
assignSpecies0.0010.0000.000
assignTaxonomy000
collapseNoMismatch2.5600.0952.810
dada2.7850.0822.886
dada_to_seq_table1.1520.0301.187
derepFastq1.1500.0771.235
evaluate_kmers0.1260.0190.145
fastqFilter1.1260.0351.169
fastqPairedFilter1.3940.0801.477
filterAndTrim0.9310.0671.002
getDadaOpt0.0010.0000.001
getErrors1.0970.0371.142
getSequences0.5800.0410.624
getUniques0.5790.0280.609
inflateErr0.0170.0000.017
isBimera0.0570.0140.071
isBimeraDenovo1.9030.0451.962
isBimeraDenovoTable3.4760.0893.703
isPhiX0.1710.0190.192
isShiftDenovo1.1500.0281.194
learnErrors8.1990.1697.629
loessErrfun0.4680.0150.484
makeSequenceTable0.8650.0390.913
mergePairs2.8230.0842.928
mergePairsByID4.1010.0634.204
mergeSequenceTables000
nwalign0.0010.0000.001
nwhamming0.0020.0000.001
plotComplementarySubstitutions4.5370.0334.691
plotErrors4.2320.0294.311
plotQualityProfile1.0850.0261.127
removeBimeraDenovo1.9120.0272.002
setDadaOpt0.0160.0000.017
uniquesToFasta0.0900.0110.102