Benjamin Callahan
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/dada2 |
| Branch: RELEASE_3_6 |
| Last Commit: 553008d |
| Last Changed Date: 2017-10-30 12:41:13 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:42:23 -0400 (Thu, 12 Apr 2018).
| Package 326/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| dada2 1.6.0 Benjamin Callahan
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ OK ] | OK | |
| Package: dada2 |
| Version: 1.6.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings dada2_1.6.0.tar.gz |
| StartedAt: 2018-04-12 02:29:18 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 02:35:06 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 348.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: dada2.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings dada2_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/dada2.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.6.0’
* 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 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
bcinstall: no visible global function definition for ‘biocLite’
makeSpeciesFasta_Silva: no visible global function definition for
‘readRNAStringSet’
makeTaxonomyFasta_RDP: no visible global function definition for
‘read.table’
makeTaxonomyFasta_Silva: no visible global function definition for
‘read.table’
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 ‘label’
plotQualityProfile: no visible binding for global variable ‘minScore’
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 biocLite indel label minScore
mismatch n0F n0R prefer read.table readRNAStringSet seqF seqR
Consider adding
importFrom("utils", "read.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 ... 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 6.05 0.152 5.468
* 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: 5 NOTEs
See
‘/Users/biocbuild/bbs-3.6-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 -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/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppParallel/include" -I/usr/local/include -fPIC -Wall -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 -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 error.o evaluate.o filter.o kmers.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-3.6-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
| name | user | system | elapsed | |
| addSpecies | 1.684 | 0.043 | 1.750 | |
| assignSpecies | 0.367 | 0.002 | 0.374 | |
| assignTaxonomy | 0.304 | 0.003 | 0.308 | |
| collapseNoMismatch | 1.551 | 0.068 | 1.644 | |
| dada | 2.048 | 0.053 | 2.141 | |
| dada_to_seq_table | 0.871 | 0.029 | 0.897 | |
| derepFastq | 0.799 | 0.091 | 0.737 | |
| evaluate_kmers | 0.133 | 0.010 | 0.145 | |
| fastqFilter | 0.605 | 0.019 | 0.634 | |
| fastqPairedFilter | 1.164 | 0.057 | 1.251 | |
| filterAndTrim | 0.811 | 0.041 | 0.874 | |
| getDadaOpt | 0.001 | 0.001 | 0.001 | |
| getErrors | 0.791 | 0.027 | 0.855 | |
| getSequences | 0.466 | 0.028 | 0.516 | |
| getUniques | 0.507 | 0.025 | 0.546 | |
| inflateErr | 0.017 | 0.000 | 0.016 | |
| isBimera | 0.053 | 0.008 | 0.064 | |
| isBimeraDenovo | 1.510 | 0.031 | 1.558 | |
| isBimeraDenovoTable | 2.592 | 0.043 | 2.707 | |
| isPhiX | 0.160 | 0.025 | 0.185 | |
| isShiftDenovo | 0.774 | 0.014 | 0.801 | |
| learnErrors | 6.050 | 0.152 | 5.468 | |
| loessErrfun | 0.333 | 0.008 | 0.348 | |
| makeSequenceTable | 0.677 | 0.032 | 0.747 | |
| mergePairs | 1.754 | 0.043 | 1.841 | |
| mergePairsByID | 4.017 | 0.155 | 3.875 | |
| mergeSequenceTables | 0.001 | 0.000 | 0.001 | |
| noqualErrfun | 1.522 | 0.065 | 1.470 | |
| nwalign | 0.001 | 0.000 | 0.001 | |
| nwhamming | 0.001 | 0.000 | 0.002 | |
| plotComplementarySubstitutions | 4.370 | 0.035 | 4.459 | |
| plotErrors | 4.362 | 0.032 | 4.481 | |
| plotQualityProfile | 1.332 | 0.045 | 1.411 | |
| removeBimeraDenovo | 1.977 | 0.028 | 2.029 | |
| setDadaOpt | 0.014 | 0.001 | 0.014 | |
| uniquesToFasta | 0.455 | 0.016 | 0.477 | |