Benjamin Callahan
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/dada2 |
| Branch: master |
| Last Commit: da23f49 |
| Last Changed Date: 2019-10-29 13:40:31 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:44:30 -0500 (Thu, 16 Jan 2020).
| Package 401/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| dada2 1.15.0 Benjamin Callahan
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: dada2 |
| Version: 1.15.0 |
| 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_1.15.0.tar.gz |
| StartedAt: 2020-01-16 03:28:27 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 03:35:12 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 404.4 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 --install=check:dada2.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings dada2_1.15.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/dada2.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.15.0’
* 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 ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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
plotComplexity: no visible binding for global variable ‘complexity’
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’
removePrimers : <anonymous>: no visible global function definition for
‘matchPattern’
Undefined global functions or variables:
Count Cum Cycle Estimated Input Mean Nominal Observed Q25 Q50 Q75
Qual Score complexity matchPattern
* 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 use of PKG_*FLAGS in Makefiles ... NOTE
PKG_CFLAGS set in ‘src/Makevars.win’ without any corresponding files
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
learnErrors 6.264 0.399 5.786
PacBioErrfun 5.537 0.161 5.702
mergePairs 4.823 0.333 5.154
* 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: 8 NOTEs
See
‘/Users/biocbuild/bbs-3.11-bioc/meat/dada2.Rcheck/00check.log’
for details.
dada2.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL dada2
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘dada2’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/4.0/Resources/library/00LOCK-dada2/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (dada2)
dada2.Rcheck/dada2-Ex.timings
| name | user | system | elapsed | |
| PacBioErrfun | 5.537 | 0.161 | 5.702 | |
| addSpecies | 3.406 | 0.042 | 3.456 | |
| assignSpecies | 1.494 | 0.005 | 1.500 | |
| assignTaxonomy | 0.440 | 0.045 | 0.433 | |
| collapseNoMismatch | 0.927 | 0.062 | 0.992 | |
| dada | 3.792 | 0.163 | 3.954 | |
| derepFastq | 1.353 | 0.179 | 1.531 | |
| fastqFilter | 0.749 | 0.025 | 0.775 | |
| fastqPairedFilter | 1.132 | 0.052 | 1.186 | |
| filterAndTrim | 1.291 | 0.050 | 1.342 | |
| getDadaOpt | 0.001 | 0.001 | 0.002 | |
| getErrors | 1.316 | 0.066 | 1.381 | |
| getSequences | 1.132 | 0.032 | 1.165 | |
| getUniques | 0.387 | 0.021 | 0.408 | |
| inflateErr | 0.001 | 0.001 | 0.001 | |
| isBimera | 0.118 | 0.028 | 0.146 | |
| isBimeraDenovo | 2.703 | 0.064 | 2.768 | |
| isBimeraDenovoTable | 2.991 | 0.104 | 3.094 | |
| isPhiX | 0.281 | 0.018 | 0.300 | |
| isShiftDenovo | 1.330 | 0.018 | 1.349 | |
| learnErrors | 6.264 | 0.399 | 5.786 | |
| loessErrfun | 0.415 | 0.010 | 0.425 | |
| makeSequenceTable | 0.812 | 0.051 | 0.863 | |
| mergePairs | 4.823 | 0.333 | 5.154 | |
| mergeSequenceTables | 0.000 | 0.001 | 0.001 | |
| noqualErrfun | 0.914 | 0.025 | 0.939 | |
| nwalign | 0.002 | 0.001 | 0.002 | |
| nwhamming | 0.001 | 0.001 | 0.002 | |
| plotComplexity | 1.403 | 0.043 | 1.447 | |
| plotErrors | 3.284 | 0.204 | 3.490 | |
| plotQualityProfile | 2.821 | 0.139 | 2.963 | |
| rc | 0.040 | 0.004 | 0.044 | |
| removeBimeraDenovo | 2.879 | 0.049 | 2.928 | |
| removePrimers | 0.382 | 0.003 | 0.386 | |
| seqComplexity | 0.056 | 0.001 | 0.057 | |
| setDadaOpt | 0.002 | 0.001 | 0.002 | |
| uniquesToFasta | 0.139 | 0.012 | 0.151 | |