Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:06:04 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
To the developers/maintainers of the dada2 package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/dada2.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 471/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
dada2 1.26.0 (landing page) Benjamin Callahan
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
Package: dada2 |
Version: 1.26.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:dada2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings dada2_1.26.0.tar.gz |
StartedAt: 2023-04-10 19:43:58 -0400 (Mon, 10 Apr 2023) |
EndedAt: 2023-04-10 19:47:33 -0400 (Mon, 10 Apr 2023) |
EllapsedTime: 215.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: dada2.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:dada2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings dada2_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/dada2.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-apple-darwin17.0 (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 ‘1.26.0’ * 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. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘C_isACGT’ ‘matchGenera’ * 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 tax.check: warning in assignTaxonomy(sq.test, fn.tax, multi = TRUE): partial argument match of 'multi' to 'multithread' 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’ tax.check: no visible binding for global variable ‘fn.spc’ Undefined global functions or variables: Count Cum Cycle Estimated Input Mean Nominal Observed Q25 Q50 Q75 Qual Score complexity fn.spc * 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 LazyData ... 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 3.109 3.511 2.563 * 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-3.16-bioc/meat/dada2.Rcheck/00check.log’ for details.
dada2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL dada2 ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’ * installing *source* package ‘dada2’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/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++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c Rmain.cpp -o Rmain.o Rmain.cpp:83:8: warning: unused variable 'HW_SSE2' [-Wunused-variable] bool HW_SSE2 = false; ^ Rmain.cpp:84:8: warning: unused variable 'HW_SSE3' [-Wunused-variable] bool HW_SSE3 = false; ^ Rmain.cpp:82:8: warning: unused variable 'HW_SSE' [-Wunused-variable] bool HW_SSE = false; ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c chimera.cpp -o chimera.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c cluster.cpp -o cluster.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c containers.cpp -o containers.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c error.cpp -o error.o error.cpp:178:51: warning: variable 'ncol' set but not used [-Wunused-but-set-variable] unsigned int i, pos, pos1, qind, j, r, s, nti0, ncol; ^ 1 warning generated. clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c evaluate.cpp -o evaluate.o 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; ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c filter.cpp -o filter.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c kmers.cpp -o kmers.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c misc.cpp -o misc.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c nwalign_endsfree.cpp -o nwalign_endsfree.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c nwalign_vectorized.cpp -o nwalign_vectorized.o nwalign_vectorized.cpp:75:21: warning: variable 'end_col' set but not used [-Wunused-but-set-variable] size_t start_col, end_col; ^ 1 warning generated. clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c pval.cpp -o pval.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c taxonomy.cpp -o taxonomy.o taxonomy.cpp:145:31: warning: variable 'boot_match' set but not used [-Wunused-but-set-variable] unsigned int boot, booti, boot_match, arraylen, arraylen_rc; ^ 1 warning generated. clang++ -mmacosx-version-min=10.13 -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/4.2/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 | 3.413 | 0.200 | 3.628 | |
addSpecies | 2.516 | 0.041 | 2.563 | |
assignSpecies | 1.219 | 0.003 | 1.222 | |
assignTaxonomy | 0.168 | 0.048 | 0.198 | |
collapseNoMismatch | 0.420 | 0.024 | 0.447 | |
dada | 2.072 | 0.050 | 2.126 | |
derepFastq | 0.681 | 0.046 | 0.728 | |
fastqFilter | 0.387 | 0.014 | 0.403 | |
fastqPairedFilter | 0.575 | 0.033 | 0.610 | |
filterAndTrim | 0.699 | 0.025 | 0.725 | |
getDadaOpt | 0.000 | 0.001 | 0.001 | |
getErrors | 0.666 | 0.027 | 0.697 | |
getSequences | 0.193 | 0.009 | 0.203 | |
getUniques | 0.196 | 0.006 | 0.203 | |
inflateErr | 0 | 0 | 0 | |
isBimera | 0.062 | 0.009 | 0.072 | |
isBimeraDenovo | 1.848 | 0.031 | 1.884 | |
isBimeraDenovoTable | 1.450 | 0.051 | 1.511 | |
isPhiX | 0.149 | 0.015 | 0.167 | |
isShiftDenovo | 0.656 | 0.025 | 0.684 | |
learnErrors | 3.109 | 3.511 | 2.563 | |
loessErrfun | 0.208 | 0.009 | 0.216 | |
makeSequenceTable | 0.377 | 0.028 | 0.407 | |
mergePairs | 2.896 | 0.143 | 3.047 | |
mergeSequenceTables | 0 | 0 | 0 | |
noqualErrfun | 0.378 | 0.011 | 0.389 | |
nwalign | 0.000 | 0.000 | 0.001 | |
nwhamming | 0.000 | 0.000 | 0.001 | |
plotComplexity | 0.239 | 0.015 | 0.255 | |
plotErrors | 1.546 | 0.032 | 1.581 | |
plotQualityProfile | 2.069 | 0.333 | 2.375 | |
rc | 0.017 | 0.003 | 0.020 | |
removeBimeraDenovo | 2.019 | 0.122 | 2.144 | |
removePrimers | 0.188 | 0.008 | 0.196 | |
seqComplexity | 0.017 | 0.000 | 0.017 | |
setDadaOpt | 0.000 | 0.000 | 0.001 | |
uniquesToFasta | 0.080 | 0.009 | 0.091 | |