| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-31 05:44:32 -0000 (Wed, 31 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4219 |
| 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: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 480/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| dada2 1.29.0 (landing page) Benjamin Callahan
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: dada2 |
| Version: 1.29.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:dada2.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings dada2_1.29.0.tar.gz |
| StartedAt: 2023-05-30 05:01:10 -0000 (Tue, 30 May 2023) |
| EndedAt: 2023-05-30 05:07:24 -0000 (Tue, 30 May 2023) |
| EllapsedTime: 373.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: dada2.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:dada2.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings dada2_1.29.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/dada2.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘dada2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dada2’ version ‘1.29.0’
* 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
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
installed size is 10.2Mb
sub-directories of 1Mb or more:
extdata 2.1Mb
libs 7.3Mb
* 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 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.
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
PacBioErrfun 8.982 0.120 9.104
learnErrors 7.135 0.347 5.933
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘dada2-intro.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 10 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/dada2.Rcheck/00check.log’
for details.
dada2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL dada2 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘dada2’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RcppParallel/include' -I/usr/local/include -fPIC -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RcppParallel/include' -I/usr/local/include -fPIC -g -O2 -c Rmain.cpp -o Rmain.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RcppParallel/include' -I/usr/local/include -fPIC -g -O2 -c chimera.cpp -o chimera.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RcppParallel/include' -I/usr/local/include -fPIC -g -O2 -c cluster.cpp -o cluster.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RcppParallel/include' -I/usr/local/include -fPIC -g -O2 -c containers.cpp -o containers.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RcppParallel/include' -I/usr/local/include -fPIC -g -O2 -c error.cpp -o error.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RcppParallel/include' -I/usr/local/include -fPIC -g -O2 -c evaluate.cpp -o evaluate.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RcppParallel/include' -I/usr/local/include -fPIC -g -O2 -c filter.cpp -o filter.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RcppParallel/include' -I/usr/local/include -fPIC -g -O2 -c kmers.cpp -o kmers.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RcppParallel/include' -I/usr/local/include -fPIC -g -O2 -c misc.cpp -o misc.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RcppParallel/include' -I/usr/local/include -fPIC -g -O2 -c nwalign_endsfree.cpp -o nwalign_endsfree.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RcppParallel/include' -I/usr/local/include -fPIC -g -O2 -c nwalign_vectorized.cpp -o nwalign_vectorized.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RcppParallel/include' -I/usr/local/include -fPIC -g -O2 -c pval.cpp -o pval.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/RcppParallel/include' -I/usr/local/include -fPIC -g -O2 -c taxonomy.cpp -o taxonomy.o g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.3.0/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 -L/home/biocbuild/R/R-4.3.0/lib -lR installing to /home/biocbuild/R/R-4.3.0/site-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 | 8.982 | 0.120 | 9.104 | |
| addSpecies | 3.544 | 0.195 | 3.742 | |
| assignSpecies | 1.665 | 0.001 | 1.664 | |
| assignTaxonomy | 0.330 | 0.024 | 0.344 | |
| collapseNoMismatch | 0.927 | 0.012 | 0.942 | |
| dada | 4.748 | 0.076 | 4.825 | |
| derepFastq | 1.020 | 0.036 | 1.056 | |
| fastqFilter | 0.603 | 0.008 | 0.611 | |
| fastqPairedFilter | 0.987 | 0.024 | 1.012 | |
| filterAndTrim | 1.067 | 0.008 | 1.075 | |
| getDadaOpt | 0 | 0 | 0 | |
| getErrors | 1.568 | 0.031 | 1.601 | |
| getSequences | 0.492 | 0.009 | 0.500 | |
| getUniques | 0.476 | 0.004 | 0.480 | |
| inflateErr | 0.001 | 0.000 | 0.000 | |
| isBimera | 0.939 | 0.044 | 0.982 | |
| isBimeraDenovo | 3.218 | 0.035 | 3.254 | |
| isBimeraDenovoTable | 3.643 | 0.020 | 3.663 | |
| isPhiX | 0.248 | 0.016 | 0.264 | |
| isShiftDenovo | 1.599 | 0.003 | 1.604 | |
| learnErrors | 7.135 | 0.347 | 5.933 | |
| loessErrfun | 0.511 | 0.011 | 0.523 | |
| makeSequenceTable | 0.917 | 0.012 | 0.930 | |
| mergePairs | 4.628 | 0.044 | 4.672 | |
| mergeSequenceTables | 0.001 | 0.000 | 0.000 | |
| noqualErrfun | 1.131 | 0.004 | 1.135 | |
| nwalign | 0.001 | 0.000 | 0.001 | |
| nwhamming | 0.001 | 0.000 | 0.001 | |
| plotComplexity | 1.217 | 0.080 | 1.297 | |
| plotErrors | 2.670 | 0.032 | 2.703 | |
| plotQualityProfile | 4.346 | 0.436 | 4.722 | |
| rc | 0.015 | 0.012 | 0.027 | |
| removeBimeraDenovo | 3.343 | 0.428 | 3.771 | |
| removePrimers | 0.296 | 0.004 | 0.303 | |
| seqComplexity | 0.031 | 0.000 | 0.032 | |
| setDadaOpt | 0.001 | 0.000 | 0.001 | |
| uniquesToFasta | 0.097 | 0.008 | 0.105 | |