Back to Mac ARM64 build report for BioC 3.20 |
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This page was generated on 2024-05-13 11:32:14 -0400 (Mon, 13 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4378 |
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 |
Package 1927/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
single 1.9.0 (landing page) Rocio Espada
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the single package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: single |
Version: 1.9.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:single.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings single_1.9.0.tar.gz |
StartedAt: 2024-05-13 03:24:32 -0400 (Mon, 13 May 2024) |
EndedAt: 2024-05-13 03:28:18 -0400 (Mon, 13 May 2024) |
EllapsedTime: 226.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: single.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:single.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings single_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/single.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘single/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘single’ version ‘1.9.0’ * package encoding: UTF-8 * 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 ‘single’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE pileup_by_QUAL: no visible binding for global variable ‘count.y’ pileup_by_QUAL: no visible binding for global variable ‘count.x’ pileup_by_QUAL: no visible binding for global variable ‘nucleotide’ pileup_by_QUAL: no visible binding for global variable ‘QUAL’ single_consensus_byBarcode: no visible binding for global variable ‘readID’ single_consensus_byBarcode: no visible binding for global variable ‘bcID’ Undefined global functions or variables: QUAL bcID count.x count.y nucleotide readID * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed single_train 5.101 0.128 5.280 fit_logregr 4.922 0.178 5.119 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/single.Rcheck/00check.log’ for details.
single.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL single ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘single’ ... ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (single)
single.Rcheck/single-Ex.timings
name | user | system | elapsed | |
evaluate_fits | 0.951 | 0.015 | 0.972 | |
fit_logregr | 4.922 | 0.178 | 5.119 | |
glm.predict. | 0.003 | 0.000 | 0.004 | |
list_mismatches | 0.196 | 0.003 | 0.200 | |
p_prior_errors | 3.730 | 0.080 | 3.847 | |
p_prior_mutations | 3.680 | 0.069 | 3.758 | |
pileup_by_QUAL | 3.623 | 0.068 | 3.701 | |
single_consensus_byBarcode | 0.326 | 0.003 | 0.331 | |
single_evaluate | 0.517 | 0.009 | 0.527 | |
single_train | 5.101 | 0.128 | 5.280 | |
weighted_consensus | 0.073 | 0.002 | 0.076 | |