Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:07:43 -0400 (Wed, 13 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
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 brendaDb package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/brendaDb.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 215/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
brendaDb 1.8.0 (landing page) Yi Zhou
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: brendaDb |
Version: 1.8.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:brendaDb.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings brendaDb_1.8.0.tar.gz |
StartedAt: 2022-04-12 11:01:57 -0400 (Tue, 12 Apr 2022) |
EndedAt: 2022-04-12 11:03:54 -0400 (Tue, 12 Apr 2022) |
EllapsedTime: 117.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: brendaDb.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:brendaDb.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings brendaDb_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/brendaDb.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘brendaDb/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘brendaDb’ version ‘1.8.0’ * 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 ... 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 ‘brendaDb’ 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 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 ... OK * 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 compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.14-bioc/meat/brendaDb.Rcheck/00check.log’ for details.
brendaDb.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL brendaDb ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘brendaDb’ ... ** 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/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c read_brenda.cpp -o read_brenda.o 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 brendaDb.so RcppExports.o read_brenda.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-brendaDb/00new/brendaDb/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (brendaDb)
brendaDb.Rcheck/tests/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(brendaDb) > > test_check("brendaDb") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 118 ] > > proc.time() user system elapsed 17.376 1.047 35.523
brendaDb.Rcheck/brendaDb-Ex.timings
name | user | system | elapsed | |
BiocycPathwayEnzymes | 0 | 0 | 0 | |
BiocycPathwayGenes | 0.000 | 0.000 | 0.001 | |
CleanECNumber | 0.244 | 0.009 | 0.254 | |
ConfigBPCores | 0.037 | 0.001 | 0.038 | |
DownloadBrenda | 0.000 | 0.001 | 0.000 | |
ExtractField | 0.507 | 0.155 | 4.643 | |
ID2Enzyme | 0.270 | 0.015 | 0.286 | |
InitBrendaDeprecatedEntry | 4.350 | 0.453 | 0.638 | |
InitBrendaEntry | 0.165 | 0.095 | 0.249 | |
ParseProtein | 0.065 | 0.010 | 0.075 | |
ParseProteinNum | 0.001 | 0.001 | 0.001 | |
ParseRecommendedName | 0.001 | 0.000 | 0.002 | |
ParseReference | 0.021 | 0.003 | 0.024 | |
ParseSystematicName | 0.001 | 0.000 | 0.000 | |
QueryBrenda | 4.116 | 0.405 | 4.380 | |
QueryBrendaBase | 3.812 | 0.163 | 3.977 | |
ReadBrenda | 0.085 | 0.004 | 0.088 | |
SeparateSubentries | 0.001 | 0.000 | 0.001 | |
ShowFields | 0.138 | 0.005 | 0.143 | |