Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:28 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the ASEB package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ASEB.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 90/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ASEB 1.36.0 (landing page) Likun Wang
| nebbiolo1 | Linux (Ubuntu 20.04.2 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: ASEB |
Version: 1.36.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ASEB.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ASEB_1.36.0.tar.gz |
StartedAt: 2021-10-14 16:21:31 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 16:22:07 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 35.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ASEB.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ASEB.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ASEB_1.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/ASEB.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ASEB/DESCRIPTION’ ... OK * this is package ‘ASEB’ version ‘1.36.0’ * 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: .git_fetch_output.txt .git_merge_output.txt 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 ‘ASEB’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘methods’ A package should be listed in only one of these fields. * 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 ... NOTE SequenceInfo: no visible global function definition for ‘new’ drawEScurve,data.frame: no visible global function definition for ‘pdf’ drawEScurve,data.frame: no visible global function definition for ‘jpeg’ drawEScurve,data.frame: no visible global function definition for ‘lines’ drawEScurve,data.frame: no visible global function definition for ‘rgb’ drawEScurve,data.frame: no visible global function definition for ‘dev.off’ drawStat,data.frame: no visible global function definition for ‘pdf’ drawStat,data.frame: no visible global function definition for ‘jpeg’ drawStat,data.frame: no visible global function definition for ‘lines’ drawStat,data.frame: no visible global function definition for ‘dev.off’ ids,SequenceInfo: no visible global function definition for ‘slot’ ids<-,SequenceInfo-character: no visible global function definition for ‘slot<-’ sequences,SequenceInfo: no visible global function definition for ‘slot’ sequences<-,SequenceInfo-character: no visible global function definition for ‘slot<-’ show,SequenceInfo: no visible global function definition for ‘show’ Undefined global functions or variables: dev.off jpeg lines new pdf rgb show slot slot<- Consider adding importFrom("grDevices", "dev.off", "jpeg", "pdf", "rgb") importFrom("graphics", "lines") importFrom("methods", "new", "show", "slot", "slot<-") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/ASEB/libs/ASEB.so’: Found ‘_rand’, possibly from ‘rand’ (C) Found ‘_srand’, possibly from ‘srand’ (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... 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: 4 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/ASEB.Rcheck/00check.log’ for details.
ASEB.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ASEB ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘ASEB’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c asebC.cpp -o asebC.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -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 ASEB.so asebC.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-ASEB/00new/ASEB/libs ** R ** 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 (ASEB)
ASEB.Rcheck/ASEB-Ex.timings
name | user | system | elapsed | |
SequenceInfo | 0.001 | 0.000 | 0.002 | |
asebProteins | 1.846 | 0.018 | 1.866 | |
asebSites | 1.334 | 0.010 | 1.346 | |
drawEScurve | 1.620 | 0.030 | 1.655 | |
drawStat | 2.004 | 0.017 | 2.026 | |
readSequence | 0.947 | 0.002 | 0.951 | |