Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-01-28 11:09:00 -0500 (Sat, 28 Jan 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" | 4465 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" | 4246 |
merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" | 4269 |
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 igvR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/igvR.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 945/2162 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
igvR 1.19.0 (landing page) Paul Shannon
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | NA | |||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
Package: igvR |
Version: 1.19.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:igvR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings igvR_1.19.0.tar.gz |
StartedAt: 2023-01-28 02:32:51 -0500 (Sat, 28 Jan 2023) |
EndedAt: 2023-01-28 02:43:17 -0500 (Sat, 28 Jan 2023) |
EllapsedTime: 625.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: igvR.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:igvR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings igvR_1.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/igvR.Rcheck’ * using R Under development (unstable) (2023-01-10 r83596) * using platform: x86_64-apple-darwin17.0 (64-bit) * R was compiled by Apple clang version 12.0.0 (clang-1200.0.32.29) GNU Fortran (GCC) 8.2.0 * running under: macOS Mojave 10.14.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘igvR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘igvR’ version ‘1.19.0’ * 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 ‘igvR’ can be installed ... OK * checking installed package size ... NOTE installed size is 16.7Mb sub-directories of 1Mb or more: browserCode 10.1Mb extdata 6.0Mb * 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 ... WARNING Vignettes with missing or empty \VignetteIndexEntry: v05.ucscTableBrowser.Rmd See sections ‘The INDEX file’ and ‘Package subdirectories’ in the ‘Writing R Extensions’ manual. * 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: ‘BrowserViz:::log’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .writeMotifLogoImagesUpdateTrackNames: no visible binding for global variable ‘MotifDb’ .writeMotifLogoImagesUpdateTrackNames: no visible global function definition for ‘seqLogo’ Undefined global functions or variables: MotifDb seqLogo * 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 include directives in Makefiles ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... WARNING Found ‘inst/doc/makefile’: should be ‘Makefile’ and will be ignored * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 3 NOTEs See ‘/Users/biocbuild/bbs-3.17-bioc/meat/igvR.Rcheck/00check.log’ for details.
igvR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL igvR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/library’ * installing *source* package ‘igvR’ ... ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (igvR)
igvR.Rcheck/igvR-Ex.timings
name | user | system | elapsed | |
BedpeInteractionsTrack-class | 0.024 | 0.003 | 0.031 | |
DataFrameAnnotationTrack-class | 0.025 | 0.003 | 0.044 | |
DataFrameQuantitativeTrack-class | 0.044 | 0.006 | 0.065 | |
GFF3Track-class | 0.026 | 0.003 | 0.039 | |
GRangesAnnotationTrack-class | 0.145 | 0.015 | 0.215 | |
GRangesQuantitativeTrack-class | 0.050 | 0.006 | 0.073 | |
GWASTrack-class | 0.256 | 0.012 | 0.363 | |
GWASUrlTrack-class | 0.006 | 0.001 | 0.011 | |
GenomicAlignmentTrack-class | 0.301 | 0.005 | 0.422 | |
UCSCBedAnnotationTrack-class | 0.712 | 0.020 | 0.991 | |
UCSCBedGraphQuantitativeTrack-class | 0.227 | 0.026 | 0.342 | |
VariantTrack-class | 1.222 | 0.068 | 1.747 | |
displayTrack | 0.002 | 0.000 | 0.002 | |
enableMotifLogoPopups | 0.002 | 0.000 | 0.003 | |
getGenomicRegion | 0.000 | 0.000 | 0.005 | |
getSupportedGenomes | 0.000 | 0.000 | 0.001 | |
getTrackNames | 0 | 0 | 0 | |
igvR-class | 0.002 | 0.000 | 0.002 | |
parseAndValidateGenomeSpec | 0.125 | 0.011 | 0.967 | |
ping | 0.000 | 0.000 | 0.001 | |
removeTracksByName | 0.004 | 0.001 | 0.004 | |
setCustomGenome | 0.002 | 0.001 | 0.002 | |
setGenome | 0.000 | 0.000 | 0.001 | |
showGenomicRegion | 0.001 | 0.000 | 0.001 | |
trackSize-DataFrameAnnotationTrack-method | 0.007 | 0.000 | 0.008 | |
trackSize-UCSCBedAnnotationTrack-method | 0.206 | 0.001 | 0.212 | |
url.exists | 0 | 0 | 0 | |