Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 1043/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
IntEREst 1.30.0 (landing page) Ali Oghabian
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the IntEREst package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/IntEREst.git to reflect on this report. See Troubleshooting Build Report for more information. - 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: IntEREst |
Version: 1.30.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:IntEREst.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings IntEREst_1.30.0.tar.gz |
StartedAt: 2024-11-19 23:14:55 -0500 (Tue, 19 Nov 2024) |
EndedAt: 2024-11-19 23:23:43 -0500 (Tue, 19 Nov 2024) |
EllapsedTime: 528.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: IntEREst.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:IntEREst.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings IntEREst_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/IntEREst.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-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 Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘IntEREst/DESCRIPTION’ ... OK * this is package ‘IntEREst’ version ‘1.30.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' NOTE Depends: includes the non-default packages: 'GenomicRanges', 'Rsamtools', 'SummarizedExperiment', 'edgeR', 'S4Vectors', 'GenomicFiles' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 ‘IntEREst’ 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 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 interestIntExAnalyseSingleStranded: no visible global function definition for ‘bamFlagAsBitMatrix’ Undefined global functions or variables: bamFlagAsBitMatrix * checking Rd files ... NOTE checkRd: (-1) interest.Rd:105: Lost braces; missing escapes or markup? 105 | regions to a different region defined in {limitRanges}. It is useful to ignore | ^ checkRd: (-1) interest.sequential.Rd:103: Lost braces; missing escapes or markup? 103 | regions to a different region defined in {limitRanges}. It is useful to ignore | ^ * 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 DEXSeqIntEREst 18.127 0.199 18.397 * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/IntEREst.Rcheck/00check.log’ for details.
IntEREst.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL IntEREst ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘IntEREst’ ... ** 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 (IntEREst)
IntEREst.Rcheck/IntEREst-Ex.timings
name | user | system | elapsed | |
DEXSeqIntEREst | 18.127 | 0.199 | 18.397 | |
addAnnotation | 0.025 | 0.001 | 0.026 | |
annotateU12 | 1.636 | 0.066 | 1.711 | |
applyOverlap | 0.124 | 0.001 | 0.126 | |
attributes | 0.018 | 0.002 | 0.020 | |
boxplot-method | 0.037 | 0.001 | 0.038 | |
buildSsTypePwms | 0.000 | 0.001 | 0.000 | |
counts-method | 0.021 | 0.002 | 0.023 | |
deseqInterest | 3.148 | 0.012 | 3.168 | |
exactTestInterest | 0.067 | 0.002 | 0.070 | |
getRepeatTable | 0 | 0 | 0 | |
glmInterest | 0.074 | 0.001 | 0.076 | |
interest | 1.044 | 0.016 | 1.065 | |
interest.sequential | 0.893 | 0.011 | 0.907 | |
interestResult | 0.013 | 0.000 | 0.013 | |
interestResultIntEx | 0.121 | 0.001 | 0.123 | |
intexIndex | 0.002 | 0.000 | 0.002 | |
lfc | 0.154 | 0.004 | 0.158 | |
mergeInterestResult | 0.052 | 0.001 | 0.054 | |
plot-method | 0.234 | 0.005 | 0.240 | |
psi | 0.524 | 0.008 | 0.533 | |
qlfInterest | 0.095 | 0.004 | 0.100 | |
readInterestResults | 0.023 | 0.003 | 0.026 | |
referencePrepare | 0.827 | 0.016 | 0.847 | |
subInterestResult | 0.025 | 0.001 | 0.025 | |
treatInterest | 0.073 | 0.002 | 0.075 | |
u12Boxplot | 0.044 | 0.001 | 0.044 | |
u12BoxplotNb | 0.052 | 0.000 | 0.052 | |
u12DensityPlot | 0.185 | 0.006 | 0.193 | |
u12Index | 0.004 | 0.000 | 0.004 | |
u12NbIndex | 0.031 | 0.001 | 0.033 | |
unionRefTr | 0.011 | 0.000 | 0.011 | |
updateRowDataCol | 0.036 | 0.001 | 0.037 | |