Back to Multiple platform build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-10-16 11:37:10 -0400 (Mon, 16 Oct 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
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 1038/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
IVAS 2.20.0 (landing page) Seonggyun Han
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the IVAS package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/IVAS.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: IVAS |
Version: 2.20.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:IVAS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings IVAS_2.20.0.tar.gz |
StartedAt: 2023-10-16 03:05:41 -0400 (Mon, 16 Oct 2023) |
EndedAt: 2023-10-16 03:18:36 -0400 (Mon, 16 Oct 2023) |
EllapsedTime: 774.9 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: IVAS.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:IVAS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings IVAS_2.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/IVAS.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.3 (clang-1403.0.22.14.1) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘IVAS/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘IVAS’ version ‘2.20.0’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘IVAS’ can be installed ... WARNING Found the following significant warnings: Note: next used in wrong context: no loop is visible See ‘/Users/biocbuild/bbs-3.17-bioc/meat/IVAS.Rcheck/00install.out’ for details. Information on the location(s) of code generating the ‘Note’s can be obtained by re-running with environment variable R_KEEP_PKG_SOURCE set to ‘yes’. * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed ASdb-class 24.221 0.435 33.764 saveBplot 24.100 0.223 33.890 sQTLsFinder 22.473 0.149 31.173 RatioFromFPKM 12.375 0.084 16.698 CalSigSNP 9.836 0.106 13.366 Splicingfinder 7.738 0.048 10.538 * 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: 1 WARNING See ‘/Users/biocbuild/bbs-3.17-bioc/meat/IVAS.Rcheck/00check.log’ for details.
IVAS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL IVAS ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’ * installing *source* package ‘IVAS’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Note: next used in wrong context: no loop is visible ** 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 (IVAS)
IVAS.Rcheck/IVAS-Ex.timings
name | user | system | elapsed | |
ASdb-class | 24.221 | 0.435 | 33.764 | |
CalSigSNP | 9.836 | 0.106 | 13.366 | |
RatioFromFPKM | 12.375 | 0.084 | 16.698 | |
Splicingfinder | 7.738 | 0.048 | 10.538 | |
chrseparate | 0.202 | 0.005 | 0.277 | |
findAlternative | 1.228 | 0.018 | 1.670 | |
findOversnp | 1.214 | 0.024 | 1.670 | |
sQTLsFinder | 22.473 | 0.149 | 31.173 | |
sampleexp | 0.006 | 0.003 | 0.010 | |
samplesnp | 0.004 | 0.004 | 0.008 | |
samplesnplocus | 0.002 | 0.004 | 0.006 | |
saveBplot | 24.100 | 0.223 | 33.890 | |