Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:05:12 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
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 octad package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/octad.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 1374/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
octad 1.0.0 (landing page) E. Chekalin
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
Package: octad |
Version: 1.0.0 |
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:octad.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings octad_1.0.0.tar.gz |
StartedAt: 2023-04-10 22:25:13 -0400 (Mon, 10 Apr 2023) |
EndedAt: 2023-04-10 22:45:23 -0400 (Mon, 10 Apr 2023) |
EllapsedTime: 1210.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: octad.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:octad.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings octad_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/octad.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘octad/DESCRIPTION’ ... OK * this is package ‘octad’ version ‘1.0.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'magrittr', 'dplyr', 'ggplot2', 'edgeR', 'RUVSeq', 'DESeq2', 'limma', 'rhdf5', 'foreach', 'Rfast', 'octad.db', 'httr', 'ExperimentHub', 'AnnotationHub', 'Biobase', 'S4Vectors' 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 ... NOTE Found the following hidden files and directories: .BBSoptions 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 ‘octad’ 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Package in Depends field not imported from: ‘httr’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE diffExp: no visible binding for global variable ‘case’ diffExp: no visible binding for global variable ‘control’ runsRGES: no visible binding for global variable ‘RGES’ topLineEval: no visible binding for global variable ‘sRGES’ topLineEval: no visible binding for global variable ‘medauc’ Undefined global functions or variables: RGES case control medauc sRGES * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed octadDrugEnrichment 75.644 2.854 79.876 topLineEval 51.881 1.908 55.934 computeCellLine 45.907 3.105 53.445 diffExp 26.381 1.419 29.712 loadOctadCounts 16.389 0.745 19.399 computeRefTissue 4.446 0.325 5.482 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘octad.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/home/biocbuild/bbs-3.16-bioc/meat/octad.Rcheck/00check.log’ for details.
octad.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL octad ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’ * installing *source* package ‘octad’ ... ** using staged installation ** R ** data ** 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 (octad)
octad.Rcheck/octad-Ex.timings
name | user | system | elapsed | |
computeCellLine | 45.907 | 3.105 | 53.445 | |
computeRefTissue | 4.446 | 0.325 | 5.482 | |
diffExp | 26.381 | 1.419 | 29.712 | |
loadOctadCounts | 16.389 | 0.745 | 19.399 | |
octadDrugEnrichment | 75.644 | 2.854 | 79.876 | |
runsRGES | 0.373 | 0.030 | 0.403 | |
topLineEval | 51.881 | 1.908 | 55.934 | |