Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:46 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
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 600/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DriverNet 1.45.0 (landing page) Jiarui Ding
| nebbiolo2 | Linux (Ubuntu 22.04.3 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 | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the DriverNet package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DriverNet.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: DriverNet |
Version: 1.45.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:DriverNet.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings DriverNet_1.45.0.tar.gz |
StartedAt: 2024-08-27 04:28:07 -0000 (Tue, 27 Aug 2024) |
EndedAt: 2024-08-27 04:29:37 -0000 (Tue, 27 Aug 2024) |
EllapsedTime: 90.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: DriverNet.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:DriverNet.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings DriverNet_1.45.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/DriverNet.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘DriverNet/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DriverNet’ version ‘1.45.0’ * 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 ‘DriverNet’ 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Package in Depends field not imported from: ‘methods’ 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 .computeDriversHelper: no visible global function definition for ‘new’ getPatientOutlierMatrix: no visible binding for global variable ‘sd’ getPatientOutlierMatrix: no visible global function definition for ‘dnorm’ resultSummary: no visible global function definition for ‘write.table’ Undefined global functions or variables: dnorm new sd write.table Consider adding importFrom("methods", "new") importFrom("stats", "dnorm", "sd") importFrom("utils", "write.table") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE checkRd: (-1) sampleDriversList.Rd:8: Lost braces 8 | An object of DriverNetResult class that obtained from running the code{computeDrivers} function. | ^ * 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 ... NOTE Argument items with no description in Rd file 'actualEvents.Rd': ‘x’ Argument items with no description in Rd file 'drivers.Rd': ‘x’ Argument items with no description in Rd file 'totalEvents.Rd': ‘x’ * 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 DriverNet-package 33.128 0.060 33.267 computeDrivers 20.432 0.015 20.492 computeRandomizedResult 15.607 0.012 15.651 * 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: 4 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/DriverNet.Rcheck/00check.log’ for details.
DriverNet.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL DriverNet ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘DriverNet’ ... ** using staged installation ** R ** data ** 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 (DriverNet)
DriverNet.Rcheck/DriverNet-Ex.timings
name | user | system | elapsed | |
DriverNet-package | 33.128 | 0.060 | 33.267 | |
DriverNetResult-class | 0.01 | 0.00 | 0.01 | |
actualEvents | 0.024 | 0.008 | 0.032 | |
computeDrivers | 20.432 | 0.015 | 20.492 | |
computeRandomizedResult | 15.607 | 0.012 | 15.651 | |
drivers | 0.025 | 0.008 | 0.034 | |
getPatientOutlierMatrix | 0.195 | 0.008 | 0.203 | |
preprocessMatrices | 0.172 | 0.000 | 0.173 | |
resultSummary | 0.205 | 0.000 | 0.206 | |
sampleDriversList | 0.01 | 0.00 | 0.01 | |
sampleGeneNames | 0.021 | 0.000 | 0.021 | |
sampleInfluenceGraph | 0.140 | 0.000 | 0.139 | |
samplePatientExpressionMatrix | 0.062 | 0.000 | 0.062 | |
samplePatientMutationMatrix | 0.009 | 0.000 | 0.009 | |
samplePatientOutlierMatrix | 0.01 | 0.00 | 0.01 | |
sampleRandomDriversResult | 0.000 | 0.001 | 0.001 | |
totalEvents | 0.008 | 0.002 | 0.010 | |