Back to Multiple platform build/check report for BioC 3.17 |
|
This page was generated on 2023-04-12 10:55:24 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
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 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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
Package 585/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DriverNet 1.39.0 (landing page) Jiarui Ding
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
Package: DriverNet |
Version: 1.39.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:DriverNet.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings DriverNet_1.39.0.tar.gz |
StartedAt: 2023-04-11 20:01:38 -0400 (Tue, 11 Apr 2023) |
EndedAt: 2023-04-11 20:04:04 -0400 (Tue, 11 Apr 2023) |
EllapsedTime: 145.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: DriverNet.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:DriverNet.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings DriverNet_1.39.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/DriverNet.Rcheck’ * using R version 4.3.0 alpha (2023-04-03 r84154) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.2 LTS * using session charset: UTF-8 * checking for file ‘DriverNet/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DriverNet’ version ‘1.39.0’ * 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 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: ‘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 ... 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 DriverNet-package 30.129 0.076 30.205 computeDrivers 18.201 0.036 18.238 computeRandomizedResult 13.615 0.024 13.639 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘DriverNet-Overview.Rnw’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/DriverNet.Rcheck/00check.log’ for details.
DriverNet.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL DriverNet ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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 | 30.129 | 0.076 | 30.205 | |
DriverNetResult-class | 0.005 | 0.004 | 0.010 | |
actualEvents | 0.009 | 0.075 | 0.085 | |
computeDrivers | 18.201 | 0.036 | 18.238 | |
computeRandomizedResult | 13.615 | 0.024 | 13.639 | |
drivers | 0.020 | 0.071 | 0.093 | |
getPatientOutlierMatrix | 0.142 | 0.001 | 0.142 | |
preprocessMatrices | 0.214 | 0.000 | 0.213 | |
resultSummary | 0.271 | 0.000 | 0.271 | |
sampleDriversList | 0.01 | 0.00 | 0.01 | |
sampleGeneNames | 0.023 | 0.000 | 0.022 | |
sampleInfluenceGraph | 0.200 | 0.000 | 0.201 | |
samplePatientExpressionMatrix | 0.077 | 0.000 | 0.076 | |
samplePatientMutationMatrix | 0.009 | 0.000 | 0.010 | |
samplePatientOutlierMatrix | 0.011 | 0.000 | 0.011 | |
sampleRandomDriversResult | 0.002 | 0.000 | 0.002 | |
totalEvents | 0.009 | 0.000 | 0.010 | |