Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1646/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
qvalue 2.38.0 (landing page) John D. Storey
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the qvalue package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/qvalue.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: qvalue |
Version: 2.38.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:qvalue.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings qvalue_2.38.0.tar.gz |
StartedAt: 2024-12-20 04:31:28 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 04:32:09 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 41.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: qvalue.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:qvalue.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings qvalue_2.38.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/qvalue.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘qvalue/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘qvalue’ version ‘2.38.0’ * 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 ‘qvalue’ 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE hist.qvalue: no visible binding for global variable ‘density’ lfdr: no visible global function definition for ‘qnorm’ lfdr: no visible global function definition for ‘density’ lfdr: no visible global function definition for ‘smooth.spline’ lfdr: no visible global function definition for ‘predict’ lfdr: no visible global function definition for ‘dnorm’ pi0est: no visible global function definition for ‘smooth.spline’ pi0est: no visible global function definition for ‘predict’ pi0est: no visible global function definition for ‘quantile’ plot.qvalue: no visible global function definition for ‘quantile’ write.qvalue: no visible global function definition for ‘write.table’ Undefined global functions or variables: density dnorm predict qnorm quantile smooth.spline write.table Consider adding importFrom("stats", "density", "dnorm", "predict", "qnorm", "quantile", "smooth.spline") importFrom("utils", "write.table") to your NAMESPACE file. * 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.20-bioc/meat/qvalue.Rcheck/00check.log’ for details.
qvalue.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL qvalue ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘qvalue’ ... ** 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 (qvalue)
qvalue.Rcheck/qvalue-Ex.timings
name | user | system | elapsed | |
empPvals | 0.078 | 0.019 | 0.098 | |
hedenfalk | 0.993 | 0.039 | 1.032 | |
hist.qvalue | 0.509 | 0.011 | 0.520 | |
lfdr | 0.276 | 0.003 | 0.279 | |
pi0est | 0.742 | 0.005 | 0.748 | |
plot.qvalue | 0.494 | 0.003 | 0.497 | |
qvalue | 0.755 | 0.001 | 0.756 | |
summary.qvalue | 0.024 | 0.000 | 0.024 | |
write.qvalue | 0.036 | 0.000 | 0.036 | |