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 1088/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
KnowSeq 1.20.0 (landing page) Daniel Castillo-Secilla
| 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 KnowSeq package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/KnowSeq.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: KnowSeq |
Version: 1.20.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:KnowSeq.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings KnowSeq_1.20.0.tar.gz |
StartedAt: 2024-12-20 01:46:03 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 01:55:51 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 587.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: KnowSeq.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:KnowSeq.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings KnowSeq_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/KnowSeq.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 ‘KnowSeq/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘KnowSeq’ version ‘1.20.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘KnowSeq’ can be installed ... OK * checking installed package size ... NOTE installed size is 7.3Mb sub-directories of 1Mb or more: extdata 6.9Mb * 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 DEGsExtraction: warning in topTable(fit, number = number, coef = 2, sort.by = "logFC", p.value = pvalue, adjust = "fdr", lfc = lfc): partial argument match of 'adjust' to 'adjust.method' RNAseqQA : outlierBarPlot: no visible binding for global variable ‘x’ RNAseqQA : outlierBarPlot: no visible binding for global variable ‘y’ RNAseqQA: no visible binding for global variable ‘Var1’ RNAseqQA: no visible binding for global variable ‘Var2’ RNAseqQA: no visible binding for global variable ‘value’ RNAseqQA: no visible binding for global variable ‘Expression’ RNAseqQA: no visible binding for global variable ‘Samples’ dataPlot: no visible binding for global variable ‘Var1’ dataPlot: no visible binding for global variable ‘Var2’ dataPlot: no visible binding for global variable ‘value’ dataPlot: no visible binding for global variable ‘Classes’ dataPlot: no visible binding for global variable ‘Value’ knn_trn: no visible global function definition for ‘knn.cv’ knowseqReport: no visible binding for global variable ‘target’ Undefined global functions or variables: Classes Expression Samples Value Var1 Var2 knn.cv target value x y * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed dataPlot 16.371 0.247 16.581 rf_trn 13.357 0.170 13.527 svm_trn 12.666 0.085 12.752 svm_test 11.802 0.046 11.848 downloadPublicSeries 0.913 0.067 43.765 * 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/KnowSeq.Rcheck/00check.log’ for details.
KnowSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL KnowSeq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘KnowSeq’ ... ** using staged installation ** R ** 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 (KnowSeq)
KnowSeq.Rcheck/KnowSeq-Ex.timings
name | user | system | elapsed | |
DEGsEvidences | 0.292 | 0.017 | 0.921 | |
DEGsExtraction | 1.103 | 0.081 | 1.185 | |
DEGsToDiseases | 0.155 | 0.002 | 0.330 | |
DEGsToPathways | 0.291 | 0.010 | 0.301 | |
RNAseqQA | 1.573 | 0.093 | 1.654 | |
batchEffectRemoval | 2.091 | 0.057 | 2.148 | |
calculateGeneExpressionValues | 0.451 | 0.001 | 0.452 | |
countsToMatrix | 0.042 | 0.001 | 0.044 | |
dataPlot | 16.371 | 0.247 | 16.581 | |
downloadPublicSeries | 0.913 | 0.067 | 43.765 | |
featureSelection | 0.018 | 0.001 | 0.015 | |
fileMove | 0 | 0 | 0 | |
gdcClientDownload | 0 | 0 | 0 | |
geneOntologyEnrichment | 0 | 0 | 0 | |
getGenesAnnotation | 0.198 | 0.001 | 0.196 | |
hisatAlignment | 0.001 | 0.000 | 0.001 | |
knn_test | 0.04 | 0.00 | 0.04 | |
knn_trn | 1.232 | 0.002 | 1.233 | |
knowseqReport | 0.006 | 0.000 | 0.005 | |
plotConfMatrix | 0.015 | 0.001 | 0.016 | |
rawAlignment | 0.001 | 0.000 | 0.002 | |
rf_test | 3.545 | 0.027 | 3.572 | |
rf_trn | 13.357 | 0.170 | 13.527 | |
sraToFastq | 0 | 0 | 0 | |
svm_test | 11.802 | 0.046 | 11.848 | |
svm_trn | 12.666 | 0.085 | 12.752 | |