Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:43 -0000 (Wed, 01 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
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To the developers/maintainers of the KnowSeq package: - Please 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 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 1018/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
KnowSeq 1.13.0 (landing page) Daniel Castillo-Secilla
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
Package: KnowSeq |
Version: 1.13.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:KnowSeq.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings KnowSeq_1.13.0.tar.gz |
StartedAt: 2023-02-28 06:50:37 -0000 (Tue, 28 Feb 2023) |
EndedAt: 2023-02-28 07:00:33 -0000 (Tue, 28 Feb 2023) |
EllapsedTime: 595.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: KnowSeq.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:KnowSeq.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings KnowSeq_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/KnowSeq.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-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 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘KnowSeq/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘KnowSeq’ version ‘1.13.0’ * package encoding: UTF-8 * 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 ‘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 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 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 29.880 0.531 30.365 svm_trn 22.356 0.196 22.553 svm_test 20.377 0.236 20.614 rf_trn 19.837 0.308 20.145 rf_test 5.310 0.172 5.482 downloadPublicSeries 0.909 0.151 29.942 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘KnowSeq.Rmd’ using ‘UTF-8’... OK NONE * 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/KnowSeq.Rcheck/00check.log’ for details.
KnowSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL KnowSeq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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 | 0.404 | 0.028 | 1.938 | |
DEGsExtraction | 1.592 | 0.156 | 1.754 | |
DEGsToDiseases | 0.247 | 0.016 | 0.906 | |
DEGsToPathways | 0.329 | 0.012 | 0.342 | |
RNAseqQA | 2.438 | 0.132 | 2.573 | |
batchEffectRemoval | 3.013 | 0.180 | 3.194 | |
calculateGeneExpressionValues | 0.702 | 0.016 | 0.718 | |
countsToMatrix | 0.065 | 0.007 | 0.079 | |
dataPlot | 29.880 | 0.531 | 30.365 | |
downloadPublicSeries | 0.909 | 0.151 | 29.942 | |
featureSelection | 0.017 | 0.000 | 0.013 | |
fileMove | 0 | 0 | 0 | |
gdcClientDownload | 0.000 | 0.001 | 0.000 | |
geneOntologyEnrichment | 0 | 0 | 0 | |
getGenesAnnotation | 0.239 | 0.006 | 0.244 | |
hisatAlignment | 0.002 | 0.000 | 0.005 | |
knn_test | 0.07 | 0.00 | 0.07 | |
knn_trn | 2.291 | 0.196 | 2.490 | |
knowseqReport | 0.004 | 0.004 | 0.008 | |
plotConfMatrix | 0.026 | 0.000 | 0.026 | |
rawAlignment | 0.002 | 0.000 | 0.001 | |
rf_test | 5.310 | 0.172 | 5.482 | |
rf_trn | 19.837 | 0.308 | 20.145 | |
sraToFastq | 0 | 0 | 0 | |
svm_test | 20.377 | 0.236 | 20.614 | |
svm_trn | 22.356 | 0.196 | 22.553 | |