Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:38 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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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 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. 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 1044/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
KnowSeq 1.13.0 (landing page) Daniel Castillo-Secilla
| 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: 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/site-library --timings KnowSeq_1.13.0.tar.gz |
StartedAt: 2023-04-12 07:03:58 -0400 (Wed, 12 Apr 2023) |
EndedAt: 2023-04-12 07:12:24 -0400 (Wed, 12 Apr 2023) |
EllapsedTime: 505.5 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/site-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) (2023-02-14 r83833) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 * running under: Ubuntu 20.04.6 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 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 22.821 0.352 23.173 rf_trn 20.227 0.304 20.532 svm_trn 20.248 0.032 20.281 svm_test 17.753 0.116 17.870 rf_test 5.481 0.028 5.508 downloadPublicSeries 1.026 0.043 14.342 * 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/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 | 0.355 | 0.008 | 0.896 | |
DEGsExtraction | 1.146 | 0.028 | 1.174 | |
DEGsToDiseases | 0.220 | 0.000 | 0.398 | |
DEGsToPathways | 0.630 | 0.012 | 0.643 | |
RNAseqQA | 2.367 | 0.140 | 2.507 | |
batchEffectRemoval | 4.376 | 0.164 | 4.541 | |
calculateGeneExpressionValues | 0.633 | 0.020 | 0.652 | |
countsToMatrix | 0.059 | 0.004 | 0.064 | |
dataPlot | 22.821 | 0.352 | 23.173 | |
downloadPublicSeries | 1.026 | 0.043 | 14.342 | |
featureSelection | 0.017 | 0.000 | 0.014 | |
fileMove | 0 | 0 | 0 | |
gdcClientDownload | 0 | 0 | 0 | |
geneOntologyEnrichment | 0 | 0 | 0 | |
getGenesAnnotation | 0.287 | 0.000 | 0.282 | |
hisatAlignment | 0.002 | 0.000 | 0.002 | |
knn_test | 0.048 | 0.000 | 0.048 | |
knn_trn | 1.669 | 0.064 | 1.733 | |
knowseqReport | 0.01 | 0.00 | 0.01 | |
plotConfMatrix | 0.025 | 0.000 | 0.025 | |
rawAlignment | 0.003 | 0.000 | 0.002 | |
rf_test | 5.481 | 0.028 | 5.508 | |
rf_trn | 20.227 | 0.304 | 20.532 | |
sraToFastq | 0 | 0 | 0 | |
svm_test | 17.753 | 0.116 | 17.870 | |
svm_trn | 20.248 | 0.032 | 20.281 | |