Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-07-03 10:21 -0400 (Wed, 03 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4480 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4511 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4469 |
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 1097/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
KnowSeq 1.18.0 (landing page) Daniel Castillo-Secilla
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 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: 1.18.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:KnowSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings KnowSeq_1.18.0.tar.gz |
StartedAt: 2024-07-01 06:42:23 -0400 (Mon, 01 Jul 2024) |
EndedAt: 2024-07-01 06:54:23 -0400 (Mon, 01 Jul 2024) |
EllapsedTime: 719.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: KnowSeq.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:KnowSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings KnowSeq_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/KnowSeq.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘KnowSeq/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘KnowSeq’ version ‘1.18.0’ * 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 7.2Mb 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 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 57.269 0.505 67.808 svm_trn 38.693 0.476 44.248 svm_test 34.552 0.336 39.212 rf_trn 32.422 0.519 38.431 rf_test 9.531 0.173 11.619 RNAseqQA 4.550 0.216 5.796 downloadPublicSeries 1.398 0.123 26.003 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/KnowSeq.Rcheck/00check.log’ for details.
KnowSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL KnowSeq ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 | 1.164 | 0.039 | 1.876 | |
DEGsExtraction | 1.239 | 0.049 | 1.528 | |
DEGsToDiseases | 0.369 | 0.012 | 0.631 | |
DEGsToPathways | 0.614 | 0.021 | 0.732 | |
RNAseqQA | 4.550 | 0.216 | 5.796 | |
batchEffectRemoval | 3.095 | 0.032 | 3.856 | |
calculateGeneExpressionValues | 1.109 | 0.028 | 1.507 | |
countsToMatrix | 0.116 | 0.011 | 0.153 | |
dataPlot | 57.269 | 0.505 | 67.808 | |
downloadPublicSeries | 1.398 | 0.123 | 26.003 | |
featureSelection | 0.020 | 0.008 | 0.029 | |
fileMove | 0.000 | 0.000 | 0.001 | |
gdcClientDownload | 0.001 | 0.000 | 0.000 | |
geneOntologyEnrichment | 0.000 | 0.000 | 0.001 | |
getGenesAnnotation | 0.395 | 0.009 | 0.440 | |
hisatAlignment | 0.003 | 0.002 | 0.010 | |
knn_test | 0.114 | 0.002 | 0.130 | |
knn_trn | 4.031 | 0.036 | 4.773 | |
knowseqReport | 0.011 | 0.002 | 0.016 | |
plotConfMatrix | 0.043 | 0.003 | 0.052 | |
rawAlignment | 0.003 | 0.001 | 0.006 | |
rf_test | 9.531 | 0.173 | 11.619 | |
rf_trn | 32.422 | 0.519 | 38.431 | |
sraToFastq | 0.001 | 0.001 | 0.000 | |
svm_test | 34.552 | 0.336 | 39.212 | |
svm_trn | 38.693 | 0.476 | 44.248 | |