Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABCDEFGHIJ[K]LMNOPQRSTUVWXYZ

This page was generated on 2025-08-28 11:43 -0400 (Thu, 28 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 1109/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
KnowSeq 1.22.0  (landing page)
Daniel Castillo-Secilla
Snapshot Date: 2025-08-25 13:40 -0400 (Mon, 25 Aug 2025)
git_url: https://git.bioconductor.org/packages/KnowSeq
git_branch: RELEASE_3_21
git_last_commit: 1e76e4c
git_last_commit_date: 2025-04-15 11:47:28 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for KnowSeq on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: KnowSeq
Version: 1.22.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:KnowSeq.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings KnowSeq_1.22.0.tar.gz
StartedAt: 2025-08-26 11:14:27 -0000 (Tue, 26 Aug 2025)
EndedAt: 2025-08-26 11:21:06 -0000 (Tue, 26 Aug 2025)
EllapsedTime: 398.4 seconds
RetCode: 0
Status:   OK  
CheckDir: KnowSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:KnowSeq.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings KnowSeq_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/KnowSeq.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘KnowSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘KnowSeq’ version ‘1.22.0’
* 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 ... INFO
  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             30.143  1.109  31.321
svm_trn              22.864  0.127  23.049
rf_trn               22.213  0.374  22.639
svm_test             20.628  0.204  20.885
rf_test               6.111  0.212   6.334
downloadPublicSeries  0.727  0.019  42.387
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/KnowSeq.Rcheck/00check.log’
for details.


Installation output

KnowSeq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL KnowSeq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘KnowSeq’ ...
** this is package ‘KnowSeq’ version ‘1.22.0’
** 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)

Tests output


Example timings

KnowSeq.Rcheck/KnowSeq-Ex.timings

nameusersystemelapsed
DEGsEvidences0.3750.0161.629
DEGsExtraction1.7300.0391.782
DEGsToDiseases0.2300.0080.851
DEGsToPathways0.3740.0160.393
RNAseqQA2.6460.1032.760
batchEffectRemoval3.3070.2203.533
calculateGeneExpressionValues0.7460.0040.752
countsToMatrix0.0660.0080.084
dataPlot30.143 1.10931.321
downloadPublicSeries 0.727 0.01942.387
featureSelection0.0120.0030.014
fileMove000
gdcClientDownload0.0000.0000.001
geneOntologyEnrichment000
getGenesAnnotation0.2980.0280.326
hisatAlignment0.0030.0000.003
knn_test0.0750.0000.076
knn_trn2.4160.1322.552
knowseqReport0.0090.0000.009
plotConfMatrix0.0270.0040.030
rawAlignment0.0020.0000.002
rf_test6.1110.2126.334
rf_trn22.213 0.37422.639
sraToFastq0.0010.0000.000
svm_test20.628 0.20420.885
svm_trn22.864 0.12723.049