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This page was generated on 2025-10-09 12:07 -0400 (Thu, 09 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4854
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4642
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4587
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4584
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 1111/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
KnowSeq 1.23.0  (landing page)
Daniel Castillo-Secilla
Snapshot Date: 2025-10-08 14:17 -0400 (Wed, 08 Oct 2025)
git_url: https://git.bioconductor.org/packages/KnowSeq
git_branch: devel
git_last_commit: 23de926
git_last_commit_date: 2025-04-15 11:47:28 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  YES
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for KnowSeq on taishan

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: 1.23.0
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_1.23.0.tar.gz
StartedAt: 2025-10-07 09:07:59 -0000 (Tue, 07 Oct 2025)
EndedAt: 2025-10-07 09:14:26 -0000 (Tue, 07 Oct 2025)
EllapsedTime: 387.4 seconds
RetCode: 0
Status:   OK  
CheckDir: KnowSeq.Rcheck
Warnings: 0

Command output

##############################################################################
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### 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_1.23.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/KnowSeq.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘KnowSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘KnowSeq’ version ‘1.23.0’
* 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             31.540  0.542  32.183
svm_trn              22.990  0.124  23.196
rf_trn               20.788  0.092  20.949
svm_test             20.275  0.107  20.451
rf_test               5.587  0.184   5.790
downloadPublicSeries  0.659  0.231  21.049
* 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-3.22-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-4.5.0/site-library’
* installing *source* package ‘KnowSeq’ ...
** this is package ‘KnowSeq’ version ‘1.23.0’
** 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
DEGsEvidences0.4970.0424.644
DEGsExtraction1.5540.1041.672
DEGsToDiseases0.2930.0161.158
DEGsToPathways0.3420.0040.349
RNAseqQA3.8760.4864.377
batchEffectRemoval2.8150.2043.026
calculateGeneExpressionValues0.7080.0360.747
countsToMatrix0.0760.0000.092
dataPlot31.540 0.54232.183
downloadPublicSeries 0.659 0.23121.049
featureSelection0.0190.0000.016
fileMove000
gdcClientDownload000
geneOntologyEnrichment000
getGenesAnnotation0.2470.0160.264
hisatAlignment0.0020.0020.004
knn_test0.0760.0240.102
knn_trn2.4370.3972.843
knowseqReport0.0110.0000.011
plotConfMatrix0.0280.0040.033
rawAlignment0.0000.0020.003
rf_test5.5870.1845.790
rf_trn20.788 0.09220.949
sraToFastq0.0010.0000.000
svm_test20.275 0.10720.451
svm_trn22.990 0.12423.196