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This page was generated on 2024-05-04 11:36:44 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 1097/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
KnowSeq 1.18.0  (landing page)
Daniel Castillo-Secilla
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/KnowSeq
git_branch: RELEASE_3_19
git_last_commit: 2fa8987
git_last_commit_date: 2024-04-30 11:15:37 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for KnowSeq on nebbiolo1


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.

raw results


Summary

Package: KnowSeq
Version: 1.18.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:KnowSeq.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings KnowSeq_1.18.0.tar.gz
StartedAt: 2024-05-04 00:29:56 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 00:36:20 -0400 (Sat, 04 May 2024)
EllapsedTime: 384.5 seconds
RetCode: 0
Status:   OK  
CheckDir: KnowSeq.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:KnowSeq.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings KnowSeq_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/KnowSeq.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 ... OK
* 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             17.303  0.312  17.560
rf_trn               14.071  0.360  14.431
svm_trn              14.168  0.092  14.261
svm_test             13.083  0.132  13.215
downloadPublicSeries  0.888  0.061  18.107
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/KnowSeq.Rcheck/00check.log’
for details.


Installation output

KnowSeq.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL KnowSeq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-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)

Tests output


Example timings

KnowSeq.Rcheck/KnowSeq-Ex.timings

nameusersystemelapsed
DEGsEvidences0.8930.0371.494
DEGsExtraction0.7630.0640.830
DEGsToDiseases0.2020.0120.384
DEGsToPathways0.3270.0000.328
RNAseqQA1.9220.1282.021
batchEffectRemoval2.8170.1843.002
calculateGeneExpressionValues0.5430.0480.591
countsToMatrix0.0550.0040.061
dataPlot17.303 0.31217.560
downloadPublicSeries 0.888 0.06118.107
featureSelection0.0160.0000.014
fileMove0.0010.0000.000
gdcClientDownload0.0000.0000.001
geneOntologyEnrichment000
getGenesAnnotation0.2130.0160.226
hisatAlignment0.0030.0000.002
knn_test0.0460.0000.046
knn_trn1.4100.0681.478
knowseqReport0.0030.0040.006
plotConfMatrix0.0190.0000.019
rawAlignment0.0020.0000.001
rf_test4.0170.1684.185
rf_trn14.071 0.36014.431
sraToFastq000
svm_test13.083 0.13213.215
svm_trn14.168 0.09214.261