Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABCDEFGHIJ[K]LMNOPQRSTUVWXYZ

This page was generated on 2024-06-25 11:38 -0400 (Tue, 25 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4690
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4404
kjohnson3macOS 13.6.5 Venturaarm644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4353
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 1066/2242HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
KnowSeq 1.19.0  (landing page)
Daniel Castillo-Secilla
Snapshot Date: 2024-06-24 14:00 -0400 (Mon, 24 Jun 2024)
git_url: https://git.bioconductor.org/packages/KnowSeq
git_branch: devel
git_last_commit: 8ad5145
git_last_commit_date: 2024-04-30 11:15:37 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  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
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for KnowSeq on nebbiolo2

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: 1.19.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:KnowSeq.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings KnowSeq_1.19.0.tar.gz
StartedAt: 2024-06-25 00:12:52 -0400 (Tue, 25 Jun 2024)
EndedAt: 2024-06-25 00:19:02 -0400 (Tue, 25 Jun 2024)
EllapsedTime: 369.8 seconds
RetCode: 0
Status:   OK  
CheckDir: KnowSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:KnowSeq.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings KnowSeq_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/KnowSeq.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* 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 ‘1.19.0’
* 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 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             17.398  0.224  17.563
svm_trn              14.762  0.080  14.842
rf_trn               14.162  0.176  14.339
svm_test             13.214  0.060  13.273
downloadPublicSeries  0.877  0.030  15.820
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/KnowSeq.Rcheck/00check.log’
for details.


Installation output

KnowSeq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL KnowSeq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-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
DEGsEvidences0.8760.0281.427
DEGsExtraction0.7120.0290.740
DEGsToDiseases0.2010.0120.382
DEGsToPathways0.3020.0080.310
RNAseqQA1.9290.1122.014
batchEffectRemoval2.4140.0562.470
calculateGeneExpressionValues0.5470.0040.551
countsToMatrix0.0490.0000.050
dataPlot17.398 0.22417.563
downloadPublicSeries 0.877 0.03015.820
featureSelection0.0190.0000.017
fileMove000
gdcClientDownload000
geneOntologyEnrichment0.0010.0000.000
getGenesAnnotation0.2000.0000.198
hisatAlignment0.0010.0000.002
knn_test0.0410.0000.041
knn_trn1.3410.0041.345
knowseqReport0.0060.0000.006
plotConfMatrix0.0180.0000.018
rawAlignment0.0020.0000.001
rf_test3.9870.0284.014
rf_trn14.162 0.17614.339
sraToFastq000
svm_test13.214 0.06013.273
svm_trn14.762 0.08014.842