Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-02-04 11:05:50 -0500 (Sat, 04 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4483
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4249
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4272
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

CHECK results for signifinder on palomino3


To the developers/maintainers of the signifinder package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/signifinder.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1858/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
signifinder 1.1.0  (landing page)
Stefania Pirrotta
Snapshot Date: 2023-02-03 14:00:22 -0500 (Fri, 03 Feb 2023)
git_url: https://git.bioconductor.org/packages/signifinder
git_branch: master
git_last_commit: 74ba189
git_last_commit_date: 2022-11-01 11:27:46 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    NA  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: signifinder
Version: 1.1.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:signifinder.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings signifinder_1.1.0.tar.gz
StartedAt: 2023-02-04 06:37:37 -0500 (Sat, 04 Feb 2023)
EndedAt: 2023-02-04 06:48:36 -0500 (Sat, 04 Feb 2023)
EllapsedTime: 659.2 seconds
RetCode: 0
Status:   OK  
CheckDir: signifinder.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:signifinder.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings signifinder_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/signifinder.Rcheck'
* using R Under development (unstable) (2023-01-10 r83596 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'signifinder/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'signifinder' version '1.1.0'
* 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 whether package 'signifinder' 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 R 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 ... OK
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
multipleSign    120.03   0.27  120.30
consensusOVSign  62.62   0.14   62.77
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

signifinder.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL signifinder
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'signifinder' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (signifinder)

Tests output

signifinder.Rcheck/tests/testthat.Rout


R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(signifinder)

> 
> test_check("signifinder")
'select()' returned 1:1 mapping between keys and columns
Loading required package: edgeR
Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

pyroptosisSignShao is using 100% of signature genes
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
ferroptosisSignYe is using 100% of signature genes
'select()' returned 1:1 mapping between keys and columns
lipidMetabolismSign is using 100% of signature genes
StemCellCD49fSign is using 100% of signature genes
glycolysisSignZhang is using 100% of signature genes
autophagySignXu is using 100% of signature genes
'select()' returned 1:1 mapping between keys and columns
autophagySignChenM is using 27% of OS signature genes
autophagySignChenM is using 100% of DFS signature genes
'select()' returned 1:1 mapping between keys and columns
autophagySignChenM is using 27% of OS signature genes
TinflamSign is using 100% of signature genes
EMTSignMiow is using 0% of epithelial signature genes
EMTSignMiow is using 100% of mesenchymal signature genes
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
EMTSignMiow is using 0% of epithelial signature genes
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
EMTSignMak is using 100% of epithelial signature genes
EMTSignMak is using 100% of mesenchymal signature genes
EMTSignMak is using 100% of mesenchymal signature genes
EMTSignCheng is using 100% of signature genes
ASCSign is using 100% of signature genes
ChemokineSign is using 100% of signature genes
'select()' returned 1:1 mapping between keys and columns
PassONSign is using 100% of signature genes
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
'select()' returned 1:1 mapping between keys and columns
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
CISSign is using 100% of up signature genes
CISSign is using 100% of down signature genes
CISSign is using 100% of down signature genes
HRDSSign is using 100% of signature genes
DNArepSign is using 100% of signature genes
'select()' returned 1:1 mapping between keys and columns
IPRESSign is using 100% of signature genes
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
'select()' returned 1:1 mapping between keys and columns
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
ECMSign is using 0% of up signature genes
ECMSign is using 100% of down signature genes
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
ECMSign is using 0% of up signature genes
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
IPSOVSign is using 100% of signature genes
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
TLSSign is using 100% of signature genes
expandedImmuneSign is using 100% of signature genes
IFNSign is using 100% of signature genes
ImmuneCytSignRooney is using 100% of signature genes
mitoticIndexSign is using 100% of signature genes
matrisomeSign is using 100% of signature genes
immunoScoreSignRoh is using 100% of signature genes
CINSign is using 100% of signature genes
CINSign is using 36% of signature genes
CINSign is using 36% of signature genes
hypoxiaSign is using 100% of signature genes
cellCycleSignLundberg is using 100% of signature genes
cellCycleSignDavoli is using 100% of signature genes
VEGFSign is using 100% of signature genes
ImmuneCytSignDavoli is using 100% of signature genes
[ FAIL 0 | WARN 11 | SKIP 0 | PASS 194 ]

[ FAIL 0 | WARN 11 | SKIP 0 | PASS 194 ]
> 
> proc.time()
   user  system elapsed 
 114.78    4.43  119.23 

Example timings

signifinder.Rcheck/signifinder-Ex.timings

nameusersystemelapsed
ASCSign0.110.020.12
CINSign0.060.000.06
CISSign0.050.000.05
DNArepSign0.030.000.03
ECMSign0.120.030.15
EMTSign0.100.030.13
HRDSSign0.060.000.06
IFNSign0.080.000.08
IPRESSign0.290.000.30
IPSOVSign0.160.010.17
IPSSign0.090.020.11
ISCSign0.030.020.05
PassONSign0.100.000.09
TLSSign0.040.000.05
TinflamSign0.050.000.04
VEGFSign0.050.000.05
autophagySign0.060.000.06
availableSignatures0.000.010.02
cellCycleSign0.030.020.04
chemokineSign0.050.000.05
consensusOVSign62.62 0.1462.77
correlationSignPlot1.580.081.65
expandedImmuneSign0.030.000.03
ferroptosisSign0.050.010.07
geneHeatmapSignPlot1.440.031.47
glycolysisSign0.040.000.04
heatmapSignPlot2.290.072.35
hypoxiaSign0.040.000.04
immuneCytSign0.050.000.05
immunoScoreSign0.060.000.06
lipidMetabolismSign0.050.000.05
matrisomeSign0.030.010.05
mitoticIndexSign0.050.000.04
multipleSign120.03 0.27120.30
oneSignPlot0.590.000.59
pyroptosisSign0.050.000.05
ridgelineSignPlot1.340.061.41
stemCellCD49fSign0.050.000.04
survivalSignPlot1.310.121.57