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This page was generated on 2024-06-07 20:27 -0400 (Fri, 07 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4755
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4489
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4520
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4466
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 1972/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
signifinder 1.6.0  (landing page)
Stefania Pirrotta
Snapshot Date: 2024-06-05 14:00:26 -0400 (Wed, 05 Jun 2024)
git_url: https://git.bioconductor.org/packages/signifinder
git_branch: RELEASE_3_19
git_last_commit: b1f9b88
git_last_commit_date: 2024-04-30 11:45:33 -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
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for signifinder on lconway

To the developers/maintainers of the signifinder package:
- 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 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: signifinder
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:signifinder.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings signifinder_1.6.0.tar.gz
StartedAt: 2024-06-05 23:10:59 -0400 (Wed, 05 Jun 2024)
EndedAt: 2024-06-05 23:27:28 -0400 (Wed, 05 Jun 2024)
EllapsedTime: 989.7 seconds
RetCode: 0
Status:   OK  
CheckDir: signifinder.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:signifinder.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings signifinder_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/signifinder.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘signifinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘signifinder’ version ‘1.6.0’
* 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 ‘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 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 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    150.974  0.779 152.042
consensusOVSign  75.429  0.442  76.036
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: OK


Installation output

signifinder.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL signifinder
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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")
pyroptosisSignLi is using 100% of signature genes
'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

ferroptosisSignYe is using 100% of signature genes
lipidMetabolismSign is using 100% of signature genes
StemCellCD49fSign is using 100% of signature genes
glycolysisSignXu is using 100% of signature genes
autophagySignChenH is using 100% of signature genes
'select()' returned 1:1 mapping between keys and columns
autophagySignChenM is using 100% of OS signature genes
autophagySignChenM is using 60% of DFS signature genes
TinflamSign is using 100% of signature genes
EMTSignMiow is using 100% of epithelial signature genes
EMTSignMiow is using 0% of mesenchymal signature genes
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
EMTSignMiow is using 0% of mesenchymal 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
EMTSignThompson is using 100% of epithelial signature genes
EMTSignThompson is using 100% of mesenchymal signature genes
'select()' returned 1:1 mapping between keys and columns
EMTSignThompson is using 100% of mesenchymal signature genes
'select()' returned 1:1 mapping between keys and columns
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..."
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..."
ECMSign is using 100% of up signature genes
ECMSign is using 0% of down signature genes
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
ECMSign is using 0% of down 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..."
'select()' returned 1:1 mapping between keys and columns
glioCellStateSign is using 100% of MES2 signature genes
glioCellStateSign is using 100% of MES1 signature genes
glioCellStateSign is using 100% of AC signature genes
glioCellStateSign is using 100% of OPC signature genes
glioCellStateSign is using 100% of NPC1 signature genes
glioCellStateSign is using 100% of NPC2 signature genes
TinflamSignThompson is using 100% of signature genes
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
EMTSignThompson is using 100% of epithelial signature genes
EMTSignThompson is using 100% of mesenchymal signature genes
'select()' returned 1:1 mapping between keys and columns
TinflamSignThompson is using 100% of signature genes
'select()' returned 1:1 mapping between keys and columns
EMTSignThompson is using 100% of mesenchymal signature genes
'select()' returned 1:1 mapping between keys and columns
TinflamSignThompson is using 100% of signature genes
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
melStateSign is using 100% of MITF signature genes
melStateSign is using 100% of AXL signature genes
'select()' returned 1:1 mapping between keys and columns
APMSign is using 100% of signature genes
'select()' returned 1:1 mapping between keys and columns
APMSign is using 100% of signature genes
'select()' returned 1:1 mapping between keys and columns
MPSSign is using 100% of signature genes
'select()' returned 1:1 mapping between keys and columns
IRGSign is using 100% of signature genes
TGFBSign is using 100% of signature genes
ADOSign is using 100% of signature genes
MITFlowPTENnegSign is using 100% of signature genes
LRRC15CAFSign is using 100% of signature genes
breastStateSign is using 100% of Basal signature genes
breastStateSign is using 100% of Her2E signature genes
breastStateSign is using 100% of LumA signature genes
breastStateSign is using 100% of LumB signature genes
breastStateSign is using 100% of Her2E signature genes
breastStateSign is using 100% of LumA signature genes
breastStateSign is using 100% of LumB signature genes
ICBResponseSign is using 0% of responder signature genes
ICBResponseSign is using 100% of nonresponder signature genes
ICBResponseSign is using 0% of responder signature genes
COXISSign is using 100% of signature genes
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 100% of signature genes
CINSign is using 100% 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 12 | SKIP 0 | PASS 270 ]

[ FAIL 0 | WARN 12 | SKIP 0 | PASS 270 ]
> 
> proc.time()
   user  system elapsed 
315.377  11.525 327.688 

Example timings

signifinder.Rcheck/signifinder-Ex.timings

nameusersystemelapsed
ADOSign1.6400.0141.657
APMSign0.2450.0120.259
ASCSign0.0570.0050.063
CINSign0.0620.0040.066
CISSign0.2030.0070.211
COXISSign0.0550.0040.062
CombinedSign0.1330.0040.138
DNArepSign0.0600.0030.064
ECMSign1.4690.0121.483
EMTSign0.2480.0040.251
HRDSSign0.0570.0030.059
ICBResponseSign0.0720.0050.076
IFNSign0.0650.0040.070
IPRESSign0.3190.0100.330
IPSOVSign0.2920.0120.305
IPSSign0.1130.0050.118
IRGSign0.0560.0040.060
ISCSign0.0680.0060.073
LRRC15CAFSign0.3240.0440.371
MITFlowPTENnegSign0.0980.0090.107
MPSSign0.0630.0040.070
PassONSign0.2920.0040.298
TGFBSign0.0610.0040.091
TLSSign0.0640.0040.068
TinflamSign0.0540.0020.057
VEGFSign0.0610.0040.064
autophagySign0.0560.0030.058
availableSignatures0.0100.0050.015
breastStateSign0.0270.0010.029
cellCycleSign0.0530.0030.056
chemokineSign0.0620.0060.068
consensusOVSign75.429 0.44276.036
correlationSignPlot1.7740.1021.886
evaluationSignPlot1.9320.0471.983
expandedImmuneSign0.0640.0040.068
ferroptosisSign0.0710.0040.075
geneHeatmapSignPlot2.7580.0872.852
getSignGenes0.0040.0060.009
glioCellStateSign0.0350.0030.038
glycolysisSign0.0570.0040.062
heatmapSignPlot2.4530.0322.489
hypoxiaSign0.0600.0030.064
immuneCytSign0.0590.0030.062
immunoScoreSign0.1270.0090.136
lipidMetabolismSign0.0610.0030.066
matrisomeSign0.0660.0030.070
melStateSign0.0430.0030.046
mitoticIndexSign0.0640.0040.068
multipleSign150.974 0.779152.042
oneSignPlot0.5150.0410.560
pyroptosisSign0.0790.0040.083
ridgelineSignPlot1.1890.0271.221
stemCellCD49fSign0.0620.0020.064
survivalSignPlot1.7060.0491.757