| Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-12-22 12:05 -0500 (Mon, 22 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4883 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4673 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4607 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4671 |
| 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 2015/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| signifinder 1.12.0 (landing page) Stefania Pirrotta
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | TIMEOUT | OK | |||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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. |
| Package: signifinder |
| Version: 1.12.0 |
| 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_1.12.0.tar.gz |
| StartedAt: 2025-12-19 11:38:00 -0500 (Fri, 19 Dec 2025) |
| EndedAt: 2025-12-19 12:18:01 -0500 (Fri, 19 Dec 2025) |
| EllapsedTime: 2400.6 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: signifinder.Rcheck |
| Warnings: NA |
##############################################################################
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###
### 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_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/signifinder.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘signifinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘signifinder’ version ‘1.12.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 27 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
ADOSign.Rd: SummarizedExperiment-class
APMSign.Rd: SummarizedExperiment-class
ASCSign.Rd: SummarizedExperiment-class
CD39CD8TcellSign.Rd: SummarizedExperiment-class
CINSign.Rd: SummarizedExperiment-class
CISSign.Rd: SummarizedExperiment-class
COXISSign.Rd: SummarizedExperiment-class
CombinedSign.Rd: SummarizedExperiment-class
DNArepSign.Rd: SummarizedExperiment-class
ECMSign.Rd: SummarizedExperiment-class
EMTSign.Rd: SummarizedExperiment-class
HRDSSign.Rd: SummarizedExperiment-class
ICBResponseSign.Rd: SummarizedExperiment-class
IFNSign.Rd: SummarizedExperiment-class
IPRESSign.Rd: SummarizedExperiment-class
IPSOVSign.Rd: SummarizedExperiment-class
IPSSign.Rd: SummarizedExperiment-class
IRGSign.Rd: SummarizedExperiment-class
ISCSign.Rd: SummarizedExperiment-class
LRRC15CAFSign.Rd: SummarizedExperiment-class
MITFlowPTENnegSign.Rd: SummarizedExperiment-class
MPSSign.Rd: SummarizedExperiment-class
PassONSign.Rd: SummarizedExperiment-class
SCSubtypeSign.Rd: SummarizedExperiment-class
TGFBSign.Rd: SummarizedExperiment-class
TLSSign.Rd: SummarizedExperiment-class
TinflamSign.Rd: SummarizedExperiment-class
VEGFSign.Rd: SummarizedExperiment-class
autophagySign.Rd: SummarizedExperiment-class
cellCycleSign.Rd: SummarizedExperiment-class
chemokineSign.Rd: SummarizedExperiment-class
consensusOVSign.Rd: SummarizedExperiment-class
correlationSignPlot.Rd: SummarizedExperiment-class
evaluationSignPlot.Rd: SummarizedExperiment-class
expandedImmuneSign.Rd: SummarizedExperiment-class
ferroptosisSign.Rd: SummarizedExperiment-class
geneHeatmapSignPlot.Rd: SummarizedExperiment-class
glycolysisSign.Rd: SummarizedExperiment-class
heatmapSignPlot.Rd: SummarizedExperiment-class
hypoxiaSign.Rd: SummarizedExperiment-class
immuneCytSign.Rd: SummarizedExperiment-class
immunoScoreSign.Rd: SummarizedExperiment-class
interferonSign.Rd: SummarizedExperiment-class
lipidMetabolismSign.Rd: SummarizedExperiment-class
matrisomeSign.Rd: SummarizedExperiment-class
metalSign.Rd: SummarizedExperiment-class
mitoticIndexSign.Rd: SummarizedExperiment-class
multipleSign.Rd: SummarizedExperiment-class
oneSignPlot.Rd: SummarizedExperiment-class
oxphosSign.Rd: SummarizedExperiment-class
pyroptosisSign.Rd: SummarizedExperiment-class
ridgelineSignPlot.Rd: SummarizedExperiment-class
stateSign.Rd: SummarizedExperiment-class
stemCellCD49fSign.Rd: SummarizedExperiment-class
stressSign.Rd: SummarizedExperiment-class
survivalSignPlot.Rd: SummarizedExperiment-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 226.792 1.236 231.245
consensusOVSign 110.227 0.725 112.513
heatmapSignPlot 6.138 0.049 6.472
evaluationSignPlot 5.389 0.239 5.661
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
signifinder.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL signifinder ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘signifinder’ ... ** this is package ‘signifinder’ version ‘1.12.0’ ** 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)
signifinder.Rcheck/tests/testthat.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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
ferroptosisSignLiang is using 100% of signature genes
lipidMetabolismSign is using 100% of signature genes
StemCellCD49fSign is using 100% of signature genes
glycolysisSignZhang is using 100% of signature genes
autophagySignChenH 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
autophagySignChenM is using 100% of OS signature genes
autophagySignChenM is using 60% of DFS signature genes
TinflamSign is using 100% of signature genes
interferonSign is using 100% of Interferon signature genes
EMTSignMiow is using 0% of epithelial signature genes
EMTSignMiow is using 100% of mesenchymal signature genes
i argument assay='norm_expr' ignored since exprData has no assay names.
i GSVA version 2.4.4
i Searching for rows with constant values
i Calculating ssGSEA scores for 1 gene sets
i Calculating ranks
i Calculating rank weights
v Calculations finished
EMTSignMiow is using 0% of epithelial signature genes
i argument assay='norm_expr' ignored since exprData has no assay names.
i GSVA version 2.4.4
i Searching for rows with constant values
i Calculating ssGSEA scores for 1 gene sets
i Calculating ranks
i Calculating rank weights
v Calculations finished
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
EMTSign is using 100% of cEMT signature genes
EMTSign is using 100% of pEMT signature genes
EMTSign is using 100% of pEMT signature genes
hipoxiaSign is using 100% of Hypoxia 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
i GSVA version 2.4.4
i Searching for rows with constant values
i Calculating ssGSEA scores for 4 gene sets
i Calculating ranks
i Calculating rank weights
i Normalizing ssGSEA scores
v Calculations finished
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
i GSVA version 2.4.4
i Searching for rows with constant values
i Calculating GSVA ranks
i kcdf='auto' (default)
i GSVA dense (classical) algorithm
i Row-wise ECDF estimation with Poisson kernels
i Calculating row ECDFs
i Calculating column ranks
i GSVA dense (classical) algorithm
i Calculating GSVA scores
v Calculations finished
ECMSign is using 0% of up signature genes
ECMSign is using 100% of down signature genes
i argument assay='norm_expr' ignored since exprData has no assay names.
i GSVA version 2.4.4
i Searching for rows with constant values
i Calculating ssGSEA scores for 1 gene sets
i Calculating ranks
i Calculating rank weights
v Calculations finished
ECMSign is using 0% of up signature genes
i argument assay='norm_expr' ignored since exprData has no assay names.
i GSVA version 2.4.4
i Searching for rows with constant values
i Calculating ssGSEA scores for 1 gene sets
i Calculating ranks
i Calculating rank weights
v Calculations finished
IPSOVSign is using 100% of signature genes
i argument assay='norm_expr' ignored since exprData has no assay names.
i GSVA version 2.4.4
i Searching for rows with constant values
! Some gene sets have size one. Consider setting minSize > 1
i Calculating ssGSEA scores for 15 gene sets
i Calculating ranks
i Calculating rank weights
v Calculations finished
i argument assay='norm_expr' ignored since exprData has no assay names.
i GSVA version 2.4.4
i Searching for rows with constant values
! Some gene sets have size one. Consider setting minSize > 1
i Calculating ssGSEA scores for 15 gene sets
i Calculating ranks
i Calculating rank weights
v Calculations finished
'select()' returned 1:1 mapping between keys and columns
stateSign is using 100% of MES2 signature genes
stateSign is using 100% of MES1 signature genes
stateSign is using 100% of AC signature genes
stateSign is using 100% of OPC signature genes
stateSign is using 100% of NPC1 signature genes
stateSign is using 100% of NPC2 signature genes
'select()' returned 1:1 mapping between keys and columns
stateSign is using 100% of MES1 signature genes
stateSign is using 100% of AC signature genes
stateSign is using 100% of OPC signature genes
stateSign is using 100% of NPC1 signature genes
stateSign is using 100% of NPC2 signature genes
stateSign is using 100% of Alveolar signature genes
stateSign is using 100% of Basal signature genes
stateSign is using 100% of Squamous signature genes
stateSign is using 100% of Glandular signature genes
stateSign is using 100% of Ciliated signature genes
stateSign is using 100% of AC signature genes
stateSign is using 100% of OPC signature genes
stateSign is using 100% of NPC signature genes
stateSign is using 100% of Basal signature genes
stateSign is using 100% of Squamous signature genes
stateSign is using 100% of Glandular signature genes
stateSign is using 100% of Ciliated signature genes
stateSign is using 100% of AC signature genes
stateSign is using 100% of OPC signature genes
stateSign is using 100% of NPC 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
cellCycleSign is using 100% of Cycle 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
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
stateSign is using 100% of MITF signature genes
stateSign is using 100% of AXL signature genes
'select()' returned 1:1 mapping between keys and columns
signifinder.Rcheck/signifinder-Ex.timings
| name | user | system | elapsed | |
| ADOSign | 2.465 | 0.025 | 2.513 | |
| APMSign | 0.951 | 0.011 | 0.966 | |
| ASCSign | 0.089 | 0.007 | 0.097 | |
| CD39CD8TcellSign | 0.185 | 0.020 | 0.205 | |
| CINSign | 0.112 | 0.010 | 0.122 | |
| CISSign | 0.094 | 0.008 | 0.103 | |
| COXISSign | 0.138 | 0.014 | 0.151 | |
| CombinedSign | 0.221 | 0.007 | 0.229 | |
| DNArepSign | 0.093 | 0.006 | 0.100 | |
| ECMSign | 0.738 | 0.012 | 0.752 | |
| EMTSign | 0.792 | 0.009 | 0.805 | |
| HRDSSign | 1.382 | 0.016 | 1.401 | |
| ICBResponseSign | 0.133 | 0.006 | 0.141 | |
| IFNSign | 0.093 | 0.005 | 0.101 | |
| IPRESSign | 0.878 | 0.012 | 0.896 | |
| IPSOVSign | 0.765 | 0.017 | 0.784 | |
| IPSSign | 0.241 | 0.013 | 0.258 | |
| IRGSign | 0.094 | 0.006 | 0.100 | |
| ISCSign | 0.112 | 0.011 | 0.131 | |
| LRRC15CAFSign | 0.098 | 0.012 | 0.111 | |
| MITFlowPTENnegSign | 0.099 | 0.010 | 0.112 | |
| MPSSign | 0.118 | 0.016 | 0.150 | |
| PassONSign | 2.096 | 0.040 | 2.153 | |
| SCSubtypeSign | 0.050 | 0.005 | 0.055 | |
| TGFBSign | 0.095 | 0.005 | 0.101 | |
| TLSSign | 0.098 | 0.005 | 0.105 | |
| TinflamSign | 0.093 | 0.006 | 0.099 | |
| VEGFSign | 0.090 | 0.005 | 0.096 | |
| autophagySign | 0.094 | 0.005 | 0.100 | |
| availableSignatures | 0.027 | 0.021 | 0.050 | |
| cellCycleSign | 0.097 | 0.006 | 0.103 | |
| chemokineSign | 0.094 | 0.006 | 0.101 | |
| consensusOVSign | 110.227 | 0.725 | 112.513 | |
| correlationSignPlot | 3.726 | 0.121 | 3.860 | |
| evaluationSignPlot | 5.389 | 0.239 | 5.661 | |
| expandedImmuneSign | 0.093 | 0.005 | 0.098 | |
| ferroptosisSign | 0.109 | 0.008 | 0.118 | |
| geneHeatmapSignPlot | 3.548 | 0.033 | 3.629 | |
| getSignGenes | 0.009 | 0.019 | 0.029 | |
| glycolysisSign | 0.102 | 0.006 | 0.107 | |
| heatmapSignPlot | 6.138 | 0.049 | 6.472 | |
| hypoxiaSign | 0.100 | 0.006 | 0.110 | |
| immuneCytSign | 0.111 | 0.006 | 0.121 | |
| immunoScoreSign | 0.114 | 0.006 | 0.124 | |
| interferonSign | 0.053 | 0.004 | 0.059 | |
| lipidMetabolismSign | 0.091 | 0.005 | 0.097 | |
| matrisomeSign | 0.091 | 0.007 | 0.099 | |
| metalSign | 0.052 | 0.006 | 0.058 | |
| mitoticIndexSign | 0.089 | 0.006 | 0.096 | |
| multipleSign | 226.792 | 1.236 | 231.245 | |
| oneSignPlot | 1.298 | 0.013 | 1.431 | |
| oxphosSign | 0.055 | 0.005 | 0.062 | |
| pyroptosisSign | 0.123 | 0.006 | 0.132 | |
| ridgelineSignPlot | 2.781 | 0.065 | 3.031 | |
| stateSign | 0.055 | 0.004 | 0.062 | |
| stemCellCD49fSign | 0.103 | 0.005 | 0.114 | |
| stressSign | 0.054 | 0.005 | 0.062 | |
| survivalSignPlot | 4.169 | 0.077 | 4.589 | |