Stefania Pirrotta
| Snapshot Date: 2025-03-26 13:40 -0400 (Wed, 26 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/signifinder |
| git_branch: devel |
| git_last_commit: c426fdd |
| git_last_commit_date: 2025-01-13 08:58:12 -0400 (Mon, 13 Jan 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-03-27 11:45 -0400 (Thu, 27 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" | 4783 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4552 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4581 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4533 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4463 |
| 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 1973/2315 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| signifinder 1.9.3 (landing page) Stefania Pirrotta
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | 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: 1.9.3 |
| 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_1.9.3.tar.gz |
| StartedAt: 2025-03-27 00:23:46 -0400 (Thu, 27 Mar 2025) |
| EndedAt: 2025-03-27 00:46:57 -0400 (Thu, 27 Mar 2025) |
| EllapsedTime: 1391.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: signifinder.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.9.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/signifinder.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* 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 ‘1.9.3’
* 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 150.056 1.187 152.136
consensusOVSign 75.862 0.610 76.896
* 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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.21-bioc/meat/signifinder.Rcheck/00check.log’
for details.
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 ‘1.9.3’ ** 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 Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"
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")
'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
pyroptosisSignYe 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
glycolysisSignXu is using 100% of signature genes
autophagySignWang 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
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
EMTSignMiow is using 0% of epithelial signature genes
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
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
! Input expression data has NA values, which will be propagated through calculations.
ECMSign is using 0% of up signature genes
ECMSign is using 100% of down signature genes
ECMSign is using 0% of up signature genes
IPSOVSign is using 100% of signature genes
! Duplicated gene IDs removed from gene set Antimicrobials
! Some gene sets have size one. Consider setting minSize > 1
! Duplicated gene IDs removed from gene set Antimicrobials
! Some gene sets have size one. Consider setting minSize > 1
'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
stateSign 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
SCSubtypeSign is using 0% of Basal signature genes
SCSubtypeSign is using 0% of Her2E signature genes
SCSubtypeSign is using 100% of LumA signature genes
SCSubtypeSign is using 0% of LumB signature genes
SCSubtypeSign is using 0% of Basal signature genes
SCSubtypeSign is using 0% of Her2E signature genes
SCSubtypeSign is using 0% of LumB signature genes
ICBResponseSign is using 100% of responder signature genes
ICBResponseSign is using 0% of nonresponder signature genes
ICBResponseSign is using 0% of nonresponder signature genes
COXISSign is using 100% of signature genes
stressSign is using 100% of Stress signature genes
oxphosSign is using 100% of Oxphos signature genes
metalSign is using 100% of Metal signature genes
CD39CD8TcellSign 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 16 | SKIP 0 | PASS 317 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 317 ]
>
> proc.time()
user system elapsed
693.436 22.455 724.565
signifinder.Rcheck/signifinder-Ex.timings
| name | user | system | elapsed | |
| ADOSign | 1.744 | 0.017 | 1.774 | |
| APMSign | 0.264 | 0.011 | 0.279 | |
| ASCSign | 0.051 | 0.004 | 0.054 | |
| CD39CD8TcellSign | 0.217 | 0.014 | 0.232 | |
| CINSign | 0.074 | 0.004 | 0.078 | |
| CISSign | 0.053 | 0.003 | 0.056 | |
| COXISSign | 0.060 | 0.004 | 0.066 | |
| CombinedSign | 0.116 | 0.005 | 0.122 | |
| DNArepSign | 1.277 | 0.013 | 1.296 | |
| ECMSign | 0.269 | 0.005 | 0.277 | |
| EMTSign | 0.287 | 0.005 | 0.292 | |
| HRDSSign | 0.063 | 0.005 | 0.068 | |
| ICBResponseSign | 0.075 | 0.005 | 0.079 | |
| IFNSign | 0.055 | 0.005 | 0.060 | |
| IPRESSign | 0.368 | 0.008 | 0.378 | |
| IPSOVSign | 0.335 | 0.019 | 0.356 | |
| IPSSign | 0.100 | 0.004 | 0.105 | |
| IRGSign | 0.054 | 0.004 | 0.058 | |
| ISCSign | 0.066 | 0.006 | 0.076 | |
| LRRC15CAFSign | 0.061 | 0.004 | 0.065 | |
| MITFlowPTENnegSign | 0.060 | 0.005 | 0.066 | |
| MPSSign | 0.064 | 0.003 | 0.068 | |
| PassONSign | 0.322 | 0.012 | 0.336 | |
| SCSubtypeSign | 0.036 | 0.003 | 0.039 | |
| TGFBSign | 0.058 | 0.004 | 0.062 | |
| TLSSign | 0.064 | 0.004 | 0.070 | |
| TinflamSign | 0.055 | 0.004 | 0.060 | |
| VEGFSign | 0.058 | 0.004 | 0.064 | |
| autophagySign | 0.060 | 0.004 | 0.065 | |
| availableSignatures | 0.017 | 0.009 | 0.025 | |
| cellCycleSign | 0.057 | 0.004 | 0.062 | |
| chemokineSign | 0.053 | 0.004 | 0.057 | |
| consensusOVSign | 75.862 | 0.610 | 76.896 | |
| correlationSignPlot | 1.709 | 0.110 | 1.837 | |
| evaluationSignPlot | 1.931 | 0.110 | 2.057 | |
| expandedImmuneSign | 0.057 | 0.004 | 0.064 | |
| ferroptosisSign | 0.064 | 0.005 | 0.069 | |
| geneHeatmapSignPlot | 1.641 | 0.034 | 1.686 | |
| getSignGenes | 0.005 | 0.008 | 0.012 | |
| glycolysisSign | 0.062 | 0.004 | 0.066 | |
| heatmapSignPlot | 2.680 | 0.024 | 2.717 | |
| hypoxiaSign | 0.060 | 0.004 | 0.066 | |
| immuneCytSign | 0.064 | 0.004 | 0.068 | |
| immunoScoreSign | 0.063 | 0.004 | 0.070 | |
| interferonSign | 0.036 | 0.002 | 0.040 | |
| lipidMetabolismSign | 0.059 | 0.004 | 0.065 | |
| matrisomeSign | 0.054 | 0.004 | 0.059 | |
| metalSign | 0.035 | 0.003 | 0.038 | |
| mitoticIndexSign | 0.053 | 0.004 | 0.056 | |
| multipleSign | 150.056 | 1.187 | 152.136 | |
| oneSignPlot | 0.437 | 0.014 | 0.470 | |
| oxphosSign | 0.037 | 0.002 | 0.040 | |
| pyroptosisSign | 0.072 | 0.004 | 0.076 | |
| ridgelineSignPlot | 2.655 | 0.072 | 2.746 | |
| stateSign | 0.037 | 0.002 | 0.041 | |
| stemCellCD49fSign | 0.058 | 0.003 | 0.061 | |
| stressSign | 0.036 | 0.003 | 0.038 | |
| survivalSignPlot | 1.873 | 0.092 | 2.027 | |