| Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-24 09:06 -0400 (Wed, 24 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4747 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4489 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4518 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4467 |
| 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 1972/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| signifinder 1.6.0 (landing page) Stefania Pirrotta
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | 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: 1.6.0 |
| 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: 2024-07-22 12:41:49 -0400 (Mon, 22 Jul 2024) |
| EndedAt: 2024-07-22 13:17:12 -0400 (Mon, 22 Jul 2024) |
| EllapsedTime: 2123.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: signifinder.Rcheck |
| Warnings: 0 |
##############################################################################
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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_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/signifinder.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 12.7.5
* 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 235.413 2.202 283.663
consensusOVSign 115.749 1.069 138.907
heatmapSignPlot 6.629 0.048 7.790
correlationSignPlot 4.401 0.324 5.651
evaluationSignPlot 4.209 0.161 5.087
* 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
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)
signifinder.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
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")
'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
ferroptosisSignLi 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
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
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
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 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
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 13 | SKIP 0 | PASS 270 ]
[ FAIL 0 | WARN 13 | SKIP 0 | PASS 270 ]
>
> proc.time()
user system elapsed
631.557 14.554 763.282
signifinder.Rcheck/signifinder-Ex.timings
| name | user | system | elapsed | |
| ADOSign | 3.574 | 0.034 | 4.208 | |
| APMSign | 0.405 | 0.016 | 0.555 | |
| ASCSign | 0.090 | 0.006 | 0.106 | |
| CINSign | 0.120 | 0.006 | 0.144 | |
| CISSign | 0.262 | 0.011 | 0.310 | |
| COXISSign | 0.100 | 0.006 | 0.118 | |
| CombinedSign | 0.233 | 0.008 | 0.266 | |
| DNArepSign | 0.099 | 0.007 | 0.128 | |
| ECMSign | 2.048 | 0.023 | 2.418 | |
| EMTSign | 0.660 | 0.010 | 0.783 | |
| HRDSSign | 0.117 | 0.006 | 0.142 | |
| ICBResponseSign | 0.138 | 0.005 | 0.171 | |
| IFNSign | 0.097 | 0.007 | 0.120 | |
| IPRESSign | 0.755 | 0.019 | 0.906 | |
| IPSOVSign | 0.684 | 0.019 | 0.812 | |
| IPSSign | 0.240 | 0.008 | 0.287 | |
| IRGSign | 0.095 | 0.007 | 0.119 | |
| ISCSign | 0.111 | 0.008 | 0.136 | |
| LRRC15CAFSign | 0.671 | 0.052 | 0.848 | |
| MITFlowPTENnegSign | 0.152 | 0.012 | 0.197 | |
| MPSSign | 0.112 | 0.005 | 0.137 | |
| PassONSign | 0.649 | 0.011 | 0.754 | |
| TGFBSign | 0.097 | 0.005 | 0.114 | |
| TLSSign | 0.101 | 0.007 | 0.119 | |
| TinflamSign | 0.092 | 0.007 | 0.122 | |
| VEGFSign | 0.092 | 0.006 | 0.115 | |
| autophagySign | 0.096 | 0.006 | 0.117 | |
| availableSignatures | 0.025 | 0.020 | 0.063 | |
| breastStateSign | 0.053 | 0.007 | 0.073 | |
| cellCycleSign | 0.095 | 0.007 | 0.122 | |
| chemokineSign | 0.119 | 0.010 | 0.152 | |
| consensusOVSign | 115.749 | 1.069 | 138.907 | |
| correlationSignPlot | 4.401 | 0.324 | 5.651 | |
| evaluationSignPlot | 4.209 | 0.161 | 5.087 | |
| expandedImmuneSign | 0.098 | 0.008 | 0.121 | |
| ferroptosisSign | 0.111 | 0.006 | 0.134 | |
| geneHeatmapSignPlot | 3.866 | 0.057 | 4.598 | |
| getSignGenes | 0.010 | 0.018 | 0.031 | |
| glioCellStateSign | 0.055 | 0.005 | 0.072 | |
| glycolysisSign | 0.108 | 0.007 | 0.134 | |
| heatmapSignPlot | 6.629 | 0.048 | 7.790 | |
| hypoxiaSign | 0.101 | 0.007 | 0.129 | |
| immuneCytSign | 0.111 | 0.007 | 0.134 | |
| immunoScoreSign | 0.119 | 0.005 | 0.148 | |
| lipidMetabolismSign | 0.090 | 0.006 | 0.114 | |
| matrisomeSign | 0.098 | 0.006 | 0.119 | |
| melStateSign | 0.055 | 0.005 | 0.067 | |
| mitoticIndexSign | 0.093 | 0.008 | 0.122 | |
| multipleSign | 235.413 | 2.202 | 283.663 | |
| oneSignPlot | 0.958 | 0.013 | 1.227 | |
| pyroptosisSign | 0.121 | 0.007 | 0.156 | |
| ridgelineSignPlot | 2.649 | 0.052 | 3.251 | |
| stemCellCD49fSign | 0.105 | 0.005 | 0.129 | |
| survivalSignPlot | 3.734 | 0.082 | 4.699 | |