Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-09-03 17:37 -0400 (Tue, 03 Sep 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" | 4758 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4495 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4473 |
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 | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | NA | |||||||||
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: 2024-09-03 10:28:59 -0400 (Tue, 03 Sep 2024) |
EndedAt: 2024-09-03 10:48:37 -0400 (Tue, 03 Sep 2024) |
EllapsedTime: 1177.5 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_1.6.0.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: aarch64-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 Ventura 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘signifinder/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘signifinder’ version ‘1.6.0’ * 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 199.360 1.330 217.894 consensusOVSign 102.237 0.653 107.659 * 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-arm64/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: aarch64-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 'select()' returned 1:1 mapping between keys and columns ferroptosisSignLiu 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 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..." '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 13 | SKIP 0 | PASS 270 ] [ FAIL 0 | WARN 13 | SKIP 0 | PASS 270 ] > > proc.time() user system elapsed 339.892 10.243 365.185
signifinder.Rcheck/signifinder-Ex.timings
name | user | system | elapsed | |
ADOSign | 2.947 | 0.021 | 3.065 | |
APMSign | 0.240 | 0.010 | 0.258 | |
ASCSign | 0.074 | 0.005 | 0.079 | |
CINSign | 0.095 | 0.006 | 0.105 | |
CISSign | 0.232 | 0.008 | 0.247 | |
COXISSign | 0.079 | 0.005 | 0.089 | |
CombinedSign | 0.142 | 0.007 | 0.155 | |
DNArepSign | 0.078 | 0.006 | 0.086 | |
ECMSign | 1.839 | 0.017 | 1.918 | |
EMTSign | 0.306 | 0.008 | 0.331 | |
HRDSSign | 0.086 | 0.006 | 0.094 | |
ICBResponseSign | 0.090 | 0.006 | 0.099 | |
IFNSign | 0.075 | 0.005 | 0.082 | |
IPRESSign | 0.353 | 0.013 | 0.381 | |
IPSOVSign | 0.349 | 0.013 | 0.372 | |
IPSSign | 0.124 | 0.006 | 0.134 | |
IRGSign | 0.078 | 0.005 | 0.084 | |
ISCSign | 0.084 | 0.007 | 0.094 | |
LRRC15CAFSign | 0.368 | 0.029 | 0.411 | |
MITFlowPTENnegSign | 0.118 | 0.008 | 0.130 | |
MPSSign | 0.088 | 0.005 | 0.095 | |
PassONSign | 0.311 | 0.006 | 0.332 | |
TGFBSign | 0.078 | 0.004 | 0.086 | |
TLSSign | 0.077 | 0.004 | 0.085 | |
TinflamSign | 0.076 | 0.004 | 0.082 | |
VEGFSign | 0.075 | 0.005 | 0.082 | |
autophagySign | 0.077 | 0.005 | 0.086 | |
availableSignatures | 0.016 | 0.006 | 0.025 | |
breastStateSign | 0.057 | 0.004 | 0.062 | |
cellCycleSign | 0.078 | 0.006 | 0.090 | |
chemokineSign | 0.101 | 0.007 | 0.115 | |
consensusOVSign | 102.237 | 0.653 | 107.659 | |
correlationSignPlot | 1.784 | 0.095 | 1.981 | |
evaluationSignPlot | 1.923 | 0.098 | 2.114 | |
expandedImmuneSign | 0.085 | 0.005 | 0.101 | |
ferroptosisSign | 0.089 | 0.004 | 0.096 | |
geneHeatmapSignPlot | 1.580 | 0.032 | 1.734 | |
getSignGenes | 0.006 | 0.007 | 0.015 | |
glioCellStateSign | 0.064 | 0.004 | 0.076 | |
glycolysisSign | 0.086 | 0.005 | 0.101 | |
heatmapSignPlot | 2.711 | 0.033 | 3.119 | |
hypoxiaSign | 0.090 | 0.006 | 0.114 | |
immuneCytSign | 0.092 | 0.005 | 0.108 | |
immunoScoreSign | 0.093 | 0.006 | 0.109 | |
lipidMetabolismSign | 0.082 | 0.006 | 0.111 | |
matrisomeSign | 0.080 | 0.006 | 0.107 | |
melStateSign | 0.066 | 0.004 | 0.079 | |
mitoticIndexSign | 0.084 | 0.005 | 0.108 | |
multipleSign | 199.360 | 1.330 | 217.894 | |
oneSignPlot | 0.452 | 0.010 | 0.477 | |
pyroptosisSign | 0.101 | 0.007 | 0.111 | |
ridgelineSignPlot | 1.299 | 0.041 | 1.386 | |
stemCellCD49fSign | 0.092 | 0.005 | 0.104 | |
survivalSignPlot | 1.847 | 0.056 | 1.989 | |