| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-31 17:03:15 -0400 (Fri, 31 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
| 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 |  | ||||||||
| kjohnson3 | macOS 13.6.5 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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:signifinder.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings signifinder_1.6.0.tar.gz |
| StartedAt: 2024-05-31 08:15:25 -0400 (Fri, 31 May 2024) |
| EndedAt: 2024-05-31 08:32:56 -0400 (Fri, 31 May 2024) |
| EllapsedTime: 1051.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: signifinder.Rcheck |
| Warnings: 0 |
##############################################################################
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### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:signifinder.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings signifinder_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/signifinder.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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 145.115 0.875 145.995
consensusOVSign 70.760 0.409 71.175
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
signifinder.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL signifinder ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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
pyroptosisSignLin 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
autophagySignXu 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 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 12 | SKIP 0 | PASS 270 ]
[ FAIL 0 | WARN 12 | SKIP 0 | PASS 270 ]
>
> proc.time()
user system elapsed
280.977 6.334 287.311
signifinder.Rcheck/signifinder-Ex.timings
| name | user | system | elapsed | |
| ADOSign | 2.019 | 0.020 | 2.040 | |
| APMSign | 0.214 | 0.013 | 0.225 | |
| ASCSign | 0.054 | 0.004 | 0.057 | |
| CINSign | 0.072 | 0.004 | 0.075 | |
| CISSign | 0.168 | 0.012 | 0.180 | |
| COXISSign | 0.058 | 0.000 | 0.059 | |
| CombinedSign | 0.105 | 0.004 | 0.110 | |
| DNArepSign | 0.056 | 0.000 | 0.056 | |
| ECMSign | 1.476 | 0.108 | 1.584 | |
| EMTSign | 0.238 | 0.000 | 0.238 | |
| HRDSSign | 0.051 | 0.012 | 0.063 | |
| ICBResponseSign | 0.069 | 0.000 | 0.069 | |
| IFNSign | 0.060 | 0.004 | 0.064 | |
| IPRESSign | 0.272 | 0.012 | 0.285 | |
| IPSOVSign | 0.264 | 0.020 | 0.285 | |
| IPSSign | 0.096 | 0.000 | 0.097 | |
| IRGSign | 0.049 | 0.008 | 0.057 | |
| ISCSign | 0.064 | 0.000 | 0.063 | |
| LRRC15CAFSign | 0.300 | 0.012 | 0.312 | |
| MITFlowPTENnegSign | 0.086 | 0.000 | 0.086 | |
| MPSSign | 0.060 | 0.000 | 0.061 | |
| PassONSign | 0.234 | 0.003 | 0.238 | |
| TGFBSign | 0.057 | 0.001 | 0.057 | |
| TLSSign | 0.059 | 0.000 | 0.060 | |
| TinflamSign | 0.058 | 0.000 | 0.058 | |
| VEGFSign | 0.057 | 0.000 | 0.057 | |
| autophagySign | 0.052 | 0.012 | 0.064 | |
| availableSignatures | 0.007 | 0.008 | 0.016 | |
| breastStateSign | 0.037 | 0.003 | 0.040 | |
| cellCycleSign | 0.063 | 0.001 | 0.063 | |
| chemokineSign | 0.083 | 0.007 | 0.091 | |
| consensusOVSign | 70.760 | 0.409 | 71.175 | |
| correlationSignPlot | 1.643 | 0.084 | 1.727 | |
| evaluationSignPlot | 1.539 | 0.112 | 1.650 | |
| expandedImmuneSign | 0.061 | 0.004 | 0.064 | |
| ferroptosisSign | 0.062 | 0.004 | 0.066 | |
| geneHeatmapSignPlot | 1.302 | 0.044 | 1.346 | |
| getSignGenes | 0.004 | 0.004 | 0.008 | |
| glioCellStateSign | 0.041 | 0.000 | 0.040 | |
| glycolysisSign | 0.06 | 0.00 | 0.06 | |
| heatmapSignPlot | 2.18 | 0.02 | 2.20 | |
| hypoxiaSign | 0.052 | 0.008 | 0.060 | |
| immuneCytSign | 0.052 | 0.012 | 0.064 | |
| immunoScoreSign | 0.066 | 0.008 | 0.073 | |
| lipidMetabolismSign | 0.054 | 0.004 | 0.058 | |
| matrisomeSign | 0.059 | 0.000 | 0.059 | |
| melStateSign | 0.034 | 0.008 | 0.042 | |
| mitoticIndexSign | 0.054 | 0.004 | 0.058 | |
| multipleSign | 145.115 | 0.875 | 145.995 | |
| oneSignPlot | 0.367 | 0.001 | 0.367 | |
| pyroptosisSign | 0.066 | 0.003 | 0.069 | |
| ridgelineSignPlot | 1.082 | 0.032 | 1.114 | |
| stemCellCD49fSign | 0.061 | 0.000 | 0.060 | |
| survivalSignPlot | 1.467 | 0.020 | 1.488 | |