| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-02 09:00:51 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| 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 | ||||
|
To the developers/maintainers of the signifinder package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1852/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| signifinder 1.1.0 (landing page) Stefania Pirrotta
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
| Package: signifinder |
| Version: 1.1.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:signifinder.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings signifinder_1.1.0.tar.gz |
| StartedAt: 2022-12-29 03:35:33 -0500 (Thu, 29 Dec 2022) |
| EndedAt: 2022-12-29 03:44:22 -0500 (Thu, 29 Dec 2022) |
| EllapsedTime: 528.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: signifinder.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:signifinder.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings signifinder_1.1.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/signifinder.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'signifinder/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'signifinder' version '1.1.0'
* 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 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 R 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 107.27 0.14 107.40
consensusOVSign 54.99 0.11 55.09
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... 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: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL signifinder ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/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 Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
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
pyroptosisSignShao is using 100% of signature genes
'select()' returned 1:1 mapping between keys and columns
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
'select()' returned 1:1 mapping between keys and columns
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
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..."
'select()' returned 1:1 mapping between keys and columns
[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..."
'select()' returned 1:1 mapping between keys and columns
[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..."
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 36% of signature genes
CINSign is using 36% 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 9 | SKIP 0 | PASS 194 ]
[ FAIL 0 | WARN 9 | SKIP 0 | PASS 194 ]
>
> proc.time()
user system elapsed
82.29 3.31 85.93
signifinder.Rcheck/signifinder-Ex.timings
| name | user | system | elapsed | |
| ASCSign | 0.08 | 0.01 | 0.09 | |
| CINSign | 0.04 | 0.00 | 0.05 | |
| CISSign | 0.03 | 0.00 | 0.03 | |
| DNArepSign | 0.05 | 0.00 | 0.05 | |
| ECMSign | 0.11 | 0.00 | 0.11 | |
| EMTSign | 0.11 | 0.00 | 0.11 | |
| HRDSSign | 0.04 | 0.00 | 0.05 | |
| IFNSign | 0.05 | 0.00 | 0.04 | |
| IPRESSign | 0.19 | 0.02 | 0.21 | |
| IPSOVSign | 0.11 | 0.01 | 0.12 | |
| IPSSign | 0.07 | 0.02 | 0.09 | |
| ISCSign | 0.07 | 0.00 | 0.07 | |
| PassONSign | 0.09 | 0.00 | 0.09 | |
| TLSSign | 0.02 | 0.01 | 0.03 | |
| TinflamSign | 0.03 | 0.00 | 0.03 | |
| VEGFSign | 0.03 | 0.00 | 0.03 | |
| autophagySign | 0.04 | 0.02 | 0.05 | |
| availableSignatures | 0.01 | 0.00 | 0.01 | |
| cellCycleSign | 0.05 | 0.00 | 0.05 | |
| chemokineSign | 0.01 | 0.02 | 0.03 | |
| consensusOVSign | 54.99 | 0.11 | 55.09 | |
| correlationSignPlot | 1.23 | 0.17 | 1.43 | |
| expandedImmuneSign | 0.03 | 0.00 | 0.04 | |
| ferroptosisSign | 0.05 | 0.00 | 0.05 | |
| geneHeatmapSignPlot | 1.17 | 0.00 | 1.22 | |
| glycolysisSign | 0.03 | 0.00 | 0.04 | |
| heatmapSignPlot | 1.61 | 0.05 | 1.65 | |
| hypoxiaSign | 0.02 | 0.02 | 0.03 | |
| immuneCytSign | 0.03 | 0.01 | 0.05 | |
| immunoScoreSign | 0.03 | 0.02 | 0.05 | |
| lipidMetabolismSign | 0.03 | 0.00 | 0.03 | |
| matrisomeSign | 0.03 | 0.01 | 0.04 | |
| mitoticIndexSign | 0.03 | 0.00 | 0.04 | |
| multipleSign | 107.27 | 0.14 | 107.40 | |
| oneSignPlot | 0.41 | 0.05 | 0.46 | |
| pyroptosisSign | 0.04 | 0.00 | 0.04 | |
| ridgelineSignPlot | 0.93 | 0.03 | 0.97 | |
| stemCellCD49fSign | 0.04 | 0.00 | 0.05 | |
| survivalSignPlot | 2.05 | 0.09 | 2.23 | |