| Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:31 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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 | ||||
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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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1896/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| signifinder 1.1.1 (landing page) Stefania Pirrotta
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
| Package: signifinder |
| Version: 1.1.1 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:signifinder.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings signifinder_1.1.1.tar.gz |
| StartedAt: 2023-04-11 23:35:31 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 23:49:58 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 866.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: signifinder.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:signifinder.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings signifinder_1.1.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/signifinder.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘signifinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘signifinder’ version ‘1.1.1’
* 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 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 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 154.598 0.536 155.135
consensusOVSign 76.454 0.344 76.803
* 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 ...
‘signifinder.Rmd’ using ‘UTF-8’... OK
NONE
* 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-3.17-bioc/R/bin/R CMD INSTALL signifinder ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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 4.3.0 alpha (2023-04-03 r84154)
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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
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
'select()' returned 1:1 mapping between keys and columns
autophagySignChenM is using 27% of OS signature genes
TinflamSign is using 100% of signature genes
EMTSignMiow is using 100% of epithelial signature genes
EMTSignMiow is using 0% of mesenchymal signature genes
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
EMTSignMiow is using 0% of mesenchymal 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 11 | SKIP 0 | PASS 198 ]
[ FAIL 0 | WARN 11 | SKIP 0 | PASS 198 ]
>
> proc.time()
user system elapsed
112.695 4.408 117.096
signifinder.Rcheck/signifinder-Ex.timings
| name | user | system | elapsed | |
| ASCSign | 0.107 | 0.024 | 0.131 | |
| CINSign | 0.045 | 0.015 | 0.061 | |
| CISSign | 0.048 | 0.004 | 0.052 | |
| DNArepSign | 0.041 | 0.007 | 0.050 | |
| ECMSign | 0.206 | 0.008 | 0.214 | |
| EMTSign | 0.093 | 0.012 | 0.105 | |
| HRDSSign | 0.045 | 0.004 | 0.049 | |
| IFNSign | 0.035 | 0.008 | 0.043 | |
| IPRESSign | 0.224 | 0.016 | 0.240 | |
| IPSOVSign | 0.141 | 0.004 | 0.144 | |
| IPSSign | 0.086 | 0.000 | 0.087 | |
| ISCSign | 0.047 | 0.012 | 0.059 | |
| PassONSign | 0.089 | 0.028 | 0.117 | |
| TLSSign | 0.044 | 0.003 | 0.048 | |
| TinflamSign | 0.041 | 0.004 | 0.045 | |
| VEGFSign | 0.039 | 0.008 | 0.047 | |
| autophagySign | 0.046 | 0.000 | 0.046 | |
| availableSignatures | 0.006 | 0.003 | 0.010 | |
| cellCycleSign | 0.043 | 0.004 | 0.047 | |
| chemokineSign | 0.143 | 0.016 | 0.159 | |
| consensusOVSign | 76.454 | 0.344 | 76.803 | |
| correlationSignPlot | 1.451 | 0.124 | 1.575 | |
| evaluationSignPlot | 3.746 | 0.147 | 3.894 | |
| expandedImmuneSign | 0.049 | 0.000 | 0.050 | |
| ferroptosisSign | 0.055 | 0.000 | 0.055 | |
| geneHeatmapSignPlot | 1.449 | 0.091 | 1.540 | |
| glycolysisSign | 0.050 | 0.001 | 0.050 | |
| heatmapSignPlot | 2.223 | 0.016 | 2.239 | |
| hypoxiaSign | 0.047 | 0.004 | 0.051 | |
| immuneCytSign | 0.056 | 0.000 | 0.056 | |
| immunoScoreSign | 0.053 | 0.004 | 0.057 | |
| lipidMetabolismSign | 0.044 | 0.003 | 0.049 | |
| matrisomeSign | 0.043 | 0.003 | 0.048 | |
| mitoticIndexSign | 0.045 | 0.000 | 0.046 | |
| multipleSign | 154.598 | 0.536 | 155.135 | |
| oneSignPlot | 0.559 | 0.028 | 0.588 | |
| pyroptosisSign | 0.059 | 0.000 | 0.059 | |
| ridgelineSignPlot | 1.273 | 0.047 | 1.321 | |
| stemCellCD49fSign | 0.050 | 0.001 | 0.050 | |
| survivalSignPlot | 1.34 | 0.04 | 1.38 | |