| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-10 10:04:41 -0000 (Wed, 10 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6211 |
| 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 1884/2194 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| signifinder 1.3.0 (landing page) Stefania Pirrotta
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: signifinder |
| Version: 1.3.0 |
| 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_1.3.0.tar.gz |
| StartedAt: 2023-05-10 04:49:29 -0000 (Wed, 10 May 2023) |
| EndedAt: 2023-05-10 05:06:18 -0000 (Wed, 10 May 2023) |
| EllapsedTime: 1008.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: signifinder.Rcheck |
| Warnings: NA |
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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_1.3.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/signifinder.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-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 ‘1.3.0’
* 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 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 164.876 0.564 165.444
consensusOVSign 84.352 0.652 85.005
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
cellCycleSignDavoli is using 100% of signature genes
VEGFSign is using 100% of signature genes
ImmuneCytSignDavoli is using 100% of signature genes
[ FAIL 1 | WARN 9 | SKIP 0 | PASS 197 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-Plots.R:30:5'): correlationSignPlot returns a list ───────────
is(res, "list") is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 1 | WARN 9 | SKIP 0 | PASS 197 ]
Error: Test failures
Execution halted
* 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: 1 ERROR
See
‘/home/biocbuild/bbs-3.17-bioc/meat/signifinder.Rcheck/00check.log’
for details.
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-devel_2023-03-12_r83975-bin/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.fail
R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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
pyroptosisSignLin 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 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..."
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 1 | WARN 9 | SKIP 0 | PASS 197 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-Plots.R:30:5'): correlationSignPlot returns a list ───────────
is(res, "list") is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 1 | WARN 9 | SKIP 0 | PASS 197 ]
Error: Test failures
Execution halted
signifinder.Rcheck/signifinder-Ex.timings
| name | user | system | elapsed | |
| ASCSign | 0.116 | 0.000 | 0.116 | |
| CINSign | 0.056 | 0.008 | 0.064 | |
| CISSign | 0.053 | 0.000 | 0.053 | |
| DNArepSign | 0.046 | 0.004 | 0.050 | |
| ECMSign | 0.215 | 0.004 | 0.219 | |
| EMTSign | 0.120 | 0.004 | 0.124 | |
| HRDSSign | 0.055 | 0.004 | 0.059 | |
| IFNSign | 0.047 | 0.000 | 0.047 | |
| IPRESSign | 0.420 | 0.012 | 0.433 | |
| IPSOVSign | 1.451 | 0.132 | 1.583 | |
| IPSSign | 0.119 | 0.004 | 0.123 | |
| ISCSign | 0.063 | 0.000 | 0.063 | |
| PassONSign | 0.129 | 0.004 | 0.132 | |
| TLSSign | 0.050 | 0.004 | 0.054 | |
| TinflamSign | 0.049 | 0.000 | 0.049 | |
| VEGFSign | 0.047 | 0.004 | 0.051 | |
| autophagySign | 0.051 | 0.000 | 0.051 | |
| availableSignatures | 0.009 | 0.000 | 0.009 | |
| cellCycleSign | 0.044 | 0.008 | 0.052 | |
| chemokineSign | 0.051 | 0.000 | 0.051 | |
| consensusOVSign | 84.352 | 0.652 | 85.005 | |
| correlationSignPlot | 2.029 | 0.080 | 2.109 | |
| evaluationSignPlot | 2.518 | 0.095 | 2.614 | |
| expandedImmuneSign | 0.048 | 0.000 | 0.048 | |
| ferroptosisSign | 0.056 | 0.004 | 0.060 | |
| geneHeatmapSignPlot | 1.821 | 0.011 | 1.833 | |
| glycolysisSign | 0.047 | 0.004 | 0.051 | |
| heatmapSignPlot | 4.434 | 0.112 | 4.547 | |
| hypoxiaSign | 0.05 | 0.00 | 0.05 | |
| immuneCytSign | 0.054 | 0.000 | 0.055 | |
| immunoScoreSign | 0.056 | 0.000 | 0.056 | |
| lipidMetabolismSign | 0.045 | 0.000 | 0.045 | |
| matrisomeSign | 0.043 | 0.004 | 0.047 | |
| mitoticIndexSign | 0.042 | 0.004 | 0.046 | |
| multipleSign | 164.876 | 0.564 | 165.444 | |
| oneSignPlot | 0.577 | 0.024 | 0.601 | |
| pyroptosisSign | 0.063 | 0.004 | 0.067 | |
| ridgelineSignPlot | 1.531 | 0.048 | 1.579 | |
| stemCellCD49fSign | 0.05 | 0.00 | 0.05 | |
| survivalSignPlot | 1.794 | 0.028 | 1.822 | |