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This page was generated on 2024-06-28 17:40 -0400 (Fri, 28 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4760
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4494
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4508
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4466
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4362
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 1972/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
signifinder 1.6.0  (landing page)
Stefania Pirrotta
Snapshot Date: 2024-06-26 14:00 -0400 (Wed, 26 Jun 2024)
git_url: https://git.bioconductor.org/packages/signifinder
git_branch: RELEASE_3_19
git_last_commit: b1f9b88
git_last_commit_date: 2024-04-30 11:45:33 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  ERROR    ERROR  skippedskipped
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  ERROR    ERROR  skippedskipped


CHECK results for signifinder on nebbiolo1

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.

raw results


Summary

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: 2024-06-27 03:50:58 -0400 (Thu, 27 Jun 2024)
EndedAt: 2024-06-27 04:07:20 -0400 (Thu, 27 Jun 2024)
EllapsedTime: 982.0 seconds
RetCode: 0
Status:   OK  
CheckDir: signifinder.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* 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    140.815  0.768 141.583
consensusOVSign  70.494  0.447  70.947
* 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


Installation output

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)

Tests output

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

pyroptosisSignYe 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 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 100% of responder signature genes
ICBResponseSign is using 0% of nonresponder signature genes
ICBResponseSign is using 0% of nonresponder 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 
248.450   4.134 252.578 

Example timings

signifinder.Rcheck/signifinder-Ex.timings

nameusersystemelapsed
ADOSign2.0010.0092.008
APMSign0.1870.0370.223
ASCSign0.0570.0000.056
CINSign0.0710.0030.076
CISSign0.1620.0090.169
COXISSign0.0510.0070.058
CombinedSign0.1080.0000.108
DNArepSign0.0540.0030.058
ECMSign1.3300.0921.422
EMTSign0.2390.0000.239
HRDSSign0.0620.0010.063
ICBResponseSign0.0630.0040.067
IFNSign0.0520.0030.055
IPRESSign0.2700.0050.274
IPSOVSign0.2600.0080.268
IPSSign0.0930.0030.097
IRGSign0.0550.0000.055
ISCSign0.0620.0000.062
LRRC15CAFSign0.2890.0150.305
MITFlowPTENnegSign0.0870.0000.087
MPSSign0.0530.0080.061
PassONSign0.2350.0040.240
TGFBSign0.0560.0010.057
TLSSign0.0580.0000.058
TinflamSign0.0560.0000.056
VEGFSign0.0560.0000.056
autophagySign0.0490.0080.057
availableSignatures0.0040.0120.016
breastStateSign0.040.000.04
cellCycleSign0.0480.0120.059
chemokineSign0.0630.0070.071
consensusOVSign70.494 0.44770.947
correlationSignPlot1.6040.1321.737
evaluationSignPlot1.4810.1121.593
expandedImmuneSign0.0590.0000.059
ferroptosisSign0.0550.0080.063
geneHeatmapSignPlot1.2950.0121.307
getSignGenes0.0040.0040.008
glioCellStateSign0.040.000.04
glycolysisSign0.0610.0000.061
heatmapSignPlot2.1930.0042.197
hypoxiaSign0.060.000.06
immuneCytSign0.0610.0040.065
immunoScoreSign0.0610.0080.068
lipidMetabolismSign0.0530.0040.057
matrisomeSign0.0570.0040.061
melStateSign0.0340.0080.042
mitoticIndexSign0.0520.0040.056
multipleSign140.815 0.768141.583
oneSignPlot0.3840.0240.408
pyroptosisSign0.0730.0000.073
ridgelineSignPlot1.0890.0561.144
stemCellCD49fSign0.060.000.06
survivalSignPlot1.4080.0401.448