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This page was generated on 2025-10-09 11:41 -0400 (Thu, 09 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4832
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4613
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4554
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4585
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 1435/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
netDx 1.20.0  (landing page)
Shraddha Pai
Snapshot Date: 2025-10-06 13:40 -0400 (Mon, 06 Oct 2025)
git_url: https://git.bioconductor.org/packages/netDx
git_branch: RELEASE_3_21
git_last_commit: ba098e1
git_last_commit_date: 2025-04-15 11:54:11 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
merida1macOS 12.7.5 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.6.6 Ventura / arm64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for netDx on kunpeng2

To the developers/maintainers of the netDx package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/netDx.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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: netDx
Version: 1.20.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:netDx.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings netDx_1.20.0.tar.gz
StartedAt: 2025-10-07 12:20:31 -0000 (Tue, 07 Oct 2025)
EndedAt: 2025-10-07 12:41:28 -0000 (Tue, 07 Oct 2025)
EllapsedTime: 1257.1 seconds
RetCode: 0
Status:   OK  
CheckDir: netDx.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:netDx.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings netDx_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/netDx.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘netDx/DESCRIPTION’ ... OK
* this is package ‘netDx’ version ‘1.20.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘netDx’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   6.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Found the following CITATION file in a non-standard place:
  CITATION.cff
Most likely ‘inst/CITATION’ should be used instead.
* 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 whether startup messages can be suppressed ... 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 ... NOTE
checkRd: (-1) getEnr.Rd:53: Lost braces; missing escapes or markup?
    53 | {(+,-),(-,+),(-,-)} interactions. 
       | ^
checkRd: (-1) predict.Rd:27: Lost braces; missing escapes or markup?
    27 | e.g. keys could include {'clinical','rna','methylation'}, and values within 'rna' could include pathway names {'cell cycle', 'DNA repair'}, etc.,
       |                         ^
checkRd: (-1) predict.Rd:27: Lost braces; missing escapes or markup?
    27 | e.g. keys could include {'clinical','rna','methylation'}, and values within 'rna' could include pathway names {'cell cycle', 'DNA repair'}, etc.,
       |                                                                                                               ^
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
buildPredictor             26.804  1.274  53.738
createPSN_MultiData        26.141  1.182  66.894
RR_featureTally            19.796  0.263  23.608
sim.pearscale              10.085  0.035  11.800
smoothMutations_LabelProp   9.593  0.424  53.431
runFeatureSelection         7.028  0.350   8.554
getPatientPredictions       7.197  0.096   8.210
getSimilarity               7.177  0.011   8.056
compileFeatures             6.623  0.260  38.302
plotPerf                    6.463  0.024   7.744
thresholdSmoothedMutations  4.978  0.184  45.375
sparsify2                   4.288  0.095   5.184
runQuery                    3.098  0.214   6.984
enrichLabelNets             1.904  0.059  89.633
getEnr                      0.944  0.135  15.411
makePSN_NamedMatrix         0.093  0.008  14.315
countIntType_batch          0.017  0.010  15.652
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/netDx.Rcheck/00check.log’
for details.


Installation output

netDx.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL netDx
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘netDx’ ...
** this is package ‘netDx’ version ‘1.20.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'netDx' is deprecated and will be removed from Bioconductor
  version 3.22
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'netDx' is deprecated and will be removed from Bioconductor
  version 3.22
** testing if installed package keeps a record of temporary installation path
* DONE (netDx)

Tests output

netDx.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(netDx)

Attaching package: 'netDx'

The following object is masked from 'package:stats':

    predict

Warning message:
In fun(libname, pkgname) :
  Package 'netDx' is deprecated and will be removed from Bioconductor
  version 3.22
> 
> test_check("netDx")
         TT_STATUS
STATUS    TEST TRAIN
  LumA      52   178
  notLumA   52   243
         PRED_CLASS
STATUS    LumA notLumA
  LumA      41      11
  notLumA   17      35
[1] TRUE
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 39 ]
> 
> proc.time()
   user  system elapsed 
 79.055   4.686 402.433 

Example timings

netDx.Rcheck/netDx-Ex.timings

nameusersystemelapsed
MB.pheno0.0080.0000.015
RR_featureTally19.796 0.26323.608
avgNormDiff0.050.000.05
buildPredictor26.804 1.27453.738
buildPredictor_sparseGenetic0.7450.0172.919
callFeatSel0.1380.0040.283
callOverallSelectedFeatures0.1260.0160.192
cleanPathwayName0.0010.0000.000
cnv_GR0.0380.0000.037
cnv_TTstatus0.0040.0040.008
cnv_netPass0.0030.0000.004
cnv_netScores0.0030.0040.007
cnv_patientNetCount0.1220.0080.130
cnv_pheno0.010.000.01
compareShortestPath0.0290.0080.037
compileFeatureScores0.0100.0000.021
compileFeatures 6.623 0.26038.302
confmat0.0020.0000.007
confusionMatrix0.1080.0000.216
convertToMAE0.1720.0040.341
countIntType0.0020.0000.002
countIntType_batch 0.017 0.01015.652
countPatientsInNet0.0010.0020.007
createPSN_MultiData26.141 1.18266.894
dataList2List0.4880.0161.021
enrichLabelNets 1.904 0.05989.633
featScores0.0340.0040.078
fetchPathwayDefinitions0.3820.0482.293
genes0.0030.0000.008
getEMapInput1.0170.0692.013
getEMapInput_many1.0890.1001.749
getEnr 0.944 0.13515.411
getFeatureScores0.0170.0000.017
getFileSep000
getGMjar_path0.1900.0350.487
getNetConsensus0.0200.0000.041
getOR0.0030.0000.004
getPatientPredictions7.1970.0968.210
getPatientRankings0.1390.0000.273
getRegionOL0.4440.0040.737
getResults0.1570.0000.156
getSimilarity7.1770.0118.056
makePSN_NamedMatrix 0.093 0.00814.315
makePSN_RangeSets0.0100.0040.014
makeQueries0.010.000.01
makeSymmetric0.0010.0000.001
mapNamedRangesToSets0.0480.0040.052
modelres0.0030.0000.003
normDiff0.0010.0000.002
npheno0.0020.0000.002
pathwayList0.0030.0000.003
pathway_GR0.0890.0160.106
perfCalc0.0010.0010.003
pheno0.0080.0030.015
pheno_full0.0000.0020.003
plotEmap1.0470.0732.040
plotPerf6.4630.0247.744
plotPerf_multi0.0450.0070.052
predRes0.0040.0010.004
predictPatientLabels0.0110.0000.011
pruneNets0.0090.0030.013
randAlphanumString0.0010.0000.001
readPathways1.0400.0801.991
runFeatureSelection7.0280.3508.554
runQuery3.0980.2146.984
setupFeatureDB0.0620.0040.111
silh0.0030.0000.004
sim.eucscale0.5190.0200.762
sim.pearscale10.085 0.03511.800
simpleCap0.0000.0000.001
smoothMutations_LabelProp 9.593 0.42453.431
sparsify24.2880.0955.184
sparsify31.4380.0161.876
splitTestTrain0.0280.0000.057
splitTestTrain_resampling0.0070.0000.015
tSNEPlotter1.4990.0242.382
thresholdSmoothedMutations 4.978 0.18445.375
toymodel1.2010.4371.974
updateNets0.0030.0080.011
writeNetsSIF0.0050.0040.009
writeQueryBatchFile0.0040.0000.004
writeQueryFile0.0080.0000.008
xpr0.0300.0040.035