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This page was generated on 2025-09-29 11:41 -0400 (Mon, 29 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4827
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4608
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4549
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4580
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: 2025-09-25 13:40 -0400 (Thu, 25 Sep 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: 2025-09-26 13:20:33 -0000 (Fri, 26 Sep 2025)
EndedAt: 2025-09-26 13:39:18 -0000 (Fri, 26 Sep 2025)
EllapsedTime: 1125.0 seconds
RetCode: 0
Status:   OK  
CheckDir: netDx.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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             28.555  1.417  53.050
createPSN_MultiData        27.093  1.015  60.424
RR_featureTally            19.365  0.235  21.142
smoothMutations_LabelProp   9.863  0.496  45.789
sim.pearscale              10.099  0.040  10.392
getSimilarity               7.288  0.016   7.758
getPatientPredictions       6.928  0.089   7.490
compileFeatures             6.410  0.231  33.620
runFeatureSelection         6.040  0.359   7.345
plotPerf                    5.914  0.032   6.254
thresholdSmoothedMutations  5.247  0.390  42.495
runQuery                    2.919  0.191   5.384
enrichLabelNets             1.979  0.084  83.521
getEnr                      0.926  0.151  14.369
makePSN_NamedMatrix         0.082  0.020  12.841
countIntType_batch          0.025  0.004  13.145
* 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

##############################################################################
##############################################################################
###
### 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 
 78.438   4.291 364.764 

Example timings

netDx.Rcheck/netDx-Ex.timings

nameusersystemelapsed
MB.pheno0.0070.0000.006
RR_featureTally19.365 0.23521.142
avgNormDiff0.050.000.05
buildPredictor28.555 1.41753.050
buildPredictor_sparseGenetic0.7540.0402.373
callFeatSel0.1500.0040.204
callOverallSelectedFeatures0.1340.0120.147
cleanPathwayName0.0000.0000.001
cnv_GR0.0370.0040.041
cnv_TTstatus0.0080.0000.007
cnv_netPass0.0040.0000.004
cnv_netScores0.0070.0000.007
cnv_patientNetCount0.1190.0160.136
cnv_pheno0.010.000.01
compareShortestPath0.0350.0040.039
compileFeatureScores0.0110.0000.023
compileFeatures 6.410 0.23133.620
confmat0.0030.0000.009
confusionMatrix0.1100.0000.218
convertToMAE0.1780.0050.356
countIntType0.0010.0000.002
countIntType_batch 0.025 0.00413.145
countPatientsInNet0.0020.0000.003
createPSN_MultiData27.093 1.01560.424
dataList2List0.4470.0080.585
enrichLabelNets 1.979 0.08483.521
featScores0.0410.0080.055
fetchPathwayDefinitions0.4120.0161.967
genes0.0050.0080.017
getEMapInput1.0200.0481.496
getEMapInput_many1.0730.1111.766
getEnr 0.926 0.15114.369
getFeatureScores0.0160.0000.016
getFileSep000
getGMjar_path0.1710.0320.235
getNetConsensus0.020.000.02
getOR0.0000.0040.004
getPatientPredictions6.9280.0897.490
getPatientRankings0.1400.0040.206
getRegionOL0.4600.0200.481
getResults0.1620.0000.163
getSimilarity7.2880.0167.758
makePSN_NamedMatrix 0.082 0.02012.841
makePSN_RangeSets0.0140.0000.025
makeQueries0.0110.0000.024
makeSymmetric0.0020.0000.001
mapNamedRangesToSets0.0550.0040.120
modelres0.0010.0030.007
normDiff0.0000.0010.006
npheno0.0020.0000.008
pathwayList0.0030.0000.008
pathway_GR0.0960.0200.216
perfCalc0.0020.0000.002
pheno0.0110.0000.023
pheno_full0.0020.0000.008
plotEmap1.0890.1002.250
plotPerf5.9140.0326.254
plotPerf_multi0.0480.0040.053
predRes0.0030.0000.004
predictPatientLabels0.0060.0040.011
pruneNets0.0120.0000.013
randAlphanumString0.0000.0000.001
readPathways1.0030.0591.811
runFeatureSelection6.0400.3597.345
runQuery2.9190.1915.384
setupFeatureDB0.0600.0120.073
silh0.0040.0000.004
sim.eucscale0.4850.0120.497
sim.pearscale10.099 0.04010.392
simpleCap000
smoothMutations_LabelProp 9.863 0.49645.789
sparsify24.2720.1324.724
sparsify31.4510.0041.459
splitTestTrain0.0260.0000.026
splitTestTrain_resampling0.0060.0000.006
tSNEPlotter1.4670.0481.519
thresholdSmoothedMutations 5.247 0.39042.495
toymodel1.2020.4061.726
updateNets0.0030.0070.010
writeNetsSIF0.0090.0000.008
writeQueryBatchFile0.0040.0000.004
writeQueryFile0.0070.0000.007
xpr0.0320.0040.037