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This page was generated on 2025-09-25 11:42 -0400 (Thu, 25 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" 4581
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: 2025-09-22 13:40 -0400 (Mon, 22 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: 2025-09-23 12:45:26 -0000 (Tue, 23 Sep 2025)
EndedAt: 2025-09-23 13:08:02 -0000 (Tue, 23 Sep 2025)
EllapsedTime: 1355.7 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
createPSN_MultiData        26.453  1.441  70.255
buildPredictor             25.986  1.343  53.834
RR_featureTally            19.463  0.199  24.017
smoothMutations_LabelProp   9.755  0.447  55.976
sim.pearscale              10.064  0.047  15.223
getSimilarity               7.299  0.015   9.434
getPatientPredictions       6.902  0.104  10.733
compileFeatures             6.563  0.305  39.201
runFeatureSelection         6.588  0.264   8.523
plotPerf                    5.972  0.023   7.668
thresholdSmoothedMutations  5.216  0.276  48.203
sparsify2                   4.330  0.127   5.248
runQuery                    3.007  0.172   6.607
enrichLabelNets             1.954  0.064  97.518
getEnr                      0.894  0.180  19.078
makePSN_NamedMatrix         0.099  0.024  14.941
countIntType_batch          0.022  0.014  14.440
* 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 
 81.558   4.019 461.724 

Example timings

netDx.Rcheck/netDx-Ex.timings

nameusersystemelapsed
MB.pheno0.0070.0000.006
RR_featureTally19.463 0.19924.017
avgNormDiff0.0470.0000.047
buildPredictor25.986 1.34353.834
buildPredictor_sparseGenetic0.6870.0442.434
callFeatSel0.1540.0000.219
callOverallSelectedFeatures0.1300.0160.146
cleanPathwayName000
cnv_GR0.0400.0020.042
cnv_TTstatus0.0070.0000.007
cnv_netPass0.0040.0000.004
cnv_netScores0.0040.0040.008
cnv_patientNetCount0.1280.0200.149
cnv_pheno0.0110.0000.010
compareShortestPath0.0410.0000.040
compileFeatureScores0.0070.0040.012
compileFeatures 6.563 0.30539.201
confmat0.0030.0000.003
confusionMatrix0.1100.0000.223
convertToMAE0.1820.0080.314
countIntType0.0000.0020.002
countIntType_batch 0.022 0.01414.440
countPatientsInNet0.0030.0000.002
createPSN_MultiData26.453 1.44170.255
dataList2List0.4800.0200.995
enrichLabelNets 1.954 0.06497.518
featScores0.0330.0050.069
fetchPathwayDefinitions0.4310.0202.454
genes0.0030.0000.004
getEMapInput0.9490.0561.453
getEMapInput_many1.0400.1402.189
getEnr 0.894 0.18019.078
getFeatureScores0.0160.0000.017
getFileSep000
getGMjar_path0.1960.0180.475
getNetConsensus0.0150.0040.040
getOR0.0030.0000.008
getPatientPredictions 6.902 0.10410.733
getPatientRankings0.1290.0080.176
getRegionOL0.4110.0280.440
getResults0.1610.0000.161
getSimilarity7.2990.0159.434
makePSN_NamedMatrix 0.099 0.02414.941
makePSN_RangeSets0.0140.0000.026
makeQueries0.0110.0000.024
makeSymmetric0.0020.0000.002
mapNamedRangesToSets0.060.000.12
modelres0.0030.0000.008
normDiff0.0000.0020.005
npheno0.0010.0020.003
pathwayList0.0020.0000.009
pathway_GR0.1110.0040.138
perfCalc0.0030.0000.003
pheno0.0110.0000.012
pheno_full0.0030.0000.002
plotEmap1.0410.0682.127
plotPerf5.9720.0237.668
plotPerf_multi0.0510.0040.055
predRes0.0040.0000.004
predictPatientLabels0.0070.0040.011
pruneNets0.0090.0040.013
randAlphanumString000
readPathways1.0510.0922.374
runFeatureSelection6.5880.2648.523
runQuery3.0070.1726.607
setupFeatureDB0.0720.0000.144
silh0.0040.0000.008
sim.eucscale0.4830.0040.492
sim.pearscale10.064 0.04715.223
simpleCap000
smoothMutations_LabelProp 9.755 0.44755.976
sparsify24.3300.1275.248
sparsify31.4540.0281.816
splitTestTrain0.0310.0000.064
splitTestTrain_resampling0.0070.0000.015
tSNEPlotter1.4220.0321.960
thresholdSmoothedMutations 5.216 0.27648.203
toymodel1.1690.3312.099
updateNets0.0100.0000.014
writeNetsSIF0.0080.0000.008
writeQueryBatchFile0.0040.0000.004
writeQueryFile0.0040.0030.008
xpr0.0310.0050.036