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This page was generated on 2025-01-04 11:46 -0500 (Sat, 04 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4756
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4475
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4435
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4390
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4383
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 1400/2275HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
netDx 1.19.1  (landing page)
Shraddha Pai
Snapshot Date: 2025-01-03 13:40 -0500 (Fri, 03 Jan 2025)
git_url: https://git.bioconductor.org/packages/netDx
git_branch: devel
git_last_commit: 11cd9eb
git_last_commit_date: 2024-12-17 11:22:06 -0500 (Tue, 17 Dec 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    ERROR  skipped
palomino7Windows Server 2022 Datacenter / x64... NOT SUPPORTED ...
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.7.1 Ventura / arm64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 22.03 LTS-SP1) / 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: 1.19.1
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_1.19.1.tar.gz
StartedAt: 2025-01-04 08:47:16 -0000 (Sat, 04 Jan 2025)
EndedAt: 2025-01-04 09:04:10 -0000 (Sat, 04 Jan 2025)
EllapsedTime: 1014.3 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_1.19.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/netDx.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* 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)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘netDx/DESCRIPTION’ ... OK
* this is package ‘netDx’ version ‘1.19.1’
* 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 ... NOTE
Warning: program compiled against libxml 212 using older 211
* 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             25.819  0.551  47.802
createPSN_MultiData        22.140  1.127  53.692
RR_featureTally            18.892  0.132  19.744
sim.pearscale              10.040  0.021  10.108
smoothMutations_LabelProp   9.134  0.458  35.207
getSimilarity               7.178  0.016   7.548
getPatientPredictions       6.832  0.103   7.410
thresholdSmoothedMutations  6.098  0.238  31.567
compileFeatures             5.625  0.280  33.659
plotPerf                    5.864  0.025   6.662
runFeatureSelection         5.434  0.329   7.702
runQuery                    2.495  0.165   6.443
enrichLabelNets             1.769  0.170  71.439
getEnr                      0.826  0.206  13.351
makePSN_NamedMatrix         0.091  0.008  11.328
countIntType_batch          0.025  0.004  12.076
* 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: 5 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-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘netDx’ ...
** 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) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 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 
 73.362   6.417 334.152 

Example timings

netDx.Rcheck/netDx-Ex.timings

nameusersystemelapsed
MB.pheno0.0060.0000.005
RR_featureTally18.892 0.13219.744
avgNormDiff0.0520.0000.052
buildPredictor25.819 0.55147.802
buildPredictor_sparseGenetic0.6660.0162.492
callFeatSel0.1320.0000.199
callOverallSelectedFeatures0.1110.0080.119
cleanPathwayName000
cnv_GR0.0330.0040.044
cnv_TTstatus0.0040.0040.008
cnv_netPass0.0000.0040.016
cnv_netScores0.0070.0000.007
cnv_patientNetCount0.1170.0280.256
cnv_pheno0.0090.0000.010
compareShortestPath0.0370.0000.046
compileFeatureScores0.0060.0040.023
compileFeatures 5.625 0.28033.659
confmat0.0030.0000.003
confusionMatrix0.1150.0120.256
convertToMAE0.1780.0120.371
countIntType0.0010.0000.001
countIntType_batch 0.025 0.00412.076
countPatientsInNet0.0020.0000.007
createPSN_MultiData22.140 1.12753.692
dataList2List0.4310.0120.457
enrichLabelNets 1.769 0.17071.439
featScores0.0350.0010.037
fetchPathwayDefinitions0.3540.0241.686
genes0.0030.0000.003
getEMapInput0.9280.0641.333
getEMapInput_many0.9710.1101.367
getEnr 0.826 0.20613.351
getFeatureScores0.0170.0000.037
getFileSep0.0010.0000.000
getGMjar_path0.1610.0210.422
getNetConsensus0.0190.0000.038
getOR0.0040.0000.008
getPatientPredictions6.8320.1037.410
getPatientRankings0.1100.0120.122
getRegionOL0.4240.0040.429
getResults0.1540.0040.157
getSimilarity7.1780.0167.548
makePSN_NamedMatrix 0.091 0.00811.328
makePSN_RangeSets0.0110.0040.018
makeQueries0.0070.0040.012
makeSymmetric0.0020.0000.002
mapNamedRangesToSets0.0520.0040.059
modelres0.0040.0000.004
normDiff0.0010.0000.002
npheno0.0000.0020.003
pathwayList0.0010.0010.003
pathway_GR0.1010.0070.110
perfCalc0.0020.0000.002
pheno0.0110.0000.011
pheno_full0.0030.0000.002
plotEmap0.9620.0591.954
plotPerf5.8640.0256.662
plotPerf_multi0.0510.0000.051
predRes0.0000.0030.004
predictPatientLabels0.0060.0040.010
pruneNets0.0120.0010.012
randAlphanumString0.0010.0000.000
readPathways0.9620.1112.002
runFeatureSelection5.4340.3297.702
runQuery2.4950.1656.443
setupFeatureDB0.0680.0000.090
silh0.0030.0000.004
sim.eucscale0.4470.0190.466
sim.pearscale10.040 0.02110.108
simpleCap0.0000.0000.001
smoothMutations_LabelProp 9.134 0.45835.207
sparsify24.3490.1394.851
sparsify31.4000.0241.427
splitTestTrain0.0280.0000.028
splitTestTrain_resampling0.0060.0000.007
tSNEPlotter1.4420.0201.465
thresholdSmoothedMutations 6.098 0.23831.567
toymodel1.0840.3711.461
updateNets0.0080.0000.008
writeNetsSIF0.0080.0000.007
writeQueryBatchFile0.0040.0000.004
writeQueryFile0.0020.0040.006
xpr0.0340.0040.039