Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 1406/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
netDx 1.18.0  (landing page)
Shraddha Pai
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/netDx
git_branch: RELEASE_3_20
git_last_commit: 070163e
git_last_commit_date: 2024-10-29 10:43:07 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    ERROR  skipped
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    ERROR  skipped
palomino8Windows Server 2022 Datacenter / x64... NOT SUPPORTED ...
lconwaymacOS 12.7.1 Monterey / x86_64  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: 1.18.0
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_1.18.0.tar.gz
StartedAt: 2024-11-20 10:28:00 -0000 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 10:44:47 -0000 (Wed, 20 Nov 2024)
EllapsedTime: 1006.8 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_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/netDx.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘netDx/DESCRIPTION’ ... OK
* this is package ‘netDx’ version ‘1.18.0’
* 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 ... 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 ... NOTE
  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               26.426  1.755  46.406
createPSN_MultiData          24.407  2.957  55.234
RR_featureTally              22.158  0.599  22.850
sim.pearscale                11.208  0.028  11.273
smoothMutations_LabelProp     9.246  0.480  33.604
getSimilarity                 8.149  0.012   8.166
getPatientPredictions         6.650  0.172   6.833
runFeatureSelection           5.851  0.377   4.873
plotPerf                      5.790  0.036   5.847
compileFeatures               4.810  0.397  27.189
thresholdSmoothedMutations    3.628  0.081  27.992
enrichLabelNets               2.158  0.982  73.408
getEnr                        0.988  0.267  13.210
buildPredictor_sparseGenetic  0.775  0.086  20.314
makePSN_NamedMatrix           0.096  0.005  11.631
countIntType_batch            0.021  0.006  11.944
* 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-3.20-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-4.4.1/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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (netDx)

Tests output

netDx.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
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

> 
> 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 
 73.581   4.356 312.553 

Example timings

netDx.Rcheck/netDx-Ex.timings

nameusersystemelapsed
MB.pheno0.0030.0040.006
RR_featureTally22.158 0.59922.850
avgNormDiff0.0510.0000.052
buildPredictor26.426 1.75546.406
buildPredictor_sparseGenetic 0.775 0.08620.314
callFeatSel0.1330.0160.150
callOverallSelectedFeatures0.1270.0120.139
cleanPathwayName0.0010.0000.000
cnv_GR0.0400.0040.044
cnv_TTstatus0.0030.0040.008
cnv_netPass0.0040.0000.004
cnv_netScores0.0030.0040.007
cnv_patientNetCount0.1260.0120.139
cnv_pheno0.010.000.01
compareShortestPath0.0260.0120.038
compileFeatureScores0.0120.0000.013
compileFeatures 4.810 0.39727.189
confmat0.0000.0030.003
confusionMatrix0.1100.0040.175
convertToMAE0.1700.0200.191
countIntType0.0020.0000.001
countIntType_batch 0.021 0.00611.944
countPatientsInNet0.0000.0020.003
createPSN_MultiData24.407 2.95755.234
dataList2List0.4780.0120.491
enrichLabelNets 2.158 0.98273.408
featScores0.0360.0040.039
fetchPathwayDefinitions0.4430.0151.642
genes0.0040.0000.004
getEMapInput1.0310.1401.412
getEMapInput_many1.0670.2831.586
getEnr 0.988 0.26713.210
getFeatureScores0.0150.0080.023
getFileSep000
getGMjar_path0.1790.0510.228
getNetConsensus0.0260.0000.025
getOR0.0040.0000.005
getPatientPredictions6.6500.1726.833
getPatientRankings0.1210.0080.130
getRegionOL0.4130.0080.421
getResults0.1610.0040.165
getSimilarity8.1490.0128.166
makePSN_NamedMatrix 0.096 0.00511.631
makePSN_RangeSets0.0150.0000.015
makeQueries0.0100.0010.011
makeSymmetric0.0010.0000.002
mapNamedRangesToSets0.0530.0040.058
modelres0.0040.0000.004
normDiff0.0010.0000.001
npheno0.0020.0000.002
pathwayList0.0020.0000.002
pathway_GR0.0970.0150.113
perfCalc0.0000.0030.003
pheno0.0110.0000.012
pheno_full0.0030.0010.002
plotEmap1.0510.0511.874
plotPerf5.7900.0365.847
plotPerf_multi0.0510.0000.052
predRes0.0040.0000.004
predictPatientLabels0.0110.0000.010
pruneNets0.0050.0080.013
randAlphanumString000
readPathways1.0830.1031.896
runFeatureSelection5.8510.3774.873
runQuery2.4360.3094.440
setupFeatureDB0.0670.0080.076
silh0.0040.0000.003
sim.eucscale0.5500.0160.567
sim.pearscale11.208 0.02811.273
simpleCap000
smoothMutations_LabelProp 9.246 0.48033.604
sparsify24.6700.1124.790
sparsify32.2990.1402.443
splitTestTrain0.0250.0000.025
splitTestTrain_resampling0.0040.0020.006
tSNEPlotter1.4180.0211.353
thresholdSmoothedMutations 3.628 0.08127.992
toymodel1.0760.3361.414
updateNets0.0090.0000.009
writeNetsSIF0.0040.0040.008
writeQueryBatchFile0.0030.0000.004
writeQueryFile0.0070.0000.008
xpr0.0370.0000.038