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This page was generated on 2024-05-04 11:36:53 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 1418/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
netDx 1.16.0  (landing page)
Shraddha Pai
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/netDx
git_branch: RELEASE_3_19
git_last_commit: 3e00d1b
git_last_commit_date: 2024-04-30 11:20:33 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    TIMEOUT  
palomino3Windows 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  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for netDx on nebbiolo1


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.

raw results


Summary

Package: netDx
Version: 1.16.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:netDx.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings netDx_1.16.0.tar.gz
StartedAt: 2024-05-04 01:37:10 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 02:17:10 -0400 (Sat, 04 May 2024)
EllapsedTime: 2400.5 seconds
RetCode: None
Status:   TIMEOUT  
CheckDir: netDx.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:netDx.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings netDx_1.16.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/netDx.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘netDx/DESCRIPTION’ ... OK
* this is package ‘netDx’ version ‘1.16.0’
* 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 ... OK
* 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        20.233  1.554  33.202
buildPredictor             20.346  0.724  22.883
RR_featureTally             7.496  0.760   8.255
smoothMutations_LabelProp   7.459  0.609  31.075
runFeatureSelection         6.918  0.431   4.526
compileFeatures             6.729  0.394  22.783
thresholdSmoothedMutations  2.391  0.124  27.673
enrichLabelNets             2.174  0.281  60.256
getEnr                      0.869  0.195  10.750
makePSN_NamedMatrix         0.078  0.004   9.447
countIntType_batch          0.021  0.000   9.512
* 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 re-building of vignette outputs ...

Installation output

netDx.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL netDx
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/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 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 
 65.108   5.579 249.810 

Example timings

netDx.Rcheck/netDx-Ex.timings

nameusersystemelapsed
MB.pheno0.0060.0000.006
RR_featureTally7.4960.7608.255
avgNormDiff0.0440.0030.047
buildPredictor20.346 0.72422.883
buildPredictor_sparseGenetic0.6730.0161.146
callFeatSel0.0730.0000.072
callOverallSelectedFeatures0.0750.0120.086
cleanPathwayName0.0010.0000.000
cnv_GR0.0320.0000.031
cnv_TTstatus0.0050.0200.025
cnv_netPass0.0030.0000.004
cnv_netScores0.0040.0200.023
cnv_patientNetCount0.1120.1040.216
cnv_pheno0.0050.0040.009
compareShortestPath0.0230.0040.028
compileFeatureScores0.0080.0000.009
compileFeatures 6.729 0.39422.783
confmat0.0050.0000.005
confusionMatrix0.1310.0080.140
convertToMAE0.1310.0000.132
countIntType0.0010.0000.002
countIntType_batch0.0210.0009.512
countPatientsInNet0.0030.0000.004
createPSN_MultiData20.233 1.55433.202
dataList2List0.3110.0200.330
enrichLabelNets 2.174 0.28160.256
featScores0.0270.0240.051
fetchPathwayDefinitions0.3340.0200.570
genes0.0030.0000.003
getEMapInput0.7030.0680.800
getEMapInput_many0.7560.0880.869
getEnr 0.869 0.19510.750
getFeatureScores0.0160.0000.016
getFileSep000
getGMjar_path0.1260.0420.146
getNetConsensus0.0120.0000.012
getOR0.0030.0000.004
getPatientPredictions1.7480.0361.786
getPatientRankings0.0870.0040.091
getRegionOL0.2710.0360.308
getResults0.1280.0080.137
getSimilarity0.1990.0080.208
makePSN_NamedMatrix0.0780.0049.447
makePSN_RangeSets0.0150.0000.015
makeQueries0.0080.0000.008
makeSymmetric0.0010.0000.001
mapNamedRangesToSets0.0310.0070.038
modelres0.0010.0020.003
normDiff0.0000.0010.001
npheno0.0000.0020.002
pathwayList0.0000.0070.007
pathway_GR0.0650.0050.070
perfCalc0.0020.0000.002
pheno0.0050.0030.009
pheno_full0.0020.0000.002
plotEmap0.8480.0411.046
plotPerf1.2270.0241.251
plotPerf_multi0.0380.0000.038
predRes0.0030.0000.003
predictPatientLabels0.0020.0050.007
pruneNets0.000.010.01
randAlphanumString0.0000.0000.001
readPathways0.7800.0730.880
runFeatureSelection6.9180.4314.526
runQuery2.8050.2504.206
setupFeatureDB0.0990.0040.103
silh0.0040.0000.004
sim.eucscale0.2600.0320.292
sim.pearscale0.6040.0440.648
simpleCap0.0010.0000.000
smoothMutations_LabelProp 7.459 0.60931.075
sparsify20.9490.1281.077
sparsify32.1060.1552.261
splitTestTrain0.0170.0040.022
splitTestTrain_resampling0.0020.0040.006
tSNEPlotter0.8240.0320.856
thresholdSmoothedMutations 2.391 0.12427.673
toymodel0.9222.0652.986
updateNets0.0010.0090.010
writeNetsSIF0.0060.0010.008
writeQueryBatchFile0.0020.0010.004
writeQueryFile0.0060.0020.007
xpr0.0500.0160.065