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This page was generated on 2024-05-04 11:40:51 -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 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: 1.16.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:netDx.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings netDx_1.16.0.tar.gz
StartedAt: 2024-05-04 10:05:12 -0000 (Sat, 04 May 2024)
EndedAt: 2024-05-04 10:21:39 -0000 (Sat, 04 May 2024)
EllapsedTime: 986.8 seconds
RetCode: 0
Status:   OK  
CheckDir: netDx.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:netDx.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --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: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    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 ‘1.16.0’
* 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 ... 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             26.241  0.543  43.862
createPSN_MultiData        22.779  0.473  50.708
RR_featureTally            20.891  0.487  21.421
sim.pearscale              11.396  0.040  11.458
smoothMutations_LabelProp   9.686  0.506  34.846
getSimilarity               8.307  0.008   8.327
getPatientPredictions       6.677  0.100   6.785
thresholdSmoothedMutations  6.166  0.176  31.100
runFeatureSelection         5.605  0.475   4.875
plotPerf                    5.899  0.024   5.930
compileFeatures             4.831  0.415  26.105
enrichLabelNets             1.950  0.133  73.651
getEnr                      0.914  0.142  12.495
makePSN_NamedMatrix         0.082  0.022  11.589
countIntType_batch          0.022  0.002  11.462
* 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-3.19-bioc/meat/netDx.Rcheck/00check.log’
for details.


Installation output

netDx.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL netDx
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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: 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 
 73.768   4.899 319.387 

Example timings

netDx.Rcheck/netDx-Ex.timings

nameusersystemelapsed
MB.pheno0.0060.0000.007
RR_featureTally20.891 0.48721.421
avgNormDiff0.0480.0040.053
buildPredictor26.241 0.54343.862
buildPredictor_sparseGenetic0.6890.0283.520
callFeatSel0.1360.0010.137
callOverallSelectedFeatures0.1190.0120.132
cleanPathwayName0.0010.0000.000
cnv_GR0.0350.0080.043
cnv_TTstatus0.0030.0040.008
cnv_netPass0.0040.0000.004
cnv_netScores0.0030.0040.007
cnv_patientNetCount0.1110.0280.139
cnv_pheno0.010.000.01
compareShortestPath0.0350.0040.039
compileFeatureScores0.0110.0000.013
compileFeatures 4.831 0.41526.105
confmat0.0030.0000.003
confusionMatrix0.1030.0040.108
convertToMAE0.1630.0000.164
countIntType0.0010.0000.002
countIntType_batch 0.022 0.00211.462
countPatientsInNet0.0020.0000.002
createPSN_MultiData22.779 0.47350.708
dataList2List0.5180.0280.547
enrichLabelNets 1.950 0.13373.651
featScores0.0340.0040.038
fetchPathwayDefinitions0.4290.0363.131
genes0.0040.0000.004
getEMapInput0.9990.0631.311
getEMapInput_many0.9920.0951.329
getEnr 0.914 0.14212.495
getFeatureScores0.0170.0000.017
getFileSep000
getGMjar_path0.1560.0070.163
getNetConsensus0.0170.0000.018
getOR0.0030.0000.004
getPatientPredictions6.6770.1006.785
getPatientRankings0.1240.0080.133
getRegionOL0.4350.0000.435
getResults0.1660.0040.170
getSimilarity8.3070.0088.327
makePSN_NamedMatrix 0.082 0.02211.589
makePSN_RangeSets0.0150.0000.015
makeQueries0.0110.0000.011
makeSymmetric0.0020.0000.002
mapNamedRangesToSets0.0590.0000.059
modelres0.0010.0030.003
normDiff0.0000.0010.001
npheno0.0000.0020.003
pathwayList0.0030.0000.002
pathway_GR0.1010.0160.118
perfCalc0.0040.0000.005
pheno0.0130.0000.014
pheno_full0.0030.0000.003
plotEmap1.1310.0761.915
plotPerf5.8990.0245.930
plotPerf_multi0.0480.0040.052
predRes0.0000.0030.003
predictPatientLabels0.0110.0000.011
pruneNets0.0090.0030.013
randAlphanumString000
readPathways1.0690.1001.881
runFeatureSelection5.6050.4754.875
runQuery2.4680.2504.391
setupFeatureDB0.0730.0040.077
silh0.0040.0000.003
sim.eucscale0.5280.0120.540
sim.pearscale11.396 0.04011.458
simpleCap0.0000.0000.001
smoothMutations_LabelProp 9.686 0.50634.846
sparsify24.8740.0884.968
sparsify31.3250.0001.327
splitTestTrain0.0280.0000.028
splitTestTrain_resampling0.0070.0000.006
tSNEPlotter1.4670.0121.481
thresholdSmoothedMutations 6.166 0.17631.100
toymodel1.1240.3191.446
updateNets0.0080.0000.008
writeNetsSIF0.0080.0000.008
writeQueryBatchFile0.0040.0000.003
writeQueryFile0.0060.0000.006
xpr0.0290.0080.037