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This page was generated on 2024-12-24 11:47 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 1399/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
netDx 1.19.1  (landing page)
Shraddha Pai
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
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: 2024-12-24 09:17:55 -0000 (Tue, 24 Dec 2024)
EndedAt: 2024-12-24 09:34:17 -0000 (Tue, 24 Dec 2024)
EllapsedTime: 981.3 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             24.341  1.741  43.994
createPSN_MultiData        23.436  1.415  52.775
RR_featureTally            18.402  0.188  18.628
sim.pearscale              10.073  0.015  10.105
smoothMutations_LabelProp   9.436  0.309  34.343
getPatientPredictions       7.428  0.088   7.528
getSimilarity               7.175  0.004   7.185
plotPerf                    6.697  0.019   6.726
thresholdSmoothedMutations  5.939  0.215  30.184
runFeatureSelection         5.461  0.418   5.380
compileFeatures             5.105  0.388  28.728
enrichLabelNets             1.863  0.058  72.981
getEnr                      0.927  0.156  12.815
makePSN_NamedMatrix         0.105  0.006  11.859
countIntType_batch          0.022  0.004  12.111
* 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 
 73.030   5.428 319.791 

Example timings

netDx.Rcheck/netDx-Ex.timings

nameusersystemelapsed
MB.pheno0.0060.0000.006
RR_featureTally18.402 0.18818.628
avgNormDiff0.050.000.05
buildPredictor24.341 1.74143.994
buildPredictor_sparseGenetic0.6590.0082.830
callFeatSel0.1320.0000.133
callOverallSelectedFeatures0.1150.0080.123
cleanPathwayName000
cnv_GR0.0400.0000.041
cnv_TTstatus0.0030.0040.008
cnv_netPass0.0030.0000.004
cnv_netScores0.0030.0040.007
cnv_patientNetCount0.1140.0160.130
cnv_pheno0.010.000.01
compareShortestPath0.0380.0120.050
compileFeatureScores0.0040.0080.013
compileFeatures 5.105 0.38828.728
confmat0.0030.0000.003
confusionMatrix0.1080.0040.111
convertToMAE0.1700.0040.175
countIntType0.0010.0000.002
countIntType_batch 0.022 0.00412.111
countPatientsInNet0.0030.0000.002
createPSN_MultiData23.436 1.41552.775
dataList2List0.4580.0040.468
enrichLabelNets 1.863 0.05872.981
featScores0.0330.0040.037
fetchPathwayDefinitions0.3900.0241.637
genes0.0030.0000.003
getEMapInput0.9810.0441.277
getEMapInput_many1.0130.0881.345
getEnr 0.927 0.15612.815
getFeatureScores0.0180.0000.018
getFileSep0.0010.0000.000
getGMjar_path0.1460.0300.179
getNetConsensus0.0180.0000.018
getOR0.0030.0000.003
getPatientPredictions7.4280.0887.528
getPatientRankings0.1230.0000.124
getRegionOL0.4110.0160.428
getResults0.1620.0000.162
getSimilarity7.1750.0047.185
makePSN_NamedMatrix 0.105 0.00611.859
makePSN_RangeSets0.0160.0000.032
makeQueries0.0080.0040.025
makeSymmetric0.0010.0000.002
mapNamedRangesToSets0.0530.0040.113
modelres0.0040.0000.008
normDiff0.0020.0000.002
npheno0.0030.0000.003
pathwayList0.0030.0000.003
pathway_GR0.1000.0080.113
perfCalc0.0020.0000.003
pheno0.0110.0000.011
pheno_full0.0030.0000.002
plotEmap1.0240.1801.930
plotPerf6.6970.0196.726
plotPerf_multi0.0570.0000.057
predRes0.0000.0040.004
predictPatientLabels0.0070.0040.011
pruneNets0.0100.0040.014
randAlphanumString0.0010.0000.001
readPathways1.0790.1321.969
runFeatureSelection5.4610.4185.380
runQuery2.3270.2854.455
setupFeatureDB0.0690.0040.073
silh0.0040.0000.004
sim.eucscale0.4780.0310.511
sim.pearscale10.073 0.01510.105
simpleCap000
smoothMutations_LabelProp 9.436 0.30934.343
sparsify24.1930.0964.295
sparsify31.3650.0081.375
splitTestTrain0.0190.0080.027
splitTestTrain_resampling0.0070.0000.007
tSNEPlotter1.3970.0161.415
thresholdSmoothedMutations 5.939 0.21530.184
toymodel1.1310.2961.429
updateNets0.0080.0000.008
writeNetsSIF0.0070.0000.008
writeQueryBatchFile0.0040.0000.004
writeQueryFile0.0070.0000.007
xpr0.0290.0080.036