| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-31 05:44:39 -0000 (Wed, 31 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4219 |
| 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 | ||||
|
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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1352/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| netDx 1.13.0 (landing page) Shraddha Pai
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: netDx |
| Version: 1.13.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:netDx.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings netDx_1.13.0.tar.gz |
| StartedAt: 2023-05-30 13:40:46 -0000 (Tue, 30 May 2023) |
| EndedAt: 2023-05-30 14:14:59 -0000 (Tue, 30 May 2023) |
| EllapsedTime: 2052.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: netDx.Rcheck |
| Warnings: 0 |
##############################################################################
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### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:netDx.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings netDx_1.13.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/netDx.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘netDx/DESCRIPTION’ ... OK
* this is package ‘netDx’ version ‘1.13.0’
* 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 R 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 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 ... OK
* 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 26.385 2.148 58.707
buildPredictor 25.899 1.136 46.036
RR_featureTally 19.551 0.648 20.199
sim.pearscale 12.125 0.180 12.305
smoothMutations_LabelProp 8.499 0.336 44.010
getSimilarity 8.354 0.012 8.367
runFeatureSelection 7.152 0.511 5.087
getPatientPredictions 6.697 0.200 6.900
compileFeatures 6.054 0.518 28.587
plotPerf 5.835 0.040 5.876
sparsify2 5.037 0.144 5.181
thresholdSmoothedMutations 3.793 0.388 39.410
enrichLabelNets 1.984 0.245 75.497
plotEmap 1.228 0.104 5.991
getEnr 0.972 0.144 13.304
makePSN_NamedMatrix 0.092 0.010 12.174
countIntType_batch 0.026 0.000 12.336
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘ThreeWayClassifier.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/netDx.Rcheck/00check.log’
for details.
netDx.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL netDx ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/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)
netDx.Rcheck/tests/testthat.Rout
R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
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
80.134 5.491 336.649
netDx.Rcheck/netDx-Ex.timings
| name | user | system | elapsed | |
| MB.pheno | 0.155 | 0.056 | 0.211 | |
| RR_featureTally | 19.551 | 0.648 | 20.199 | |
| avgNormDiff | 0.048 | 0.004 | 0.053 | |
| buildPredictor | 25.899 | 1.136 | 46.036 | |
| buildPredictor_sparseGenetic | 0.834 | 0.034 | 3.194 | |
| callFeatSel | 0.142 | 0.004 | 0.147 | |
| callOverallSelectedFeatures | 0.130 | 0.008 | 0.138 | |
| cleanPathwayName | 0 | 0 | 0 | |
| cnv_GR | 0.040 | 0.000 | 0.039 | |
| cnv_TTstatus | 0.003 | 0.012 | 0.015 | |
| cnv_netPass | 0.004 | 0.000 | 0.004 | |
| cnv_netScores | 0.003 | 0.011 | 0.014 | |
| cnv_patientNetCount | 0.200 | 0.036 | 0.235 | |
| cnv_pheno | 0.008 | 0.002 | 0.011 | |
| compareShortestPath | 0.024 | 0.001 | 0.026 | |
| compileFeatureScores | 0.010 | 0.000 | 0.011 | |
| compileFeatures | 6.054 | 0.518 | 28.587 | |
| confmat | 0.000 | 0.003 | 0.003 | |
| confusionMatrix | 0.117 | 0.008 | 0.126 | |
| convertToMAE | 0.169 | 0.020 | 0.189 | |
| countIntType | 0.002 | 0.000 | 0.002 | |
| countIntType_batch | 0.026 | 0.000 | 12.336 | |
| countPatientsInNet | 0.000 | 0.003 | 0.003 | |
| createPSN_MultiData | 26.385 | 2.148 | 58.707 | |
| dataList2List | 0.408 | 0.016 | 0.424 | |
| enrichLabelNets | 1.984 | 0.245 | 75.497 | |
| featScores | 0.030 | 0.015 | 0.045 | |
| fetchPathwayDefinitions | 0.555 | 0.033 | 1.789 | |
| genes | 0.004 | 0.000 | 0.004 | |
| getEMapInput | 1.074 | 0.128 | 1.453 | |
| getEMapInput_many | 1.075 | 0.148 | 1.459 | |
| getEnr | 0.972 | 0.144 | 13.304 | |
| getFeatureScores | 0.013 | 0.004 | 0.017 | |
| getFileSep | 0 | 0 | 0 | |
| getGMjar_path | 0.200 | 0.055 | 0.221 | |
| getNetConsensus | 0.019 | 0.000 | 0.020 | |
| getOR | 0.002 | 0.004 | 0.006 | |
| getPatientPredictions | 6.697 | 0.200 | 6.900 | |
| getPatientRankings | 0.082 | 0.012 | 0.095 | |
| getRegionOL | 0.423 | 0.076 | 0.500 | |
| getResults | 0.152 | 0.020 | 0.172 | |
| getSimilarity | 8.354 | 0.012 | 8.367 | |
| makePSN_NamedMatrix | 0.092 | 0.010 | 12.174 | |
| makePSN_RangeSets | 0.015 | 0.000 | 0.015 | |
| makeQueries | 0.012 | 0.004 | 0.016 | |
| makeSymmetric | 0.002 | 0.000 | 0.002 | |
| mapNamedRangesToSets | 0.073 | 0.076 | 0.149 | |
| modelres | 0.001 | 0.003 | 0.004 | |
| normDiff | 0.001 | 0.000 | 0.002 | |
| npheno | 0.002 | 0.000 | 0.002 | |
| pathwayList | 0.001 | 0.003 | 0.004 | |
| pathway_GR | 0.096 | 0.008 | 0.105 | |
| perfCalc | 0.003 | 0.000 | 0.003 | |
| pheno | 0.011 | 0.000 | 0.011 | |
| pheno_full | 0.002 | 0.000 | 0.003 | |
| plotEmap | 1.228 | 0.104 | 5.991 | |
| plotPerf | 5.835 | 0.040 | 5.876 | |
| plotPerf_multi | 0.051 | 0.012 | 0.064 | |
| predRes | 0.004 | 0.000 | 0.005 | |
| predictPatientLabels | 0.012 | 0.000 | 0.012 | |
| pruneNets | 0.006 | 0.008 | 0.015 | |
| randAlphanumString | 0.001 | 0.000 | 0.001 | |
| readPathways | 1.249 | 0.176 | 2.225 | |
| runFeatureSelection | 7.152 | 0.511 | 5.087 | |
| runQuery | 2.891 | 0.307 | 4.490 | |
| setupFeatureDB | 0.062 | 0.008 | 0.070 | |
| silh | 0.003 | 0.000 | 0.004 | |
| sim.eucscale | 0.497 | 0.016 | 0.514 | |
| sim.pearscale | 12.125 | 0.180 | 12.305 | |
| simpleCap | 0 | 0 | 0 | |
| smoothMutations_LabelProp | 8.499 | 0.336 | 44.010 | |
| sparsify2 | 5.037 | 0.144 | 5.181 | |
| sparsify3 | 1.083 | 0.024 | 1.107 | |
| splitTestTrain | 0.026 | 0.000 | 0.027 | |
| splitTestTrain_resampling | 0.006 | 0.000 | 0.006 | |
| tSNEPlotter | 1.417 | 0.080 | 1.496 | |
| thresholdSmoothedMutations | 3.793 | 0.388 | 39.410 | |
| toymodel | 1.293 | 0.972 | 2.265 | |
| updateNets | 0.008 | 0.002 | 0.010 | |
| writeNetsSIF | 0.008 | 0.002 | 0.009 | |
| writeQueryBatchFile | 0.004 | 0.000 | 0.005 | |
| writeQueryFile | 0.008 | 0.000 | 0.008 | |
| xpr | 0.038 | 0.008 | 0.046 | |