| Back to Multiple platform build/check report for BioC 3.17 |
|
This page was generated on 2023-04-12 10:55:39 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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 1362/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| netDx 1.11.2 (landing page) Shraddha Pai
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | ERROR | ||||||||||
| Package: netDx |
| Version: 1.11.2 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:netDx.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings netDx_1.11.2.tar.gz |
| StartedAt: 2023-04-12 07:52:04 -0400 (Wed, 12 Apr 2023) |
| EndedAt: 2023-04-12 08:13:41 -0400 (Wed, 12 Apr 2023) |
| EllapsedTime: 1296.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: netDx.Rcheck |
| Warnings: NA |
##############################################################################
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### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:netDx.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings netDx_1.11.2.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/netDx.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘netDx/DESCRIPTION’ ... OK
* this is package ‘netDx’ version ‘1.11.2’
* 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 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
buildPredictor 30.221 2.014 34.833
createPSN_MultiData 22.555 1.834 40.254
RR_featureTally 8.962 0.620 9.583
compileFeatures 8.237 0.707 25.036
smoothMutations_LabelProp 7.783 0.468 36.877
runFeatureSelection 7.583 0.540 5.013
thresholdSmoothedMutations 2.486 0.088 27.883
enrichLabelNets 2.160 0.143 71.153
getEnr 0.950 0.148 10.943
makePSN_NamedMatrix 0.116 0.000 12.840
countIntType_batch 0.028 0.004 10.036
* 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 ... ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘ThreeWayClassifier.Rmd’ using rmarkdown
Killed
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 4 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/netDx.Rcheck/00check.log’
for details.
netDx.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL netDx ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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)
netDx.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-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
85.539 6.498 297.320
netDx.Rcheck/netDx-Ex.timings
| name | user | system | elapsed | |
| MB.pheno | 0.004 | 0.004 | 0.008 | |
| RR_featureTally | 8.962 | 0.620 | 9.583 | |
| avgNormDiff | 0.042 | 0.004 | 0.046 | |
| buildPredictor | 30.221 | 2.014 | 34.833 | |
| buildPredictor_sparseGenetic | 0.912 | 0.084 | 1.833 | |
| callFeatSel | 0.125 | 0.020 | 0.144 | |
| callOverallSelectedFeatures | 0.102 | 0.004 | 0.106 | |
| cleanPathwayName | 0.000 | 0.000 | 0.001 | |
| cnv_GR | 0.036 | 0.004 | 0.040 | |
| cnv_TTstatus | 0.006 | 0.004 | 0.010 | |
| cnv_netPass | 0.004 | 0.000 | 0.004 | |
| cnv_netScores | 0.006 | 0.004 | 0.009 | |
| cnv_patientNetCount | 0.111 | 0.044 | 0.155 | |
| cnv_pheno | 0.009 | 0.000 | 0.009 | |
| compareShortestPath | 0.018 | 0.008 | 0.025 | |
| compileFeatureScores | 0.007 | 0.004 | 0.010 | |
| compileFeatures | 8.237 | 0.707 | 25.036 | |
| confmat | 0.004 | 0.000 | 0.004 | |
| confusionMatrix | 0.170 | 0.000 | 0.169 | |
| convertToMAE | 0.223 | 0.020 | 0.242 | |
| countIntType | 0.002 | 0.000 | 0.002 | |
| countIntType_batch | 0.028 | 0.004 | 10.036 | |
| countPatientsInNet | 0.003 | 0.000 | 0.003 | |
| createPSN_MultiData | 22.555 | 1.834 | 40.254 | |
| dataList2List | 0.428 | 0.008 | 0.435 | |
| enrichLabelNets | 2.160 | 0.143 | 71.153 | |
| featScores | 0.044 | 0.008 | 0.052 | |
| fetchPathwayDefinitions | 0.477 | 0.020 | 0.714 | |
| genes | 0.004 | 0.000 | 0.004 | |
| getEMapInput | 1.022 | 0.056 | 1.125 | |
| getEMapInput_many | 0.740 | 0.084 | 0.864 | |
| getEnr | 0.950 | 0.148 | 10.943 | |
| getFeatureScores | 0.02 | 0.00 | 0.02 | |
| getFileSep | 0 | 0 | 0 | |
| getGMjar_path | 0.223 | 0.028 | 0.219 | |
| getNetConsensus | 0.021 | 0.000 | 0.020 | |
| getOR | 0.005 | 0.000 | 0.005 | |
| getPatientPredictions | 2.751 | 0.116 | 2.867 | |
| getPatientRankings | 0.096 | 0.020 | 0.116 | |
| getRegionOL | 0.34 | 0.00 | 0.34 | |
| getResults | 0.133 | 0.008 | 0.141 | |
| getSimilarity | 0.199 | 0.004 | 0.203 | |
| makePSN_NamedMatrix | 0.116 | 0.000 | 12.840 | |
| makePSN_RangeSets | 0.019 | 0.008 | 0.026 | |
| makeQueries | 0.009 | 0.004 | 0.013 | |
| makeSymmetric | 0.002 | 0.000 | 0.002 | |
| mapNamedRangesToSets | 0.057 | 0.004 | 0.061 | |
| modelres | 0.000 | 0.004 | 0.005 | |
| normDiff | 0.000 | 0.002 | 0.002 | |
| npheno | 0.000 | 0.003 | 0.002 | |
| pathwayList | 0.003 | 0.001 | 0.004 | |
| pathway_GR | 0.126 | 0.000 | 0.127 | |
| perfCalc | 0.003 | 0.000 | 0.003 | |
| pheno | 0.014 | 0.000 | 0.014 | |
| pheno_full | 0.003 | 0.000 | 0.003 | |
| plotEmap | 1.147 | 0.096 | 1.378 | |
| plotPerf | 2.005 | 0.100 | 2.105 | |
| plotPerf_multi | 0.045 | 0.012 | 0.057 | |
| predRes | 0.001 | 0.004 | 0.005 | |
| predictPatientLabels | 0.011 | 0.000 | 0.011 | |
| pruneNets | 0.014 | 0.000 | 0.013 | |
| randAlphanumString | 0.001 | 0.000 | 0.000 | |
| readPathways | 0.975 | 0.088 | 1.108 | |
| runFeatureSelection | 7.583 | 0.540 | 5.013 | |
| runQuery | 3.347 | 0.332 | 4.582 | |
| setupFeatureDB | 0.083 | 0.012 | 0.095 | |
| silh | 0.003 | 0.000 | 0.004 | |
| sim.eucscale | 0.518 | 0.048 | 0.566 | |
| sim.pearscale | 0.636 | 0.044 | 0.680 | |
| simpleCap | 0 | 0 | 0 | |
| smoothMutations_LabelProp | 7.783 | 0.468 | 36.877 | |
| sparsify2 | 0.945 | 0.112 | 1.057 | |
| sparsify3 | 2.343 | 0.172 | 2.515 | |
| splitTestTrain | 0.02 | 0.00 | 0.02 | |
| splitTestTrain_resampling | 0.006 | 0.000 | 0.005 | |
| tSNEPlotter | 0.870 | 0.024 | 0.895 | |
| thresholdSmoothedMutations | 2.486 | 0.088 | 27.883 | |
| toymodel | 2.580 | 0.692 | 3.272 | |
| updateNets | 0.007 | 0.000 | 0.007 | |
| writeNetsSIF | 0.006 | 0.000 | 0.007 | |
| writeQueryBatchFile | 0.003 | 0.000 | 0.003 | |
| writeQueryFile | 0.006 | 0.000 | 0.006 | |
| xpr | 0.040 | 0.004 | 0.044 | |