Back to Mac ARM64 build report for BioC 3.18 |
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This page was generated on 2024-04-18 11:32:14 -0400 (Thu, 18 Apr 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4388 |
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 1402/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
netDx 1.14.0 (landing page) Shraddha Pai
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | ERROR | OK | ||||||||
To the developers/maintainers of the netDx package: - 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. |
Package: netDx |
Version: 1.14.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:netDx.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings netDx_1.14.0.tar.gz |
StartedAt: 2024-04-17 21:21:11 -0400 (Wed, 17 Apr 2024) |
EndedAt: 2024-04-17 21:34:27 -0400 (Wed, 17 Apr 2024) |
EllapsedTime: 796.0 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: netDx.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:netDx.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings netDx_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/netDx.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: aarch64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘netDx/DESCRIPTION’ ... OK * this is package ‘netDx’ version ‘1.14.0’ * 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 7.2Mb sub-directories of 1Mb or more: extdata 5.9Mb * 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 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 ... ERROR Running examples in ‘netDx-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: fetchPathwayDefinitions > ### Title: fetch pathway definitions from downloads.baderlab.org > ### Aliases: fetchPathwayDefinitions > > ### ** Examples > > fetchPathwayDefinitions("October",2021) Fetching https://downloads.res.oicr.on.ca/pailab/public/EM_Genesets/October_01_2021/Human/symbol/Human_AllPathways_October_01_2021_symbol.gmt Error in curl::curl_fetch_memory(url, handle = handle) : Timeout was reached: [downloads.res.oicr.on.ca] Recv failure: Connection reset by peer Calls: fetchPathwayDefinitions ... request_fetch -> request_fetch.write_memory -> <Anonymous> Execution halted * 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 ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 4 NOTEs See ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/netDx.Rcheck/00check.log’ for details.
netDx.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL netDx ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 4.3.3 (2024-02-29) -- "Angel Food Cake" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 (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 2 | SKIP 0 | PASS 39 ] [ FAIL 0 | WARN 2 | SKIP 0 | PASS 39 ] > > proc.time() user system elapsed 73.664 4.609 314.941
netDx.Rcheck/netDx-Ex.timings
name | user | system | elapsed | |
MB.pheno | 0.009 | 0.002 | 0.011 | |
RR_featureTally | 7.694 | 2.321 | 10.105 | |
avgNormDiff | 0.064 | 0.002 | 0.067 | |
buildPredictor | 31.677 | 1.594 | 40.365 | |
buildPredictor_sparseGenetic | 0.640 | 0.040 | 1.284 | |
callFeatSel | 0.080 | 0.002 | 0.088 | |
callOverallSelectedFeatures | 0.082 | 0.011 | 0.094 | |
cleanPathwayName | 0 | 0 | 0 | |
cnv_GR | 0.078 | 0.003 | 0.080 | |
cnv_TTstatus | 0.007 | 0.019 | 0.026 | |
cnv_netPass | 0.004 | 0.002 | 0.005 | |
cnv_netScores | 0.006 | 0.017 | 0.023 | |
cnv_patientNetCount | 0.113 | 0.087 | 0.200 | |
cnv_pheno | 0.012 | 0.002 | 0.014 | |
compareShortestPath | 0.031 | 0.003 | 0.035 | |
compileFeatureScores | 0.008 | 0.002 | 0.009 | |
compileFeatures | 4.115 | 0.434 | 26.814 | |
confmat | 0.002 | 0.002 | 0.004 | |
confusionMatrix | 0.147 | 0.003 | 0.151 | |
convertToMAE | 0.150 | 0.003 | 0.153 | |
countIntType | 0.001 | 0.001 | 0.002 | |
countIntType_batch | 0.021 | 0.010 | 11.224 | |
countPatientsInNet | 0.002 | 0.002 | 0.004 | |
createPSN_MultiData | 27.053 | 0.936 | 45.705 | |
dataList2List | 0.380 | 0.018 | 0.410 | |
enrichLabelNets | 1.990 | 0.104 | 70.693 | |
featScores | 0.025 | 0.036 | 0.067 | |