Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:44 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the mAPKL package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mAPKL.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1029/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
mAPKL 1.22.0 (landing page) Argiris Sakellariou
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: mAPKL |
Version: 1.22.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:mAPKL.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings mAPKL_1.22.0.tar.gz |
StartedAt: 2021-10-14 10:26:12 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 10:36:23 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 610.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: mAPKL.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:mAPKL.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings mAPKL_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/mAPKL.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘mAPKL/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘mAPKL’ version ‘1.22.0’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘mAPKL’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * 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 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed classification 114.803 1.112 115.928 netwAttr 112.431 0.608 113.002 mAPKL 111.748 0.600 112.359 preprocess 24.433 0.216 24.651 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.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: OK
mAPKL.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL mAPKL ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘mAPKL’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (mAPKL)
mAPKL.Rcheck/tests/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 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. > BiocGenerics:::testPackage("mAPKL") Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Assign 60% as train data and 40% as test data Saving density graph for breast$trainData in /home/biocbuild/bbs-3.13-bioc/meat/mAPKL.Rcheck/tests Saving density graph for breast$testData in /home/biocbuild/bbs-3.13-bioc/meat/mAPKL.Rcheck/tests b=10 b=20 b=30 b=40 b=50 b=60 b=70 b=80 b=90 b=100 b=110 b=120 b=130 b=140 b=150 b=160 b=170 b=180 b=190 b=200 b=210 b=220 b=230 b=240 b=250 b=260 b=270 b=280 b=290 b=300 b=310 b=320 b=330 b=340 b=350 b=360 b=370 b=380 b=390 b=400 b=410 b=420 b=430 b=440 b=450 b=460 b=470 b=480 b=490 b=500 b=510 b=520 b=530 b=540 b=550 b=560 b=570 b=580 b=590 b=600 b=610 b=620 b=630 b=640 b=650 b=660 b=670 b=680 b=690 b=700 b=710 b=720 b=730 b=740 b=750 b=760 b=770 b=780 b=790 b=800 b=810 b=820 b=830 b=840 b=850 b=860 b=870 b=880 b=890 b=900 b=910 b=920 b=930 b=940 b=950 b=960 b=970 b=980 b=990 b=1000 Please wait! The (KL) cluster indexing may take several minutes... Asking for 22 number of clusters fc according to limma Loading required package: hgu133plus2.db Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: IRanges Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: org.Hs.eg.db 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns Negative samples: 8 Positive samples: 4 TN=6 FP=2 TP=3 FN=1 AUC=0.75 Accuracy=75.00 MCC=0.48 Specificity=0.75 Sensitivity=0.75 Assign 60% as train data and 40% as test data RUNIT TEST PROTOCOL -- Thu Oct 14 10:36:21 2021 *********************************************** Number of test functions: 3 Number of errors: 0 Number of failures: 0 1 Test Suite : mAPKL RUnit Tests - 3 test functions, 0 errors, 0 failures Number of test functions: 3 Number of errors: 0 Number of failures: 0 Warning messages: 1: In xtfrm.data.frame(x) : cannot xtfrm data frames 2: In xtfrm.data.frame(x) : cannot xtfrm data frames 3: In xtfrm.data.frame(x) : cannot xtfrm data frames 4: In .local(s, x = x, ...) : algorithm did not converge; turn on details and call plot() to monitor net similarity. Consider increasing 'maxits' and 'convits', and, if oscillations occur also increasing damping factor 'lam'. 5: In .local(s, x = x, ...) : algorithm did not converge; turn on details and call plot() to monitor net similarity. Consider increasing 'maxits' and 'convits', and, if oscillations occur also increasing damping factor 'lam'. 6: In .local(s, x = x, ...) : algorithm did not converge; turn on details and call plot() to monitor net similarity. Consider increasing 'maxits' and 'convits', and, if oscillations occur also increasing damping factor 'lam'. 7: In .local(s, x = x, ...) : algorithm did not converge; turn on details and call plot() to monitor net similarity. Consider increasing 'maxits' and 'convits', and, if oscillations occur also increasing damping factor 'lam'. 8: In xtfrm.data.frame(x) : cannot xtfrm data frames 9: In xtfrm.data.frame(x) : cannot xtfrm data frames 10: In xtfrm.data.frame(x) : cannot xtfrm data frames > > proc.time() user system elapsed 122.871 1.624 124.484
mAPKL.Rcheck/mAPKL-Ex.timings
name | user | system | elapsed | |
annotate | 0.658 | 0.044 | 0.702 | |
classification | 114.803 | 1.112 | 115.928 | |
mAPKL | 111.748 | 0.600 | 112.359 | |
metrics | 0.002 | 0.000 | 0.001 | |
netwAttr | 112.431 | 0.608 | 113.002 | |
preprocess | 24.433 | 0.216 | 24.651 | |
probes2pathways | 0.551 | 0.036 | 0.586 | |
report | 0.001 | 0.000 | 0.000 | |
sampling | 1.105 | 0.008 | 1.112 | |