Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-10-19 13:20:46 -0400 (Wed, 19 Oct 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
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 restfulSE package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/restfulSE.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1627/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
restfulSE 1.18.0 (landing page) Shweta Gopaulakrishnan
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: restfulSE |
Version: 1.18.0 |
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:restfulSE.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings restfulSE_1.18.0.tar.gz |
StartedAt: 2022-10-18 21:26:33 -0400 (Tue, 18 Oct 2022) |
EndedAt: 2022-10-18 21:29:52 -0400 (Tue, 18 Oct 2022) |
EllapsedTime: 199.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: restfulSE.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:restfulSE.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings restfulSE_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/restfulSE.Rcheck’ * using R version 4.2.1 (2022-06-23) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘restfulSE/DESCRIPTION’ ... OK * this is package ‘restfulSE’ version ‘1.18.0’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘restfulSE’ 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 ... NOTE Namespace in Imports field not imported from: ‘methods’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE BQ3_ArraySeed: no visible global function definition for ‘is’ BQ3_ArraySeed: no visible global function definition for ‘new’ BQ3_Source: no visible global function definition for ‘slot’ BQ3_Source: no visible binding for global variable ‘SampleTypeLetterCode’ BQ3_Source: no visible global function definition for ‘new’ BQ3m2: no visible binding for global variable ‘SampleTypeLetterCode’ BQM_ArraySeed: no visible global function definition for ‘is’ BQM_ArraySeed: no visible global function definition for ‘new’ BQM_Source: no visible global function definition for ‘new’ TCGA_tablerefs: no visible global function definition for ‘new’ newDA: no visible global function definition for ‘new’ replaceSlots: no visible global function definition for ‘validObject’ seByTumor: no visible global function definition for ‘new’ unsafe_replaceSlots: no visible global function definition for ‘slot’ unsafe_replaceSlots: no visible global function definition for ‘slot<-’ coerce,BQ3_Array-BQ3_Matrix: no visible global function definition for ‘new’ coerce,BQM_Array-BQM_Matrix: no visible global function definition for ‘new’ Undefined global functions or variables: SampleTypeLetterCode is new slot slot<- validObject Consider adding importFrom("methods", "is", "new", "slot", "slot<-", "validObject") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 gtexTiss 4.569 0.687 6.375 * 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.15-bioc/meat/restfulSE.Rcheck/00check.log’ for details.
restfulSE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL restfulSE ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’ * installing *source* package ‘restfulSE’ ... ** using staged installation ** R ** 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 (restfulSE)
restfulSE.Rcheck/tests/testthat.Rout
R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid" Copyright (C) 2022 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(restfulSE) Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Attaching package: 'BiocGenerics' 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 Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Loading required package: DelayedArray Loading required package: Matrix Attaching package: 'Matrix' The following object is masked from 'package:S4Vectors': expand Attaching package: 'DelayedArray' The following objects are masked from 'package:base': aperm, apply, rowsum, scale, sweep > library(rhdf5client) > > test_check("restfulSE") [ FAIL 0 | WARN 0 | SKIP 1 | PASS 3 ] ══ Skipped tests ═══════════════════════════════════════════════════════════════ • CGC_BILLING not set (1) [ FAIL 0 | WARN 0 | SKIP 1 | PASS 3 ] > > proc.time() user system elapsed 9.853 0.516 10.357
restfulSE.Rcheck/restfulSE-Ex.timings
name | user | system | elapsed | |
BQ3_Array | 0.001 | 0.000 | 0.001 | |
BQ3_Source | 0 | 0 | 0 | |
BQM_Array | 0 | 0 | 0 | |
BQM_Source | 0 | 0 | 0 | |
bqConn | 0 | 0 | 0 | |
cgcConn | 0 | 0 | 0 | |
goPatt | 0.890 | 0.123 | 1.013 | |
gtexTiss | 4.569 | 0.687 | 6.375 | |
isbCgcDatasets | 0.001 | 0.000 | 0.000 | |
isbCgcTables | 0.000 | 0.001 | 0.000 | |
pancan_SE | 0.000 | 0.001 | 0.000 | |
seByTumor | 0.000 | 0.001 | 0.000 | |
tasicCortex | 0.000 | 0.002 | 0.001 | |