Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-02 09:00:53 -0500 (Mon, 02 Jan 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
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 TCGAutils package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 2009/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
TCGAutils 1.19.1 (landing page) Marcel Ramos
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
Package: TCGAutils |
Version: 1.19.1 |
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TCGAutils.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings TCGAutils_1.19.1.tar.gz |
StartedAt: 2022-12-29 04:07:57 -0500 (Thu, 29 Dec 2022) |
EndedAt: 2022-12-29 04:13:17 -0500 (Thu, 29 Dec 2022) |
EllapsedTime: 320.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: TCGAutils.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TCGAutils.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings TCGAutils_1.19.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/TCGAutils.Rcheck' * using R Under development (unstable) (2022-12-25 r83502 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 10.4.0 GNU Fortran (GCC) 10.4.0 * running under: Windows Server x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'TCGAutils/DESCRIPTION' ... OK * this is package 'TCGAutils' version '1.19.1' * 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 whether package 'TCGAutils' 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 Unexported objects imported by ':::' calls: 'BiocGenerics:::replaceSlots' 'GenomicRanges:::.normarg_field' 'S4Vectors:::selectSome' See the note in ?`:::` about the use of this operator. * 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 simplifyTCGA 26.45 1.69 28.44 TCGAprimaryTumors 13.13 2.34 16.16 oncoPrintTCGA 10.81 1.65 14.17 trimColData 10.97 1.28 12.53 curatedTCGAData-helpers 9.65 1.05 11.00 imputeAssay 9.47 1.02 10.79 makeSummarizedExperimentFromGISTIC 3.68 0.21 10.64 * 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 NOTE See 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/TCGAutils.Rcheck/00check.log' for details.
TCGAutils.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL TCGAutils ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'TCGAutils' ... ** 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 (TCGAutils)
TCGAutils.Rcheck/tests/testthat.Rout
R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (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(TCGAutils) > > test_check("TCGAutils") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 49 ] > > proc.time() user system elapsed 11.59 1.01 14.96
TCGAutils.Rcheck/TCGAutils-Ex.timings
name | user | system | elapsed | |
ID-translation | 1.61 | 0.07 | 3.69 | |
TCGAbarcode | 0 | 0 | 0 | |
TCGAbiospec | 0.03 | 0.00 | 0.04 | |
TCGAprimaryTumors | 13.13 | 2.34 | 16.16 | |
TCGAsampleSelect | 0.01 | 0.00 | 0.02 | |
builds | 0.18 | 0.00 | 0.17 | |
curatedTCGAData-helpers | 9.65 | 1.05 | 11.00 | |
findGRangesCols | 0 | 0 | 0 | |
generateMap | 0.02 | 0.00 | 0.02 | |
getFileName | 0.04 | 0.00 | 0.47 | |
imputeAssay | 9.47 | 1.02 | 10.79 | |
makeGRangesListFromCopyNumber | 0.49 | 0.00 | 1.05 | |
makeGRangesListFromExonFiles | 0.25 | 0.01 | 0.26 | |
makeSummarizedExperimentFromGISTIC | 3.68 | 0.21 | 10.64 | |
mergeColData | 0.20 | 0.00 | 0.21 | |
oncoPrintTCGA | 10.81 | 1.65 | 14.17 | |
simplifyTCGA | 26.45 | 1.69 | 28.44 | |
trimColData | 10.97 | 1.28 | 12.53 | |