Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-08-13 17:40 -0400 (Tue, 13 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4758 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4493 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4522 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4471 |
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 1006/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
icetea 1.22.0 (landing page) Vivek Bhardwaj
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
To the developers/maintainers of the icetea package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/icetea.git to reflect on this report. See Troubleshooting Build Report for more information. - 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: icetea |
Version: 1.22.0 |
Command: set _R_CHECK_FORCE_SUGGESTS_=0&& E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:icetea.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings icetea_1.22.0.tar.gz |
StartedAt: 2024-08-12 02:03:17 -0400 (Mon, 12 Aug 2024) |
EndedAt: 2024-08-12 02:11:54 -0400 (Mon, 12 Aug 2024) |
EllapsedTime: 517.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: icetea.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### set _R_CHECK_FORCE_SUGGESTS_=0&& E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:icetea.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings icetea_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.19-bioc/meat/icetea.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'icetea/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'icetea' version '1.22.0' * 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 whether package 'icetea' 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 code 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 ... WARNING '::' or ':::' import not declared from: 'MatrixGenerics' * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE detectTSS,CapSet : <anonymous>: no visible binding for global variable 'logFC' fitDiffTSS,CapSet: no visible binding for global variable 'ResizeReads' Undefined global functions or variables: ResizeReads logFC * 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 detectTSS 19.57 1.78 36.28 annotateTSS 9.97 0.29 10.28 getNormFactors 1.96 0.15 26.83 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 1 NOTE See 'E:/biocbuild/bbs-3.19-bioc/meat/icetea.Rcheck/00check.log' for details.
icetea.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL icetea ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.19-bioc/R/library' * installing *source* package 'icetea' ... ** 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 (icetea)
icetea.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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(icetea) > > test_check("icetea") [ FAIL 0 | WARN 1 | SKIP 0 | PASS 17 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 17 ] > > proc.time() user system elapsed 47.07 2.90 75.67
icetea.Rcheck/icetea-Ex.timings
name | user | system | elapsed | |
annotateTSS | 9.97 | 0.29 | 10.28 | |
demultiplexFASTQ | 2.45 | 0.08 | 2.53 | |
detectDiffTSS | 0 | 0 | 0 | |
detectTSS | 19.57 | 1.78 | 36.28 | |
exampleCSobject | 0.11 | 0.00 | 0.11 | |
exportTSS | 0.20 | 0.02 | 0.22 | |
filterDuplicates | 2.50 | 0.06 | 2.63 | |
fitDiffTSS | 0 | 0 | 0 | |
getGeneCounts | 1.84 | 0.16 | 2.00 | |
getNormFactors | 1.96 | 0.15 | 26.83 | |
mapCaps | 0 | 0 | 0 | |
newCapSet | 0.06 | 0.00 | 0.06 | |
plotReadStats | 0.37 | 0.02 | 0.39 | |
plotTSSprecision | 2.55 | 0.26 | 2.84 | |
sampleInfo | 0.11 | 0.04 | 0.14 | |
splitBAM_byIndex | 0.25 | 0.17 | 0.45 | |
splitBAM_byRepindex | 0.28 | 0.12 | 0.45 | |