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 17:41 -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 2256/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
VDJdive 1.6.0 (landing page) Kelly Street
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | NA | |||||||||
To the developers/maintainers of the VDJdive package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/VDJdive.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: VDJdive |
Version: 1.6.0 |
Command: E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:VDJdive.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings VDJdive_1.6.0.tar.gz |
StartedAt: 2024-08-12 06:31:52 -0400 (Mon, 12 Aug 2024) |
EndedAt: 2024-08-12 06:36:21 -0400 (Mon, 12 Aug 2024) |
EllapsedTime: 268.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: VDJdive.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:VDJdive.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings VDJdive_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.19-bioc/meat/VDJdive.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 'VDJdive/DESCRIPTION' ... OK * this is package 'VDJdive' version '1.6.0' * 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 'VDJdive' can be installed ... NOTE Found the following notes/warnings: Non-staged installation was used See 'E:/biocbuild/bbs-3.19-bioc/meat/VDJdive.Rcheck/00install.out' for details. * used C++ compiler: 'G__~1.EXE (GCC) 13.2.0' * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE abundanceVDJ,clonoStats: no visible binding for global variable 'count' abundanceVDJ,clonoStats: no visible binding for global variable 'y' barVDJ,Matrix: no visible binding for global variable 'count' boxVDJ,matrix: no visible binding for global variable 'group' boxVDJ,matrix: no visible binding for global variable 'Diversity' pieVDJ,Matrix: no visible binding for global variable 'count' scatterVDJ,matrix: no visible binding for global variable 'clono' scatterVDJ,matrix: no visible binding for global variable 'normentropy' scatterVDJ,matrix: no visible binding for global variable 'sampleType' Undefined global functions or variables: Diversity clono count group normentropy sampleType y * checking Rd files ... NOTE checkRd: (-1) clonoStats.Rd:98-102: Lost braces in \itemize; meant \describe ? checkRd: (-1) clonoStats.Rd:103-105: Lost braces in \itemize; meant \describe ? checkRd: (-1) clonoStats.Rd:106-107: Lost braces in \itemize; meant \describe ? checkRd: (-1) clonoStats.Rd:108-111: Lost braces in \itemize; meant \describe ? checkRd: (-1) clonoStats.Rd:112-114: Lost braces in \itemize; meant \describe ? * 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files for x64 is not available File 'E:/biocbuild/bbs-3.19-bioc/R/library/VDJdive/libs/x64/VDJdive.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... OK * 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: 4 NOTEs See 'E:/biocbuild/bbs-3.19-bioc/meat/VDJdive.Rcheck/00check.log' for details.
VDJdive.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL VDJdive ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.19-bioc/R/library' * installing *source* package 'VDJdive' ... ** using non-staged installation via StagedInstall field ** libs using C++ compiler: 'G__~1.EXE (GCC) 13.2.0' g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c TCR_EM.cpp -o TCR_EM.o g++ -std=gnu++17 -shared -s -static-libgcc -o VDJdive.dll tmp.def RcppExports.o TCR_EM.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR installing to E:/biocbuild/bbs-3.19-bioc/R/library/VDJdive/libs/x64 ** R ** data ** 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 * DONE (VDJdive)
VDJdive.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(VDJdive) > > test_check("VDJdive") An object of class "clonoStats" clonotypes: 7 cells: 24 groups(2): sample1 sample2 has assignment: FALSEAn object of class "clonoStats" clonotypes: 7 cells: 24 groups(2): sample1 sample2 has assignment: TRUE[ FAIL 0 | WARN 0 | SKIP 0 | PASS 125 ] > > proc.time() user system elapsed 36.53 1.01 37.57
VDJdive.Rcheck/VDJdive-Ex.timings
name | user | system | elapsed | |
abundanceVDJ | 1.58 | 0.07 | 1.64 | |
addVDJtoSCE | 0.31 | 0.01 | 0.33 | |
barVDJ | 0.86 | 0.06 | 0.92 | |
boxVDJ | 1.02 | 0.05 | 1.06 | |
calculateDiversity | 1.30 | 0.02 | 1.32 | |
clonoStats-class | 0.65 | 0.00 | 0.65 | |
clonoStats | 0.56 | 0.01 | 0.58 | |
contigs | 0.46 | 0.00 | 0.45 | |
pieVDJ | 1.12 | 0.02 | 1.14 | |
readVDJcontigs | 0.06 | 0.03 | 0.32 | |
runBreakaway | 2.41 | 0.16 | 2.98 | |
runVDJPCA | 0.81 | 0.01 | 0.83 | |
scatterVDJ | 0.86 | 0.00 | 0.86 | |
splitClonotypes | 1.22 | 0.00 | 1.23 | |
summarizeClonotypes | 0.86 | 0.02 | 0.88 | |
writeVDJcontigs | 0.06 | 0.00 | 0.06 | |