Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:44 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 2227/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
VDJdive 1.9.0 (landing page) Kelly Street
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
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: 1.9.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:VDJdive.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings VDJdive_1.9.0.tar.gz |
StartedAt: 2024-12-23 23:51:00 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 23:54:58 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 237.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: VDJdive.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:VDJdive.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings VDJdive_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/VDJdive.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘VDJdive/DESCRIPTION’ ... OK * this is package ‘VDJdive’ version ‘1.9.0’ * 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 ‘VDJdive’ can be installed ... NOTE Found the following notes/warnings: Non-staged installation was used See ‘/Users/biocbuild/bbs-3.21-bioc/meat/VDJdive.Rcheck/00install.out’ for details. * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: clonoStats.Rd: BiocParallelParam-class summarizeClonotypes.Rd: BiocParallelParam-class Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 is not available * 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: 5 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/VDJdive.Rcheck/00check.log’ for details.
VDJdive.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL VDJdive ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘VDJdive’ ... ** using non-staged installation via StagedInstall field ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c TCR_EM.cpp -o TCR_EM.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o VDJdive.so RcppExports.o TCR_EM.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/VDJdive/libs ** 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 Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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 31.578 0.828 32.574
VDJdive.Rcheck/VDJdive-Ex.timings
name | user | system | elapsed | |
abundanceVDJ | 1.257 | 0.054 | 1.314 | |
addVDJtoSCE | 0.204 | 0.006 | 0.210 | |
barVDJ | 0.855 | 0.008 | 0.866 | |
boxVDJ | 0.866 | 0.006 | 0.874 | |
calculateDiversity | 0.599 | 0.004 | 0.605 | |
clonoStats-class | 0.544 | 0.004 | 0.550 | |
clonoStats | 0.561 | 0.004 | 0.567 | |
contigs | 0.617 | 0.005 | 0.626 | |
pieVDJ | 0.991 | 0.009 | 1.007 | |
readVDJcontigs | 0.078 | 0.006 | 0.084 | |
runBreakaway | 3.160 | 0.103 | 3.289 | |
runVDJPCA | 0.804 | 0.034 | 0.844 | |
scatterVDJ | 0.671 | 0.073 | 0.749 | |
splitClonotypes | 0.768 | 0.044 | 0.815 | |
summarizeClonotypes | 0.687 | 0.010 | 0.702 | |
writeVDJcontigs | 0.041 | 0.003 | 0.043 | |