Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:43 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
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 tripr package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/tripr.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
Package 2124/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
tripr 1.5.3 (landing page) Nikolaos Pechlivanis
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||||
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | ERROR | ||||||||||
Package: tripr |
Version: 1.5.3 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:tripr.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings tripr_1.5.3.tar.gz |
StartedAt: 2023-04-12 10:01:38 -0400 (Wed, 12 Apr 2023) |
EndedAt: 2023-04-12 10:03:46 -0400 (Wed, 12 Apr 2023) |
EllapsedTime: 128.4 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: tripr.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:tripr.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings tripr_1.5.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/tripr.Rcheck’ * using R Under development (unstable) (2023-02-14 r83833) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 * running under: Ubuntu 20.04.6 LTS * using session charset: UTF-8 * checking for file ‘tripr/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘tripr’ version ‘1.5.3’ * 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 ‘tripr’ can be installed ... OK * checking installed package size ... NOTE installed size is 6.2Mb sub-directories of 1Mb or more: R 1.0Mb app 1.4Mb extdata 3.6Mb * 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 loading without being on the library search path ... 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 clonotypes: no visible global function definition for ‘:=’ clonotypes: no visible binding for global variable ‘N.uniq.seq’ clonotypes : one_run: no visible global function definition for ‘:=’ clonotypes : one_run: no visible binding for global variable ‘N.uniq.seq’ repertoires: no visible binding for global variable ‘Gene’ repertoires : one_run: no visible binding for global variable ‘Gene’ Undefined global functions or variables: := Gene N.uniq.seq * 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 ... ERROR Running examples in ‘tripr-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: run_TRIP > ### Title: Run tripr analysis via R command line > ### Aliases: run_TRIP > > ### ** Examples > > > > ## Do not run > > run_TRIP( + output_path=tools::R_user_dir("tripr", which="cache"), + filelist=c("1_Summary.txt", "2_IMGT-gapped-nt-sequences.txt", + "4_IMGT-gapped-AA-sequences.txt", "6_Junction.txt"), + cell="Bcell", + throughput="High Throughput", + preselection="1,2,3,4C:W", + selection="5", + identity_range="88:100", + cdr3_length_range="", + pipeline="1", + select_clonotype="V Gene + CDR3 Amino Acids") Datapath you provided: /home/biocbuild/bbs-3.17-bioc/R/site-library/tripr/extdata/dataset Output will be saved in: /home/biocbuild/.cache/R/tripr/output_2023.04.12_10.03.35 Error in cat(paste0("testColumnNames", "\t"), file = logFile, append = TRUE) : invalid connection Calls: run_TRIP -> testColumnNames -> cat Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: Error in `cat(paste0("testColumnNames", "\t"), file = logFile, append = TRUE)`: invalid connection Backtrace: ▆ 1. └─tripr:::testColumnNames(name, files, datapath) at test-imgtcleaning.R:31:4 2. └─base::cat(paste0("testColumnNames", "\t"), file = logFile, append = TRUE) ── Error ('test-imgtfilter.R:32:5'): dataframe after filter is not empty ─────── Error in `cat(paste0("testColumnNames", "\t"), file = logFile, append = TRUE)`: invalid connection Backtrace: ▆ 1. └─tripr:::testColumnNames(name, files, datapath) at test-imgtfilter.R:32:4 2. └─base::cat(paste0("testColumnNames", "\t"), file = logFile, append = TRUE) [ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘tripr_guide.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 2 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/tripr.Rcheck/00check.log’ for details.
tripr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL tripr ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘tripr’ ... ** 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 (tripr)
tripr.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" Copyright (C) 2023 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(tripr) Loading required package: shiny Loading required package: shinyBS Welcome to tripr! > library(fs) > > test_check("tripr") [ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-imgtcleaning.R:31:5'): dataframe after cleaning is not empty ─── Error in `cat(paste0("testColumnNames", "\t"), file = logFile, append = TRUE)`: invalid connection Backtrace: ▆ 1. └─tripr:::testColumnNames(name, files, datapath) at test-imgtcleaning.R:31:4 2. └─base::cat(paste0("testColumnNames", "\t"), file = logFile, append = TRUE) ── Error ('test-imgtfilter.R:32:5'): dataframe after filter is not empty ─────── Error in `cat(paste0("testColumnNames", "\t"), file = logFile, append = TRUE)`: invalid connection Backtrace: ▆ 1. └─tripr:::testColumnNames(name, files, datapath) at test-imgtfilter.R:32:4 2. └─base::cat(paste0("testColumnNames", "\t"), file = logFile, append = TRUE) [ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ] Error: Test failures Execution halted
tripr.Rcheck/tripr-Ex.timings
name | user | system | elapsed |