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###
### 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
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/tripr.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 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 ... 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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... 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_00.16.35
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, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/tripr.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL tripr
###
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* 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)

R version 4.3.0 alpha (2023-04-03 r84154)
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