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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:IMMAN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings IMMAN_1.26.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/IMMAN.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘IMMAN/DESCRIPTION’ ... OK
* this is package ‘IMMAN’ version ‘1.26.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘IMMAN’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
IMMAN: no visible binding for global variable ‘tem’
IMMAN : <anonymous>: no visible binding for global variable ‘tem’
Undefined global functions or variables:
  tem
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘IMMAN-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: IMMAN
> ### Title: Interlog protein network reconstruction by Mapping and Mining
> ###   ANalysis
> ### Aliases: IMMAN
> 
> ### ** Examples
> 
> 
> data(FruitFly)
> data(Celegance)
> 
> subFruitFly <- as.character(FruitFly$V1)[1:10]
> subCelegance <- as.character(Celegance$V1)[1:10]
> 
> ProteinLists = list(subFruitFly, subCelegance)
> 
> List1_Species_ID = 7227  # taxonomy ID FruitFly
> List2_Species_ID = 6239  # taxonomy ID Celegance
> 
> Species_IDs  = c(List1_Species_ID, List2_Species_ID)
> 
> identityU = 30
> substitutionMatrix = "BLOSUM62"
> gapOpening = -8
> gapExtension = -8
> NetworkShrinkage = FALSE
> coverage = 1
> BestHit = TRUE
> score_threshold = 400
> STRINGversion="11"
> 
> # Run the IMMAN function for the parameters
> output = IMMAN(ProteinLists, fileNames=NULL, Species_IDs,
+               identityU, substitutionMatrix,
+               gapOpening, gapExtension, BestHit,
+               coverage, NetworkShrinkage,
+               score_threshold, STRINGversion,
+               InputDirectory = getwd())
Step 1/4:Downloading amino acid sequences...
Downloading amino acid sequences of List1
Downloading amino acid sequences of List2
Step 2/4: Alignment...
Align List1 with List2
Step 3/4: Detection in STRING...
Warning in open.connection(file, "rt") :
  cannot open URL 'https://string-db.org/api/tsv-no-header/version': HTTP status was '400 Bad Request'
Error in open.connection(file, "rt") : 
  cannot open the connection to 'https://string-db.org/api/tsv-no-header/version'
Calls: IMMAN ... <Anonymous> -> read.table -> open -> open.connection
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:
  Backtrace:
      ▆
   1. └─IMMAN::IMMAN(...) at test_IMMAN.R:6:2
   2.   └─STRINGdb$new(...)
   3.     └─methods::new(def, ...)
   4.       ├─methods::initialize(value, ...)
   5.       └─methods::initialize(value, ...)
   6.         └─.Object$initialize(...)
   7.           └─utils::read.table(...)
   8.             ├─base::open(file, "rt")
   9.             └─base::open.connection(file, "rt")
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
* 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: 2 ERRORs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/IMMAN.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL IMMAN
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘IMMAN’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (IMMAN)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
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(IMMAN)
> 
> test_check("IMMAN")
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_IMMAN.R:6:2'): IMMAN reconstruct the interlog protein network ──
Error in `open.connection(file, "rt")`: cannot open the connection to 'https://string-db.org/api/tsv-no-header/version'
Backtrace:
    ▆
 1. └─IMMAN::IMMAN(...) at test_IMMAN.R:6:2
 2.   └─STRINGdb$new(...)
 3.     └─methods::new(def, ...)
 4.       ├─methods::initialize(value, ...)
 5.       └─methods::initialize(value, ...)
 6.         └─.Object$initialize(...)
 7.           └─utils::read.table(...)
 8.             ├─base::open(file, "rt")
 9.             └─base::open.connection(file, "rt")

[ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted