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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:IMMAN.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings IMMAN_1.27.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/IMMAN.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘IMMAN/DESCRIPTION’ ... OK
* this is package ‘IMMAN’ version ‘1.27.0’
* 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 ‘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 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
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...
Detecting List1 in STRING
trying URL 'https://stringdb-downloads.org/download/protein.aliases.v11.0/7227.protein.aliases.v11.0.txt.gz'
Content type 'application/octet-stream' length 4188915 bytes (4.0 MB)
==================================================
downloaded 4.0 MB

trying URL 'https://stringdb-downloads.org/download/protein.info.v11.0/7227.protein.info.v11.0.txt.gz'
Content type 'application/octet-stream' length 687988 bytes (671 KB)
==================================================
downloaded 671 KB

Detecting List2 in STRING
trying URL 'https://stringdb-downloads.org/download/protein.aliases.v11.0/6239.protein.aliases.v11.0.txt.gz'
Content type 'application/octet-stream' length 2902021 bytes (2.8 MB)
==================================================
downloaded 2.8 MB

trying URL 'https://stringdb-downloads.org/download/protein.info.v11.0/6239.protein.info.v11.0.txt.gz'
Content type 'application/octet-stream' length 675823 bytes (659 KB)
==================================================
downloaded 659 KB

Step 4/4: Retrieving String Network...
Retrieving List1
trying URL 'https://stringdb-downloads.org/download/protein.links.v11.0/7227.protein.links.v11.0.txt.gz'
Content type 'application/octet-stream' length 22010066 bytes (21.0 MB)
==================================================
downloaded 21.0 MB

Retrieving List2
trying URL 'https://stringdb-downloads.org/download/protein.links.v11.0/6239.protein.links.v11.0.txt.gz'
Content type 'application/octet-stream' length 48132415 bytes (45.9 MB)
==============
downloaded 13.3 MB

Warning in download.file(urlStr, temp) :
  downloaded length 13975290 != reported length 48132415
Warning in download.file(urlStr, temp) :
  URL 'https://stringdb-downloads.org/download/protein.links.v11.0/6239.protein.links.v11.0.txt.gz': Timeout of 600 seconds was reached
Error in download.file(urlStr, temp) : 
  download from 'https://stringdb-downloads.org/download/protein.links.v11.0/6239.protein.links.v11.0.txt.gz' failed
Calls: IMMAN ... <Anonymous> -> load -> downloadAbsentFile -> download.file
Execution halted
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/IMMAN.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL IMMAN
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘IMMAN’ ...
** this is package ‘IMMAN’ version ‘1.27.0’
** 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 Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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")
trying URL 'https://stringdb-downloads.org/download/protein.aliases.v11.0/6239.protein.aliases.v11.0.txt.gz'
Content type 'application/octet-stream' length 2902021 bytes (2.8 MB)
==================================================
downloaded 2.8 MB

trying URL 'https://stringdb-downloads.org/download/protein.info.v11.0/6239.protein.info.v11.0.txt.gz'
Content type 'application/octet-stream' length 675823 bytes (659 KB)
==================================================
downloaded 659 KB

trying URL 'https://stringdb-downloads.org/download/protein.aliases.v11.0/7227.protein.aliases.v11.0.txt.gz'
Content type 'application/octet-stream' length 4188915 bytes (4.0 MB)
==================================================
downloaded 4.0 MB

trying URL 'https://stringdb-downloads.org/download/protein.info.v11.0/7227.protein.info.v11.0.txt.gz'
Content type 'application/octet-stream' length 687988 bytes (671 KB)
==================================================
downloaded 671 KB

trying URL 'https://stringdb-downloads.org/download/protein.links.v11.0/6239.protein.links.v11.0.txt.gz'
Content type 'application/octet-stream' length 48132415 bytes (45.9 MB)
==================================================
downloaded 45.9 MB

trying URL 'https://stringdb-downloads.org/download/protein.links.v11.0/7227.protein.links.v11.0.txt.gz'
Content type 'application/octet-stream' length 22010066 bytes (21.0 MB)
==================================================
downloaded 21.0 MB

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
> 
> proc.time()
   user  system elapsed 
 61.400   3.342 187.931