############################################################################## ############################################################################## ### ### 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 ### ############################################################################## ############################################################################## * 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 : : 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 ... -> 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.