############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings DECIPHER_3.3.5.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/DECIPHER.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 ‘DECIPHER/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DECIPHER’ version ‘3.3.5’ * 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 ‘DECIPHER’ can be installed ... OK * used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * checking installed package size ... INFO installed size is 13.9Mb sub-directories of 1Mb or more: R 1.4Mb data 7.5Mb extdata 2.8Mb libs 1.6Mb * 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 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 AlignSeqs: no visible binding for global variable ‘deltaGrulesRNA’ DesignSignatures: no visible binding for global variable ‘deltaHrules’ FindGenes: no visible binding for global variable ‘deltaHrulesRNA’ FindNonCoding: no visible binding for global variable ‘deltaHrulesRNA’ LearnNonCoding: no visible binding for global variable ‘deltaHrulesRNA’ PredictDBN: no visible binding for global variable ‘deltaGrulesRNA’ Treeline: multiple local function definitions for ‘.NNI’ with different formal arguments Treeline: multiple local function definitions for ‘.minimize’ with different formal arguments Undefined global functions or variables: deltaGrulesRNA deltaHrules deltaHrulesRNA * 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 data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘DECIPHER-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: AlignSeqs > ### Title: Align a Set of Unaligned Sequences > ### Aliases: AlignSeqs > > ### ** Examples > > fas <- system.file("extdata", "Bacteria_175seqs.fas", package="DECIPHER") > dna <- readDNAStringSet(fas) > dna <- RemoveGaps(dna) > alignedDNA <- AlignSeqs(dna) Determining distance matrix based on shared 9-mers: ================================================================================ Time difference of 1.05 secs Clustering into groups by similarity: ================================================================================ Time difference of 0.03 secs Aligning Sequences: ================================================================================ Time difference of 1.69 secs Iteration 1 of 2: Determining distance matrix based on alignment: ================================================================================ Time difference of 0.15 secs Reclustering into groups by similarity: ================================================================================ Time difference of 0.04 secs Realigning Sequences: ================================================================================ Time difference of 1.16 secs Iteration 2 of 2: Determining distance matrix based on alignment: ================================================================================ Time difference of 0.16 secs Reclustering into groups by similarity: ================================================================================ Time difference of 0.07 secs Realigning Sequences: ================================================================================ Time difference of 0.32 secs > BrowseSeqs(alignedDNA, highlight=1) > > # use secondary structure with RNA sequences > alignedRNA <- AlignSeqs(RNAStringSet(dna)) Predicting structures based on free energies: ================================================================================ Time difference of 120.29 secs Determining distance matrix based on shared 9-mers: ================================================================================ Time difference of 1.09 secs Clustering into groups by similarity: ================================================================================ Time difference of 0.02 secs Aligning Sequences: ================================================================================ Time difference of 2.52 secs Iteration 1 of 2: Predicting RNA Secondary Structures: ================================================================================ Time difference of 2.8 secs Determining distance matrix based on alignment: ================================================================================ Time difference of 0.08 secs Reclustering into groups by similarity: ================================================================================ Time difference of 0.04 secs Realigning Sequences: ================================================================================ Time difference of 1.64 secs Iteration 2 of 2: Predicting RNA Secondary Structures: ================================================================================ Time difference of 2.61 secs Determining distance matrix based on alignment: ================================================================================ Time difference of 0.08 secs Reclustering into groups by similarity: ================================================================================ Time difference of 0.03 secs Realigning Sequences: ================================================================================ Time difference of 0.46 secs > BrowseSeqs(alignedRNA, highlight=1) Error in writeLines(html, htmlfile) : Error writing to connection: No space left on device Calls: BrowseSeqs -> writeLines Execution halted * 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, 2 NOTEs See ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/DECIPHER.Rcheck/00check.log’ for details.