############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings DECIPHER_2.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/DECIPHER.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘DECIPHER/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DECIPHER’ version ‘2.30.0’ * 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 (GCC) 10.3.1’ * checking installed package size ... NOTE installed size is 13.2Mb sub-directories of 1Mb or more: R 1.3Mb data 7.5Mb extdata 2.3Mb 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 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 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 ‘.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: LearnNonCoding > ### Title: Learn a Non-Coding RNA Model > ### Aliases: LearnNonCoding > > ### ** Examples > > # import a family of non-coding RNAs > fas_path <- system.file("extdata", + "IhtA.fas", + package="DECIPHER") > rna <- readRNAStringSet(fas_path) > rna RNAStringSet object of length 27: width seq names [1] 103 AAGAUGAUAUUCUGCGCCAUGGA...UGAUUGUUGUUUUCUUGGCUUU KE360988.1/6443-6... [2] 105 AAGAUGAUAUUCUCCGCCGUGGA...AACUUUAUGUUUUCUUGGCUUU AE002161.1/54676-... [3] 107 AAGUUGGUAUUCUAACGCCAUGG...UAUCUCCGGUUCUCUUGGCUUU AE001273.1/773281... [4] 107 AAGUUGGUAUUCUAACGCCAUGG...UGUCUCCAGUUCUCUUGGCUUU AE002160.2/53054-... [5] 103 AAGAUGAUAUUCUACGCCAUGGA...UGAUUGUUGUUUUCUUGGCUUU AE015925.1/52097-... ... ... ... [23] 107 AAGUUGGUAUUCUAACGCCAUGG...UAUCUCCGGUUCUCUUGGCUUU CP006674.1 Chlamy... [24] 103 AAGAUGAUAUUCUGCGCCAUGGA...UGAUUGUUGUUUUCUUGGCUUU KE356008.1 Chlamy... [25] 108 AAGUUGGUAUUCUAACGCCAUGG...UAUCUCCGGUUCUCUUGGCUUU CVNC01000001.1 Ch... [26] 103 AAGAUGAUAUUCUGCGCCAUGGA...UGAUUGUUGUUUUCUUGGCUUU AP006861.1 Chlamy... [27] 101 AAGAUGAUAUUCUACGCCAUGGA...AUGAUGUUGUUUUCUUGGCUUU CP015840.1 Chlamy... > > # align the sequences > RNA <- AlignSeqs(rna) Predicting structures based on free energies: ================================================================================ Time difference of 0.83 secs Determining distance matrix based on shared 7-mers: ================================================================================ Time difference of 0 secs Clustering into groups by similarity: ================================================================================ Time difference of 0.01 secs Aligning Sequences: ================================================================================ Time difference of 0.21 secs Iteration 1 of 2: Determining distance matrix based on alignment: ================================================================================ Time difference of 0 secs Reclustering into groups by similarity: ================================================================================ Time difference of 0.01 secs Realigning Sequences: ================================================================================ Time difference of 0.11 secs Iteration 2 of 2: Determining distance matrix based on alignment: ================================================================================ Time difference of 0 secs Reclustering into groups by similarity: ================================================================================ Time difference of 0.01 secs Realigning Sequences: ================================================================================ Time difference of 0.02 secs > RNA RNAStringSet object of length 27: width seq names [1] 113 AAGAUGAUAUUCUG-CGCCAUGG...GAUUGU-UGUUUUCUUGGCUUU KE360988.1/6443-6... [2] 113 AAGAUGAUAUUCUC-CGCCGUGG...AACUUUAUGUUUUCUUGGCUUU AE002161.1/54676-... [3] 113 AAGUUGGUAUUCUAACGCCAUGG...--UCUCCGGUUCUCUUGGCUUU AE001273.1/773281... [4] 113 AAGUUGGUAUUCUAACGCCAUGG...--UCUCCAGUUCUCUUGGCUUU AE002160.2/53054-... [5] 113 AAGAUGAUAUUCUA-CGCCAUGG...GAUUGU-UGUUUUCUUGGCUUU AE015925.1/52097-... ... ... ... [23] 113 AAGUUGGUAUUCUAACGCCAUGG...--UCUCCGGUUCUCUUGGCUUU CP006674.1 Chlamy... [24] 113 AAGAUGAUAUUCUG-CGCCAUGG...GAUUGU-UGUUUUCUUGGCUUU KE356008.1 Chlamy... [25] 113 AAGUUGGUAUUCUAACGCCAUGG...--UCUCCGGUUCUCUUGGCUUU CVNC01000001.1 Ch... [26] 113 AAGAUGAUAUUCUG-CGCCAUGG...GAUUGU-UGUUUUCUUGGCUUU AP006861.1 Chlamy... [27] 113 AAGAUGAUAUUCUA-CGCCAUGG...GA-UGU-UGUUUUCUUGGCUUU CP015840.1 Chlamy... > > y <- LearnNonCoding(RNA) * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 3 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/DECIPHER.Rcheck/00check.log’ for details.