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### Running command:
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###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:enhancerHomologSearch.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings enhancerHomologSearch_1.8.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/enhancerHomologSearch.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 ‘enhancerHomologSearch/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘enhancerHomologSearch’ version ‘1.8.2’
* 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 ‘enhancerHomologSearch’ can be installed ... WARNING
Found the following significant warnings:
  Muscle/domuscle.cpp:74:26: warning: argument to ‘sizeof’ in ‘int snprintf(char*, size_t, const char*, ...)’ call is the same expression as the destination; did you mean to provide an explicit length? [-Wsizeof-pointer-memaccess]
  Muscle/typetostr.cpp:35:17: warning: argument to ‘sizeof’ in ‘int snprintf(char*, size_t, const char*, ...)’ call is the same expression as the destination; did you mean to provide an explicit length? [-Wsizeof-pointer-memaccess]
  Muscle/typetostr.cpp:52:17: warning: argument to ‘sizeof’ in ‘int snprintf(char*, size_t, const char*, ...)’ call is the same expression as the destination; did you mean to provide an explicit length? [-Wsizeof-pointer-memaccess]
  Muscle/typetostr.cpp:35:32: warning: ‘%8g’ directive output may be truncated writing between 8 and 13 bytes into a region of size 8 [-Wformat-truncation=]
  Muscle/typetostr.cpp:52:32: warning: ‘%.3g’ directive output may be truncated writing between 1 and 10 bytes into a region of size 8 [-Wformat-truncation=]
See ‘/home/biocbuild/bbs-3.18-bioc/meat/enhancerHomologSearch.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 10.3.1’
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking installed package size ... NOTE
  installed size is 30.9Mb
  sub-directories of 1Mb or more:
    libs  29.7Mb
* 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 ... OK
* 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 ... NOTE
  Note: found 28 marked UTF-8 strings
* 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 ‘enhancerHomologSearch-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: conservedMotifs
> ### Title: check the conserved motifs in the orthologs
> ### Aliases: conservedMotifs
> 
> ### ** Examples
> 
> library(BSgenome.Hsapiens.UCSC.hg38)
Loading required package: GenomeInfoDb
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:utils’:

    findMatches

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: BSgenome
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

Loading required package: BiocIO
Loading required package: rtracklayer

Attaching package: ‘rtracklayer’

The following object is masked from ‘package:BiocIO’:

    FileForFormat

> library(BSgenome.Mmusculus.UCSC.mm10)
> library(BSgenome.Drerio.UCSC.danRer10)
> LEN <- GRanges("chr4", IRanges(19050041, 19051709))
> seqEN <- getSeq(BSgenome.Drerio.UCSC.danRer10, LEN)
> aln_hs <- readRDS(system.file("extdata", "aln_hs.rds",
+                package="enhancerHomologSearch"))
> genome(aln_hs) <- Hsapiens
> aln_mm <- readRDS(system.file("extdata", "aln_mm.rds",
+                package="enhancerHomologSearch"))
> genome(aln_mm) <- Mmusculus
> al <- alignment(seqEN, list(human=aln_hs, mouse=aln_mm),
+                 method="ClustalW", order="input")
> data(motifs)
> conservedMotifs(al[[1]], list(human=aln_hs, mouse=aln_mm),
+                 motifs[["dist60"]], Drerio)
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’/home/biocbuild/R/R-4.3.1/bin/BATCH: line 60: 990716 Killed                  ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1

 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  [1] TRUE
  > require("TxDb.Hsapiens.UCSC.hg38.knownGene") || stop("unable to load TxDb.Hsapiens.UCSC.hg38.knownGene")
  Loading required package: TxDb.Hsapiens.UCSC.hg38.knownGene
  Loading required package: GenomicFeatures
  [1] TRUE
  > require("BiocParallel") || stop("unable to load BiocParallel")
  Loading required package: BiocParallel
  [1] TRUE
  > require("testthat") || stop("unable to load testthat")
  Loading required package: testthat
  [1] TRUE
  > test_check("enhancerHomologSearch")
  
    |                                                                            
    |                                                                      |   0%
* 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: 2 ERRORs, 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/enhancerHomologSearch.Rcheck/00check.log’
for details.