• using R version 4.5.2 (2025-10-31)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (Debian 14.3.0-10) 14.3.0     GNU Fortran (Debian 14.3.0-10) 14.3.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘seqminer/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘seqminer’ version ‘9.7’
• 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 executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking serialization versions ... OK
• checking whether package ‘seqminer’ can be installed ... OK See the install log for details.
• used C compiler: ‘gcc-14 (Debian 14.3.0-10) 14.3.0’
• used C++ compiler: ‘g++-14 (Debian 14.3.0-10) 14.3.0’
• checking C++ specification ... OK
• checking package directory ... OK
• checking for future file timestamps ... 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 ... [0s/1s] OK
• checking whether the package can be loaded with stated dependencies ... [0s/1s] OK
• checking whether the package can be unloaded cleanly ... [0s/1s] OK
• checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
• checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
• checking loading without being on the library search path ... [0s/1s] OK
• checking whether startup messages can be suppressed ... [0s/1s] OK
• checking use of S3 registration ... 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 ... [6s/8s] OK
• checking Rd files ... [0s/1s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... 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 line endings in shell scripts ... 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 ... INFO GNU make is a SystemRequirements.
• checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking use of PKG_*FLAGS in Makefiles ... OK
• checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
• checking include directives in Makefiles ... OK
• checking pragmas in C/C++ headers and code ... OK
• checking compilation flags used ... OK
• checking compiled code ... OK
• checking examples ... [1s/2s] OK
• checking for unstated dependencies in ‘demo’ ... OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [3s/5s] ERROR   Running ‘testthat.R’ [3s/4s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > ## follow http://adv-r.had.co.nz/Testing.html   > print(sprintf("Test seqminer [version %s]", packageVersion("seqminer")))   [1] "Test seqminer [version 9.7]"   > print("Platform")   [1] "Platform"   > print(str(.Platform))   List of 8    $ OS.type : chr "unix"    $ file.sep : chr "/"    $ dynlib.ext: chr ".so"    $ GUI : chr "X11"    $ endian : chr "little"    $ pkgType : chr "source"    $ path.sep : chr ":"    $ r_arch : chr ""   NULL   >   > print("Sys.info()")   [1] "Sys.info()"   > print(Sys.info())                                                  sysname                                                  "Linux"                                                  release                                          "6.12.22-amd64"                                                  version   "#1 SMP PREEMPT_DYNAMIC Debian 6.12.22-1 (2025-04-10)"                                                 nodename                                                 "gimli2"                                                  machine                                                 "x86_64"                                                    login                                                 "hornik"                                                     user                                                 "hornik"                                           effective_user                                                 "hornik"   >   > print(citation("seqminer"))   To cite package 'seqminer' in publications use:        Zhan X, Liu D (2015). "SEQMINER: An R-Package to Facilitate the     Functional Interpretation of Sequence-Based Associations." _Genetic     Epidemiology_, *39*(8), 1242. doi:10.1002/gepi.21918     <https://doi.org/10.1002/gepi.21918>, seqminer version 9.7,     <http://dx.doi.org/10.1002/gepi.21918>.      A BibTeX entry for LaTeX users is        @Article{,       title = {SEQMINER: An R-Package to Facilitate the Functional Interpretation of Sequence-Based Associations},       author = {Xiaowei Zhan and Dajiang J Liu},       journal = {Genetic Epidemiology},       volume = {39},       number = {8},       pages = {1242},       year = {2015},       note = {seqminer version 9.7},       web = {http:/zhanxw.github.io/seqminer},       publisher = {Wiley Online Library},       url = {http://dx.doi.org/10.1002/gepi.21918},       doi = {10.1002/gepi.21918},     }   >   > library(testthat)   > library(seqminer)   > ## ## test code are under inst/tests   > ## ## test_package("seqminer", reporter="tap")   > ## test_package("seqminer")   > test_check("seqminer")   1 gene/region to be extracted.   Read score tests...   In study 0   Done read score file: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/seqminer/test-triallelic/bi.MetaScore.assoc.gz   Read cov files ...   In study 0   Done read cov file: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/seqminer/test-triallelic/bi.MetaCov.assoc.gz   Finished calculation.   [1] "1:1" "1:2" "1:3"   [[1]]   [1] "G" "G" "G"      [[1]]              [,1] [,2] [,3]   [1,] 0.5126420 -0.0427202 0.0427202   [2,] -0.0427202 0.1993610 -0.0284801   [3,] 0.0427202 -0.0284801 0.1139210      Skipped: encounter a duplicated site: [ 1:1 ] in file [ /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/seqminer/test-triallelic/tri.MetaScore.assoc.gz ]   1 gene/region to be extracted.   Read score tests...   In study 0   Error: encounter a duplicated location: [ 1:1 ] in file [ /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/seqminer/test-triallelic/tri.MetaScore.assoc.gz ], will overwrite previous results!   Done read score file: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/seqminer/test-triallelic/tri.MetaScore.assoc.gz   Read cov files ...   In study 0   Done read cov file: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/seqminer/test-triallelic/tri.MetaCov.assoc.gz   Finished calculation.   [1] "1:1" "1:3"   [[1]]   [1] "T" "G"      [[1]]              [,1] [,2]   [1,] 0.1993610 -0.0284801   [2,] -0.0284801 0.1139210      1 gene/region to be extracted.   Read score tests...   In study 0   Done read score file: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/seqminer/test-triallelic/tri.MetaScore.assoc.gz   Read cov files ...   In study 0   Done read cov file: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/seqminer/test-triallelic/tri.MetaCov.assoc.gz   Finished calculation.   [1] "1:1_A/G" "1:1_A/T" "1:3_A/G"   [[1]]   [1] "G" "T" "G"      [[1]]              [,1] [,2] [,3]   [1,] 0.5126420 -0.0427202 0.0427202   [2,] -0.0427202 0.1993610 -0.0284801   [3,] 0.0427202 -0.0284801 0.1139210      [1] "============="   Total 3 line loaded, now put them to matrix [ 3 x 3 ] in R ...              1:1 1:2 1:3   1:1 0.5126420 -0.0427202 0.0427202   1:2 -0.0427202 0.1993610 -0.0284801   1:3 0.0427202 -0.0284801 0.1139210              1:1 1:2 1:3   1:1 0.5126420 -0.0427202 0.0427202   1:2 -0.0427202 0.1993610 -0.0284801   1:3 0.0427202 -0.0284801 0.1139210   Total 3 line loaded, now put them to matrix [ 3 x 3 ] in R ...                1:1 1:1/1 1:3   1:1 0.5126420 -0.0427202 0.0427202   1:1/1 -0.0427202 0.1993610 -0.0284801   1:3 0.0427202 -0.0284801 0.1139210   [1] "============="   $pos   [1] 1 2 3      $ref   [1] "A" "A" "A"      $alt   [1] "G" "G" "G"      $nSample   [1] 9 9 9      $af   [1] 0.3333330 0.1111110 0.0555556      $ac   [1] 6 2 1      $callRate   [1] 1 1 1      $hwe   [1] "1" "1" "1"      $nref   [1] 4 7 8      $nhet   [1] 4 2 1      $nalt   [1] 1 0 0      $ustat   [1] 0.283603 0.000000 0.325521      $vstat   [1] 2.14797 1.33950 1.01256      $effect   [1] 0.0614687 0.0000000 0.3174930      $pVal   [1] 0.894958 1.000000 0.747845      $anno   [1] "" "" ""      $annoFull   [1] "" "" ""      $pos   [1] 1 1 3      $ref   [1] "A" "A" "A"      $alt   [1] "G" "T" "G"      $nSample   [1] 9 9 9      $af   [1] 0.3333330 0.1111110 0.0555556      $ac   [1] 6 2 1      $callRate   [1] 1 1 1      $hwe   [1] "1" "1" "1"      $nref   [1] 4 7 8      $nhet   [1] 4 2 1      $nalt   [1] 1 0 0      $ustat   [1] 0.283603 0.000000 0.325521      $vstat   [1] 2.14797 1.33950 1.01256      $effect   [1] 0.0614687 0.0000000 0.3174930      $pVal   [1] 0.894958 1.000000 0.747845      $anno   [1] "" "" ""      $annoFull   [1] "" "" ""      Skipped: encounter a duplicated site: [ 1:1 ] in file [ /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/seqminer/test-triallelic/test2.study1.MetaScore.assoc.gz ]   1 gene/region to be extracted.   Read score tests...   In study 0   Error: encounter a duplicated location: [ 1:1 ] in file [ /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/seqminer/test-triallelic/test2.study1.MetaScore.assoc.gz ], will overwrite previous results!   Done read score file: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/seqminer/test-triallelic/test2.study1.MetaScore.assoc.gz   In study 1   Done read score file: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/seqminer/test-triallelic/test2.study2.MetaScore.assoc.gz   Read cov files ...   In study 0   Done read cov file: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/seqminer/test-triallelic/test2.study1.MetaCov.assoc.gz   In study 1   Done read cov file: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/seqminer/test-triallelic/test2.study2.MetaCov.assoc.gz   Finished calculation.   1 gene/region to be extracted.   Read score tests...   In study 0   Done read score file: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/seqminer/test-triallelic/test2.study1.MetaScore.assoc.gz   In study 1   Done read score file: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/seqminer/test-triallelic/test2.study2.MetaScore.assoc.gz   Read cov files ...   In study 0   Done read cov file: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/seqminer/test-triallelic/test2.study1.MetaCov.assoc.gz   In study 1   Done read cov file: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/seqminer/test-triallelic/test2.study2.MetaCov.assoc.gz   Finished calculation.   Loading objects:     apoe     cfh     cfh.all     cfh.nonsyn     cfh.nonsyn.2     cfh.range     cfh.syn     cfh.syn.2     out.gene.1     out.gene.2     out.gene.3     out.range.1     ssss   --------------- test readVCFToMatrixByRange ---------------   1 region to be extracted.   1 region to be extracted.   2 region to be extracted.   1 region to be extracted.   1 region to be extracted.   range of [ CFH ] is [ 1:196621007-196716634 ]   1 region to be extracted.   range of [ APOE ] is [ 19:45409038-45412650 ]   1 region to be extracted.   range of [ ssss ] is [ ]   range of [ CFH ] is [ 1:196621007-196716634 ]   range = 1:196621007-196716634   range of [ CFH ] is [ 1:196621007-196716634 ]   range = 1:196621007-196716634   range of [ CFH ] is [ 1:196621007-196716634 ]   range = 1:196621007-196716634   1 region to be extracted.   1 region to be extracted.   1 region to be extracted.   range of [ CFH ] is [ 1:196621007-196716634 ]   range of [ CFH ] is [ 1:196621007-196716634 ]   range = 1:196621007-196716634   start   file = /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/seqminer/plink/all.anno.filtered.extract   Sat Nov 15 19:32:36 2025 - read bim   Sat Nov 15 19:32:36 2025 - read fam   extract 2 marker and 3 sample out of 166 marker and 3 sample   Sat Nov 15 19:32:36 2025 - read bed   Binary PLINK BED file is ready to read   build a look-up table   assigned 6 values   allocate dim and dimnames   Sat Nov 15 19:32:36 2025 - end   --------------- test openPlink ---------------   --------------- test readPlinkBySubscript ---------------   start   file = /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/seqminer/plink/all.anno.filtered.extract.bed   extract 2 marker and 3 sample out of 166 marker and 3 sample   Binary PLINK BED file is ready to read   build a look-up table   assigned 6 values   allocate dim   Sat Nov 15 19:32:36 2025 - end   --------------- test readSingleChromosomeVCFToMatrixByRange ---------------   fsize = 2688   query [0, 0]   Found 1 results   found 1 position, e.g. 0 2384   Inferred 3 samples from header   1 region to be extracted.   query [196621007, 196716634]   Found 166 results   found 166 position, e.g. 196623337 2454   --------------- test createSingleChromosomeVCFIndex ---------------   header line has 3 samples   offset = 2384   Indexing finished with 3 samples and 166 markers   created index file [ /home/hornik/tmp/scratch/RtmpmVBuaL/file8b57d3ac4f8bf ]   Saving _problems/test-vcf-167.R   --------------- test readSingleChromosomeBCFToMatrixByRange ---------------   fsize = 2688   l_text = 4206   Total contig parse = 1, total header index used = 47   Inferred 3 samples from header   1 region to be extracted.   query [196621006, 196716633]   Found 166 results   196623336 4215   found 166 position, e.g. 196623336 4215   sampleNames.size() = 3, markerNames.size() = 166   --------------- test createSingleChromosomeBCFIndex ---------------   l_text = 4206   Total contig parse = 1, total header index used = 47   offset_header = 4135   sample size = 3   last character is s[after_chrom_size-1] = 0   Indexing finished with 3 samples and 166 markers   created index file [ /home/hornik/tmp/scratch/RtmpmVBuaL/file8b57dc965ebd ]   Saving _problems/test-vcf-181.R   [ FAIL 2 | WARN 0 | SKIP 0 | PASS 72 ]      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test-vcf.R:167:5'): createSingleChromosomeVCFIndex ──────────────────   Error in `expect(nchar(cfh) > 0)`: `failure_message` must be a character vector, not absent.   Backtrace:       ▆    1. └─testthat::expect(failure_message = <empty>) at test-vcf.R:167:5    2. └─testthat:::check_character(failure_message)    3. └─testthat:::stop_input_type(...)    4. └─rlang::abort(message, ..., call = call, arg = arg)   ── Error ('test-vcf.R:181:5'): createSingleChromosomeBCFIndex ──────────────────   Error in `expect(nchar(cfh) > 0)`: `failure_message` must be a character vector, not absent.   Backtrace:       ▆    1. └─testthat::expect(failure_message = <empty>) at test-vcf.R:181:5    2. └─testthat:::check_character(failure_message)    3. └─testthat:::stop_input_type(...)    4. └─rlang::abort(message, ..., call = call, arg = arg)      [ FAIL 2 | WARN 0 | SKIP 0 | PASS 72 ]   Error:   ! Test failures.   Execution halted
• checking PDF version of manual ... [9s/13s] OK
• checking HTML version of manual ... [1s/2s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR