Last updated on 2025-12-04 07:52:02 CET.
| Package | ERROR | WARN | NOTE | OK |
|---|---|---|---|---|
| cromwellDashboard | 5 | 8 | ||
| seqminer | 9 | 2 | 1 | 1 |
Current CRAN status: NOTE: 5, OK: 8
Version: 0.5.1
Check: CRAN incoming feasibility
Result: NOTE
Maintainer: ‘Xiaowei Zhan <zhanxw@gmail.com>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: person(given = "Xiaowei",
family = "Zhan",
role = c("aut", "cre"),
email = "zhanxw@gmail.com")
as necessary.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 0.5.1
Check: LazyData
Result: NOTE
'LazyData' is specified without a 'data' directory
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Current CRAN status: ERROR: 9, WARN: 2, NOTE: 1, OK: 1
Version: 9.7
Check: tests
Result: ERROR
Running ‘testthat.R’ [3s/5s]
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-devel-clang/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-devel-clang/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-devel-clang/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-devel-clang/Work/build/Packages/seqminer/test-triallelic/tri.MetaScore.assoc.gz ], will overwrite previous results!
Done read score file: /home/hornik/tmp/R.check/r-devel-clang/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-devel-clang/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-devel-clang/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-devel-clang/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-devel-clang/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-devel-clang/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-devel-clang/Work/build/Packages/seqminer/test-triallelic/test2.study1.MetaScore.assoc.gz
In study 1
Done read score file: /home/hornik/tmp/R.check/r-devel-clang/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-devel-clang/Work/build/Packages/seqminer/test-triallelic/test2.study1.MetaCov.assoc.gz
In study 1
Done read cov file: /home/hornik/tmp/R.check/r-devel-clang/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-devel-clang/Work/build/Packages/seqminer/test-triallelic/test2.study1.MetaScore.assoc.gz
In study 1
Done read score file: /home/hornik/tmp/R.check/r-devel-clang/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-devel-clang/Work/build/Packages/seqminer/test-triallelic/test2.study1.MetaCov.assoc.gz
In study 1
Done read cov file: /home/hornik/tmp/R.check/r-devel-clang/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-devel-clang/Work/build/Packages/seqminer/plink/all.anno.filtered.extract
Tue Dec 2 08:26:25 2025 - read bim
Tue Dec 2 08:26:25 2025 - read fam
extract 2 marker and 3 sample out of 166 marker and 3 sample
Tue Dec 2 08:26:25 2025 - read bed
Binary PLINK BED file is ready to read
build a look-up table
assigned 6 values
allocate dim and dimnames
Tue Dec 2 08:26:25 2025 - end
--------------- test openPlink ---------------
--------------- test readPlinkBySubscript ---------------
start
file = /home/hornik/tmp/R.check/r-devel-clang/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
Tue Dec 2 08:26:25 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/RtmptA8BRR/file902f3516879d7 ]
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/RtmptA8BRR/file902f356e030a3 ]
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
Flavor: r-devel-linux-x86_64-debian-clang
Version: 9.7
Check: tests
Result: ERROR
Running ‘testthat.R’ [2s/3s]
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
"gimli1"
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-devel-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-devel-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-devel-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-devel-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-devel-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-devel-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-devel-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-devel-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-devel-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-devel-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-devel-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-devel-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-devel-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-devel-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-devel-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-devel-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-devel-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-devel-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-devel-gcc/Work/build/Packages/seqminer/plink/all.anno.filtered.extract
Wed Dec 3 18:26:31 2025 - read bim
Wed Dec 3 18:26:31 2025 - read fam
extract 2 marker and 3 sample out of 166 marker and 3 sample
Wed Dec 3 18:26:31 2025 - read bed
Binary PLINK BED file is ready to read
build a look-up table
assigned 6 values
allocate dim and dimnames
Wed Dec 3 18:26:31 2025 - end
--------------- test openPlink ---------------
--------------- test readPlinkBySubscript ---------------
start
file = /home/hornik/tmp/R.check/r-devel-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
Wed Dec 3 18:26:31 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 [ /tmp/RtmpufggVF/file2a39d7f11461f ]
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 [ /tmp/RtmpufggVF/file2a39d51ea9519 ]
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
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 9.7
Check: tests
Result: ERROR
Running ‘testthat.R’
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
"6.14.6-300.fc42.x86_64"
version
"#1 SMP PREEMPT_DYNAMIC Fri May 9 20:11:19 UTC 2025"
nodename
"gannet.stats.ox.ac.uk"
machine
"x86_64"
login
"ripley"
user
"ripley"
effective_user
"ripley"
>
> 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: /data/gannet/ripley/R/packages/tests-clang/seqminer.Rcheck/seqminer/test-triallelic/bi.MetaScore.assoc.gz
Read cov files ...
In study 0
Done read cov file: /data/gannet/ripley/R/packages/tests-clang/seqminer.Rcheck/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 [ /data/gannet/ripley/R/packages/tests-clang/seqminer.Rcheck/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 [ /data/gannet/ripley/R/packages/tests-clang/seqminer.Rcheck/seqminer/test-triallelic/tri.MetaScore.assoc.gz ], will overwrite previous results!
Done read score file: /data/gannet/ripley/R/packages/tests-clang/seqminer.Rcheck/seqminer/test-triallelic/tri.MetaScore.assoc.gz
Read cov files ...
In study 0
Done read cov file: /data/gannet/ripley/R/packages/tests-clang/seqminer.Rcheck/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: /data/gannet/ripley/R/packages/tests-clang/seqminer.Rcheck/seqminer/test-triallelic/tri.MetaScore.assoc.gz
Read cov files ...
In study 0
Done read cov file: /data/gannet/ripley/R/packages/tests-clang/seqminer.Rcheck/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 [ /data/gannet/ripley/R/packages/tests-clang/seqminer.Rcheck/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 [ /data/gannet/ripley/R/packages/tests-clang/seqminer.Rcheck/seqminer/test-triallelic/test2.study1.MetaScore.assoc.gz ], will overwrite previous results!
Done read score file: /data/gannet/ripley/R/packages/tests-clang/seqminer.Rcheck/seqminer/test-triallelic/test2.study1.MetaScore.assoc.gz
In study 1
Done read score file: /data/gannet/ripley/R/packages/tests-clang/seqminer.Rcheck/seqminer/test-triallelic/test2.study2.MetaScore.assoc.gz
Read cov files ...
In study 0
Done read cov file: /data/gannet/ripley/R/packages/tests-clang/seqminer.Rcheck/seqminer/test-triallelic/test2.study1.MetaCov.assoc.gz
In study 1
Done read cov file: /data/gannet/ripley/R/packages/tests-clang/seqminer.Rcheck/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: /data/gannet/ripley/R/packages/tests-clang/seqminer.Rcheck/seqminer/test-triallelic/test2.study1.MetaScore.assoc.gz
In study 1
Done read score file: /data/gannet/ripley/R/packages/tests-clang/seqminer.Rcheck/seqminer/test-triallelic/test2.study2.MetaScore.assoc.gz
Read cov files ...
In study 0
Done read cov file: /data/gannet/ripley/R/packages/tests-clang/seqminer.Rcheck/seqminer/test-triallelic/test2.study1.MetaCov.assoc.gz
In study 1
Done read cov file: /data/gannet/ripley/R/packages/tests-clang/seqminer.Rcheck/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 = /data/gannet/ripley/R/packages/tests-clang/seqminer.Rcheck/seqminer/plink/all.anno.filtered.extract
Mon Dec 1 13:46:33 2025 - read bim
Mon Dec 1 13:46:33 2025 - read fam
extract 2 marker and 3 sample out of 166 marker and 3 sample
Mon Dec 1 13:46:33 2025 - read bed
Binary PLINK BED file is ready to read
build a look-up table
assigned 6 values
allocate dim and dimnames
Mon Dec 1 13:46:33 2025 - end
--------------- test openPlink ---------------
--------------- test readPlinkBySubscript ---------------
start
file = /data/gannet/ripley/R/packages/tests-clang/seqminer.Rcheck/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
Mon Dec 1 13:46:33 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 [ /tmp/RtmpABpUty/working_dir/RtmpNsOcKs/file1de56e4eaa81a0 ]
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 [ /tmp/RtmpABpUty/working_dir/RtmpNsOcKs/file1de56e60720b7f ]
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
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 9.7
Check: tests
Result: ERROR
Running ‘testthat.R’ [4s/11s]
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
"6.14.6-300.fc42.x86_64"
version
"#1 SMP PREEMPT_DYNAMIC Fri May 9 20:11:19 UTC 2025"
nodename
"gannet.stats.ox.ac.uk"
machine
"x86_64"
login
"ripley"
user
"ripley"
effective_user
"ripley"
>
> 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: /data/gannet/ripley/R/packages/tests-devel/seqminer.Rcheck/seqminer/test-triallelic/bi.MetaScore.assoc.gz
Read cov files ...
In study 0
Done read cov file: /data/gannet/ripley/R/packages/tests-devel/seqminer.Rcheck/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 [ /data/gannet/ripley/R/packages/tests-devel/seqminer.Rcheck/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 [ /data/gannet/ripley/R/packages/tests-devel/seqminer.Rcheck/seqminer/test-triallelic/tri.MetaScore.assoc.gz ], will overwrite previous results!
Done read score file: /data/gannet/ripley/R/packages/tests-devel/seqminer.Rcheck/seqminer/test-triallelic/tri.MetaScore.assoc.gz
Read cov files ...
In study 0
Done read cov file: /data/gannet/ripley/R/packages/tests-devel/seqminer.Rcheck/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: /data/gannet/ripley/R/packages/tests-devel/seqminer.Rcheck/seqminer/test-triallelic/tri.MetaScore.assoc.gz
Read cov files ...
In study 0
Done read cov file: /data/gannet/ripley/R/packages/tests-devel/seqminer.Rcheck/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 [ /data/gannet/ripley/R/packages/tests-devel/seqminer.Rcheck/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 [ /data/gannet/ripley/R/packages/tests-devel/seqminer.Rcheck/seqminer/test-triallelic/test2.study1.MetaScore.assoc.gz ], will overwrite previous results!
Done read score file: /data/gannet/ripley/R/packages/tests-devel/seqminer.Rcheck/seqminer/test-triallelic/test2.study1.MetaScore.assoc.gz
In study 1
Done read score file: /data/gannet/ripley/R/packages/tests-devel/seqminer.Rcheck/seqminer/test-triallelic/test2.study2.MetaScore.assoc.gz
Read cov files ...
In study 0
Done read cov file: /data/gannet/ripley/R/packages/tests-devel/seqminer.Rcheck/seqminer/test-triallelic/test2.study1.MetaCov.assoc.gz
In study 1
Done read cov file: /data/gannet/ripley/R/packages/tests-devel/seqminer.Rcheck/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: /data/gannet/ripley/R/packages/tests-devel/seqminer.Rcheck/seqminer/test-triallelic/test2.study1.MetaScore.assoc.gz
In study 1
Done read score file: /data/gannet/ripley/R/packages/tests-devel/seqminer.Rcheck/seqminer/test-triallelic/test2.study2.MetaScore.assoc.gz
Read cov files ...
In study 0
Done read cov file: /data/gannet/ripley/R/packages/tests-devel/seqminer.Rcheck/seqminer/test-triallelic/test2.study1.MetaCov.assoc.gz
In study 1
Done read cov file: /data/gannet/ripley/R/packages/tests-devel/seqminer.Rcheck/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 = /data/gannet/ripley/R/packages/tests-devel/seqminer.Rcheck/seqminer/plink/all.anno.filtered.extract
Mon Nov 24 05:57:01 2025 - read bim
Mon Nov 24 05:57:01 2025 - read fam
extract 2 marker and 3 sample out of 166 marker and 3 sample
Mon Nov 24 05:57:01 2025 - read bed
Binary PLINK BED file is ready to read
build a look-up table
assigned 6 values
allocate dim and dimnames
Mon Nov 24 05:57:01 2025 - end
--------------- test openPlink ---------------
--------------- test readPlinkBySubscript ---------------
start
file = /data/gannet/ripley/R/packages/tests-devel/seqminer.Rcheck/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
Mon Nov 24 05:57:01 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 [ /tmp/Rtmpp7Kq3g/working_dir/Rtmpubvw1o/file2c66db71fd87b0 ]
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 [ /tmp/Rtmpp7Kq3g/working_dir/Rtmpubvw1o/file2c66db3c270a49 ]
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
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 9.7
Check: tests
Result: ERROR
Running 'testthat.R' [3s]
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 "windows"
$ file.sep : chr "/"
$ dynlib.ext: chr ".dll"
$ GUI : chr "RTerm"
$ endian : chr "little"
$ pkgType : chr "win.binary"
$ path.sep : chr ";"
$ r_arch : chr "x64"
NULL
>
> print("Sys.info()")
[1] "Sys.info()"
> print(Sys.info())
sysname release version nodename machine
"Windows" "Server x64" "build 20348" "CRANWIN3" "x86-64"
login user effective_user udomain
"CRAN" "CRAN" "CRAN" "CRANWIN3"
>
> 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: D:/RCompile/CRANpkg/lib/4.6/seqminer/test-triallelic/bi.MetaScore.assoc.gz
Read cov files ...
In study 0
Done read cov file: D:/RCompile/CRANpkg/lib/4.6/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 [ D:/RCompile/CRANpkg/lib/4.6/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 [ D:/RCompile/CRANpkg/lib/4.6/seqminer/test-triallelic/tri.MetaScore.assoc.gz ], will overwrite previous results!
Done read score file: D:/RCompile/CRANpkg/lib/4.6/seqminer/test-triallelic/tri.MetaScore.assoc.gz
Read cov files ...
In study 0
Done read cov file: D:/RCompile/CRANpkg/lib/4.6/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: D:/RCompile/CRANpkg/lib/4.6/seqminer/test-triallelic/tri.MetaScore.assoc.gz
Read cov files ...
In study 0
Done read cov file: D:/RCompile/CRANpkg/lib/4.6/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 [ D:/RCompile/CRANpkg/lib/4.6/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 [ D:/RCompile/CRANpkg/lib/4.6/seqminer/test-triallelic/test2.study1.MetaScore.assoc.gz ], will overwrite previous results!
Done read score file: D:/RCompile/CRANpkg/lib/4.6/seqminer/test-triallelic/test2.study1.MetaScore.assoc.gz
In study 1
Done read score file: D:/RCompile/CRANpkg/lib/4.6/seqminer/test-triallelic/test2.study2.MetaScore.assoc.gz
Read cov files ...
In study 0
Done read cov file: D:/RCompile/CRANpkg/lib/4.6/seqminer/test-triallelic/test2.study1.MetaCov.assoc.gz
In study 1
Done read cov file: D:/RCompile/CRANpkg/lib/4.6/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: D:/RCompile/CRANpkg/lib/4.6/seqminer/test-triallelic/test2.study1.MetaScore.assoc.gz
In study 1
Done read score file: D:/RCompile/CRANpkg/lib/4.6/seqminer/test-triallelic/test2.study2.MetaScore.assoc.gz
Read cov files ...
In study 0
Done read cov file: D:/RCompile/CRANpkg/lib/4.6/seqminer/test-triallelic/test2.study1.MetaCov.assoc.gz
In study 1
Done read cov file: D:/RCompile/CRANpkg/lib/4.6/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 = D:/RCompile/CRANpkg/lib/4.6/seqminer/plink/all.anno.filtered.extract
Tue Dec 2 14:49:32 2025 - read bim
Tue Dec 2 14:49:32 2025 - read fam
extract 2 marker and 3 sample out of 166 marker and 3 sample
Tue Dec 2 14:49:32 2025 - read bed
Binary PLINK BED file is ready to read
build a look-up table
assigned 6 values
allocate dim and dimnames
Tue Dec 2 14:49:32 2025 - end
--------------- test openPlink ---------------
--------------- test readPlinkBySubscript ---------------
start
file = D:/RCompile/CRANpkg/lib/4.6/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
Tue Dec 2 14:49:32 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. 1.96623e+08 2454
--------------- test createSingleChromosomeVCFIndex ---------------
header line has 3 samples
offset = 2384
Indexing finished with 3 samples and 166 markers
created index file [ D:\temp\2025_12_02_01_50_00_12944\RtmpMBdQl9\filef27c6f9a5b14 ]
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
1.96623e+08 4215
found 166 position, e.g. 1.96623e+08 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 [ D:\temp\2025_12_02_01_50_00_12944\RtmpMBdQl9\filef27c665d13af ]
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
Flavor: r-devel-windows-x86_64
Version: 9.7
Check: tests
Result: ERROR
Running ‘testthat.R’ [2s/5s]
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-patched-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-patched-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-patched-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-patched-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-patched-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-patched-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-patched-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-patched-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-patched-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-patched-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-patched-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-patched-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-patched-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-patched-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-patched-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-patched-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-patched-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-patched-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-patched-gcc/Work/build/Packages/seqminer/plink/all.anno.filtered.extract
Wed Dec 3 19:34:58 2025 - read bim
Wed Dec 3 19:34:58 2025 - read fam
extract 2 marker and 3 sample out of 166 marker and 3 sample
Wed Dec 3 19:34:58 2025 - read bed
Binary PLINK BED file is ready to read
build a look-up table
assigned 6 values
allocate dim and dimnames
Wed Dec 3 19:34:58 2025 - end
--------------- test openPlink ---------------
--------------- test readPlinkBySubscript ---------------
start
file = /home/hornik/tmp/R.check/r-patched-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
Wed Dec 3 19:34:58 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/RtmpE7bLvc/file20ca0d7b1b68c4 ]
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/RtmpE7bLvc/file20ca0d3fa23cff ]
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
Flavor: r-patched-linux-x86_64
Version: 9.7
Check: tests
Result: 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 29 19:35:02 2025 - read bim
Sat Nov 29 19:35:02 2025 - read fam
extract 2 marker and 3 sample out of 166 marker and 3 sample
Sat Nov 29 19:35:02 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 29 19:35:02 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 29 19:35:02 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/RtmpdLn4FM/file2926a76e72b3c2 ]
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/RtmpdLn4FM/file2926a717ed7e54 ]
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
Flavor: r-release-linux-x86_64
Version: 9.7
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
SingleChromosomeVCFIndex.cpp:109:51: warning: format specifies type 'long' but the argument has type 'int64_t' (aka 'long long') [-Wformat]
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.5/seqminer.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
* used C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
* used SDK: ‘MacOSX11.3.sdk’
Flavor: r-release-macos-x86_64
Version: 9.7
Check: tests
Result: ERROR
Running 'testthat.R' [3s]
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 "windows"
$ file.sep : chr "/"
$ dynlib.ext: chr ".dll"
$ GUI : chr "RTerm"
$ endian : chr "little"
$ pkgType : chr "win.binary"
$ path.sep : chr ";"
$ r_arch : chr "x64"
NULL
>
> print("Sys.info()")
[1] "Sys.info()"
> print(Sys.info())
sysname release version nodename machine
"Windows" "Server x64" "build 20348" "CRANWIN3" "x86-64"
login user effective_user udomain
"CRAN" "CRAN" "CRAN" "CRANWIN3"
>
> 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: D:/RCompile/CRANpkg/lib/4.5/seqminer/test-triallelic/bi.MetaScore.assoc.gz
Read cov files ...
In study 0
Done read cov file: D:/RCompile/CRANpkg/lib/4.5/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 [ D:/RCompile/CRANpkg/lib/4.5/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 [ D:/RCompile/CRANpkg/lib/4.5/seqminer/test-triallelic/tri.MetaScore.assoc.gz ], will overwrite previous results!
Done read score file: D:/RCompile/CRANpkg/lib/4.5/seqminer/test-triallelic/tri.MetaScore.assoc.gz
Read cov files ...
In study 0
Done read cov file: D:/RCompile/CRANpkg/lib/4.5/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: D:/RCompile/CRANpkg/lib/4.5/seqminer/test-triallelic/tri.MetaScore.assoc.gz
Read cov files ...
In study 0
Done read cov file: D:/RCompile/CRANpkg/lib/4.5/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 [ D:/RCompile/CRANpkg/lib/4.5/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 [ D:/RCompile/CRANpkg/lib/4.5/seqminer/test-triallelic/test2.study1.MetaScore.assoc.gz ], will overwrite previous results!
Done read score file: D:/RCompile/CRANpkg/lib/4.5/seqminer/test-triallelic/test2.study1.MetaScore.assoc.gz
In study 1
Done read score file: D:/RCompile/CRANpkg/lib/4.5/seqminer/test-triallelic/test2.study2.MetaScore.assoc.gz
Read cov files ...
In study 0
Done read cov file: D:/RCompile/CRANpkg/lib/4.5/seqminer/test-triallelic/test2.study1.MetaCov.assoc.gz
In study 1
Done read cov file: D:/RCompile/CRANpkg/lib/4.5/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: D:/RCompile/CRANpkg/lib/4.5/seqminer/test-triallelic/test2.study1.MetaScore.assoc.gz
In study 1
Done read score file: D:/RCompile/CRANpkg/lib/4.5/seqminer/test-triallelic/test2.study2.MetaScore.assoc.gz
Read cov files ...
In study 0
Done read cov file: D:/RCompile/CRANpkg/lib/4.5/seqminer/test-triallelic/test2.study1.MetaCov.assoc.gz
In study 1
Done read cov file: D:/RCompile/CRANpkg/lib/4.5/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 = D:/RCompile/CRANpkg/lib/4.5/seqminer/plink/all.anno.filtered.extract
Sun Nov 16 02:55:57 2025 - read bim
Sun Nov 16 02:55:57 2025 - read fam
extract 2 marker and 3 sample out of 166 marker and 3 sample
Sun Nov 16 02:55:57 2025 - read bed
Binary PLINK BED file is ready to read
build a look-up table
assigned 6 values
allocate dim and dimnames
Sun Nov 16 02:55:57 2025 - end
--------------- test openPlink ---------------
--------------- test readPlinkBySubscript ---------------
start
file = D:/RCompile/CRANpkg/lib/4.5/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
Sun Nov 16 02:55:57 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. 1.96623e+08 2454
--------------- test createSingleChromosomeVCFIndex ---------------
header line has 3 samples
offset = 2384
Indexing finished with 3 samples and 166 markers
created index file [ D:\temp\2025_11_15_13_34_13_7498\RtmpUbmiGA\fileeedc1db21f4a ]
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
1.96623e+08 4215
found 166 position, e.g. 1.96623e+08 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 [ D:\temp\2025_11_15_13_34_13_7498\RtmpUbmiGA\fileeedc43f3d58 ]
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
Flavor: r-release-windows-x86_64
Version: 9.7
Check: installed package size
Result: NOTE
installed size is 19.3Mb
sub-directories of 1Mb or more:
libs 17.8Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 9.7
Check: for GNU extensions in Makefiles
Result: NOTE
GNU make is a SystemRequirements.
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 9.7
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
SingleChromosomeVCFIndex.cpp:109:51: warning: format specifies type 'long' but the argument has type 'int64_t' (aka 'long long') [-Wformat]
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.4/seqminer.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
* used C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
* used SDK: ‘MacOSX11.3.sdk’
Flavor: r-oldrel-macos-x86_64
Version: 9.7
Check: tests
Result: ERROR
Running 'testthat.R' [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 "windows"
$ file.sep : chr "/"
$ dynlib.ext: chr ".dll"
$ GUI : chr "RTerm"
$ endian : chr "little"
$ pkgType : chr "win.binary"
$ path.sep : chr ";"
$ r_arch : chr "x64"
NULL
>
> print("Sys.info()")
[1] "Sys.info()"
> print(Sys.info())
sysname release version nodename machine
"Windows" "Server x64" "build 20348" "CRANWIN2" "x86-64"
login user effective_user
"CRAN" "CRAN" "CRAN"
>
> 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: D:/RCompile/CRANpkg/lib/4.4/seqminer/test-triallelic/bi.MetaScore.assoc.gz
Read cov files ...
In study 0
Done read cov file: D:/RCompile/CRANpkg/lib/4.4/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 [ D:/RCompile/CRANpkg/lib/4.4/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 [ D:/RCompile/CRANpkg/lib/4.4/seqminer/test-triallelic/tri.MetaScore.assoc.gz ], will overwrite previous results!
Done read score file: D:/RCompile/CRANpkg/lib/4.4/seqminer/test-triallelic/tri.MetaScore.assoc.gz
Read cov files ...
In study 0
Done read cov file: D:/RCompile/CRANpkg/lib/4.4/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: D:/RCompile/CRANpkg/lib/4.4/seqminer/test-triallelic/tri.MetaScore.assoc.gz
Read cov files ...
In study 0
Done read cov file: D:/RCompile/CRANpkg/lib/4.4/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 [ D:/RCompile/CRANpkg/lib/4.4/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 [ D:/RCompile/CRANpkg/lib/4.4/seqminer/test-triallelic/test2.study1.MetaScore.assoc.gz ], will overwrite previous results!
Done read score file: D:/RCompile/CRANpkg/lib/4.4/seqminer/test-triallelic/test2.study1.MetaScore.assoc.gz
In study 1
Done read score file: D:/RCompile/CRANpkg/lib/4.4/seqminer/test-triallelic/test2.study2.MetaScore.assoc.gz
Read cov files ...
In study 0
Done read cov file: D:/RCompile/CRANpkg/lib/4.4/seqminer/test-triallelic/test2.study1.MetaCov.assoc.gz
In study 1
Done read cov file: D:/RCompile/CRANpkg/lib/4.4/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: D:/RCompile/CRANpkg/lib/4.4/seqminer/test-triallelic/test2.study1.MetaScore.assoc.gz
In study 1
Done read score file: D:/RCompile/CRANpkg/lib/4.4/seqminer/test-triallelic/test2.study2.MetaScore.assoc.gz
Read cov files ...
In study 0
Done read cov file: D:/RCompile/CRANpkg/lib/4.4/seqminer/test-triallelic/test2.study1.MetaCov.assoc.gz
In study 1
Done read cov file: D:/RCompile/CRANpkg/lib/4.4/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 = D:/RCompile/CRANpkg/lib/4.4/seqminer/plink/all.anno.filtered.extract
Wed Dec 3 21:53:05 2025 - read bim
Wed Dec 3 21:53:05 2025 - read fam
extract 2 marker and 3 sample out of 166 marker and 3 sample
Wed Dec 3 21:53:05 2025 - read bed
Binary PLINK BED file is ready to read
build a look-up table
assigned 6 values
allocate dim and dimnames
Wed Dec 3 21:53:05 2025 - end
--------------- test openPlink ---------------
--------------- test readPlinkBySubscript ---------------
start
file = D:/RCompile/CRANpkg/lib/4.4/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
Wed Dec 3 21:53:05 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. 1.96623e+08 2454
--------------- test createSingleChromosomeVCFIndex ---------------
header line has 3 samples
offset = 2384
Indexing finished with 3 samples and 166 markers
created index file [ D:\temp\2025_12_03_01_50_00_178\Rtmp8mjxO2\file7810628677ba ]
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
1.96623e+08 4215
found 166 position, e.g. 1.96623e+08 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 [ D:\temp\2025_12_03_01_50_00_178\Rtmp8mjxO2\file781056414e7 ]
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
Flavor: r-oldrel-windows-x86_64
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