Last updated on 2025-12-28 09:51:22 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: whether package can be installed
Result: ERROR
Installation failed.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, 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
Wed Dec 24 20:20:06 2025 - read bim
Wed Dec 24 20:20:06 2025 - read fam
extract 2 marker and 3 sample out of 166 marker and 3 sample
Wed Dec 24 20:20:06 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 24 20:20:06 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
Wed Dec 24 20:20:06 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_24_01_50_00_27005\Rtmpy21kDi\file66803aa71009 ]
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_24_01_50_00_27005\Rtmpy21kDi\file66802d753a02 ]
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’ [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-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 24 19:40:23 2025 - read bim
Wed Dec 24 19:40:23 2025 - read fam
extract 2 marker and 3 sample out of 166 marker and 3 sample
Wed Dec 24 19:40:23 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 24 19:40:23 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 24 19:40:23 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/RtmpTrXJct/file8c0b168b5b169 ]
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/RtmpTrXJct/file8c0b152aece92 ]
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’ [2s/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 Dec 27 19:24:14 2025 - read bim
Sat Dec 27 19:24:14 2025 - read fam
extract 2 marker and 3 sample out of 166 marker and 3 sample
Sat Dec 27 19:24:14 2025 - read bed
Binary PLINK BED file is ready to read
build a look-up table
assigned 6 values
allocate dim and dimnames
Sat Dec 27 19:24:14 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 Dec 27 19:24:14 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/RtmpxVLxtQ/file3ec8d6733da963 ]
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/RtmpxVLxtQ/file3ec8d65572ea7c ]
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
Thu Dec 25 19:36:06 2025 - read bim
Thu Dec 25 19:36:06 2025 - read fam
extract 2 marker and 3 sample out of 166 marker and 3 sample
Thu Dec 25 19:36:06 2025 - read bed
Binary PLINK BED file is ready to read
build a look-up table
assigned 6 values
allocate dim and dimnames
Thu Dec 25 19:36:06 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
Thu Dec 25 19:36:06 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_25_01_50_00_14239\Rtmp8KgNaE\file885427531f5e ]
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_25_01_50_00_14239\Rtmp8KgNaE\file8854247b5db1 ]
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 24 22:15:39 2025 - read bim
Wed Dec 24 22:15:39 2025 - read fam
extract 2 marker and 3 sample out of 166 marker and 3 sample
Wed Dec 24 22:15:39 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 24 22:15:39 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 24 22:15:39 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_24_01_50_00_27005\RtmpoNOFNi\file132984cb6234b ]
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_24_01_50_00_27005\RtmpoNOFNi\file132986a586e8a ]
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
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.