CRAN Package Check Results for Maintainer Paul Boutros <PBoutros at sbpdiscovery.org>

CRAN Package Check Results for Maintainer ‘Paul Boutros <PBoutros at sbpdiscovery.org>’

Last updated on 2026-02-26 13:52:07 CET.

Package	ERROR	NOTE	OK
ApplyPolygenicScore	6		8
bedr			14
BoutrosLab.plotting.general			14
OmicsQC			14
OutSeekR		2	12
SeqKat		1	13
VennDiagram			14

Package ApplyPolygenicScore

Current CRAN status: ERROR: 6, OK: 8

Version: 4.0.1
Check: tests
Result: ERROR Running ‘testthat.R’ [125s/140s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat); > library(ApplyPolygenicScore); > > test_check('ApplyPolygenicScore'); Input data passed validation Input data passed validation Skipping test for >12 PGS columns as 'scales' package is available and will be used. [1] "springgreen3" [1] "darkturquoise" [1] "springgreen3" [1] "darkturquoise" Saving _problems/test-vcf-import-266.R Saving _problems/test-vcf-import-270.R [ FAIL 2 | WARN 87 | SKIP 0 | PASS 653 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-vcf-import.R:263:9'): import.vcf accurately imports INFO fields ── Expected `ncol(select.info.test.vcf$dat)` to equal `ncol.select`. Differences: `actual`: 19.0 `expected`: 18.0 ── Failure ('test-vcf-import.R:267:9'): import.vcf accurately imports INFO fields ── Expected `ncol(all.info.test.vcf$dat)` to equal `ncol.all`. Differences: `actual`: 32.0 `expected`: 31.0 [ FAIL 2 | WARN 87 | SKIP 0 | PASS 653 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 4.0.1
Check: tests
Result: ERROR Running ‘testthat.R’ [259s/296s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat); > library(ApplyPolygenicScore); > > test_check('ApplyPolygenicScore'); Input data passed validation Input data passed validation Skipping test for >12 PGS columns as 'scales' package is available and will be used. [1] "springgreen3" [1] "darkturquoise" [1] "springgreen3" [1] "darkturquoise" Saving _problems/test-vcf-import-266.R Saving _problems/test-vcf-import-270.R [ FAIL 2 | WARN 87 | SKIP 0 | PASS 653 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-vcf-import.R:263:9'): import.vcf accurately imports INFO fields ── Expected `ncol(select.info.test.vcf$dat)` to equal `ncol.select`. Differences: `actual`: 19.0 `expected`: 18.0 ── Failure ('test-vcf-import.R:267:9'): import.vcf accurately imports INFO fields ── Expected `ncol(all.info.test.vcf$dat)` to equal `ncol.all`. Differences: `actual`: 32.0 `expected`: 31.0 [ FAIL 2 | WARN 87 | SKIP 0 | PASS 653 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 4.0.1
Check: tests
Result: ERROR Running 'testthat.R' [159s] Running the tests in 'tests/testthat.R' failed. Complete output: > library(testthat); > library(ApplyPolygenicScore); > > test_check('ApplyPolygenicScore'); Input data passed validation Input data passed validation Skipping test for >12 PGS columns as 'scales' package is available and will be used. [1] "springgreen3" [1] "darkturquoise" _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices 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_cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices [1] "springgreen3" [1] "darkturquoise" _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices Saving _problems/test-vcf-import-266.R Saving _problems/test-vcf-import-270.R [ FAIL 2 | WARN 87 | SKIP 0 | PASS 653 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-vcf-import.R:263:9'): import.vcf accurately imports INFO fields ── Expected `ncol(select.info.test.vcf$dat)` to equal `ncol.select`. Differences: `actual`: 19.0 `expected`: 18.0 ── Failure ('test-vcf-import.R:267:9'): import.vcf accurately imports INFO fields ── Expected `ncol(all.info.test.vcf$dat)` to equal `ncol.all`. Differences: `actual`: 32.0 `expected`: 31.0 [ FAIL 2 | WARN 87 | SKIP 0 | PASS 653 ] Error: ! Test failures. Execution halted Flavor: r-devel-windows-x86_64

Version: 4.0.1
Check: tests
Result: ERROR Running ‘testthat.R’ [175s/222s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat); > library(ApplyPolygenicScore); > > test_check('ApplyPolygenicScore'); Input data passed validation Input data passed validation Skipping test for >12 PGS columns as 'scales' package is available and will be used. [1] "springgreen3" [1] "darkturquoise" [1] "springgreen3" [1] "darkturquoise" Saving _problems/test-vcf-import-266.R Saving _problems/test-vcf-import-270.R [ FAIL 2 | WARN 87 | SKIP 0 | PASS 653 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-vcf-import.R:263:9'): import.vcf accurately imports INFO fields ── Expected `ncol(select.info.test.vcf$dat)` to equal `ncol.select`. Differences: `actual`: 19.0 `expected`: 18.0 ── Failure ('test-vcf-import.R:267:9'): import.vcf accurately imports INFO fields ── Expected `ncol(all.info.test.vcf$dat)` to equal `ncol.all`. Differences: `actual`: 32.0 `expected`: 31.0 [ FAIL 2 | WARN 87 | SKIP 0 | PASS 653 ] Error: ! Test failures. Execution halted Flavor: r-patched-linux-x86_64

Version: 4.0.1
Check: tests
Result: ERROR Running 'testthat.R' [166s] Running the tests in 'tests/testthat.R' failed. Complete output: > library(testthat); > library(ApplyPolygenicScore); > > test_check('ApplyPolygenicScore'); Input data passed validation Input data passed validation Skipping test for >12 PGS columns as 'scales' package is available and will be used. [1] "springgreen3" [1] "darkturquoise" [1] "springgreen3" [1] "darkturquoise" Saving _problems/test-vcf-import-266.R Saving _problems/test-vcf-import-270.R [ FAIL 2 | WARN 87 | SKIP 0 | PASS 653 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-vcf-import.R:263:9'): import.vcf accurately imports INFO fields ── Expected `ncol(select.info.test.vcf$dat)` to equal `ncol.select`. Differences: `actual`: 19.0 `expected`: 18.0 ── Failure ('test-vcf-import.R:267:9'): import.vcf accurately imports INFO fields ── Expected `ncol(all.info.test.vcf$dat)` to equal `ncol.all`. Differences: `actual`: 32.0 `expected`: 31.0 [ FAIL 2 | WARN 87 | SKIP 0 | PASS 653 ] Error: ! Test failures. Execution halted Flavor: r-release-windows-x86_64

Version: 4.0.1
Check: tests
Result: ERROR Running 'testthat.R' [201s] Running the tests in 'tests/testthat.R' failed. Complete output: > library(testthat); > library(ApplyPolygenicScore); > > test_check('ApplyPolygenicScore'); Input data passed validation Input data passed validation Skipping test for >12 PGS columns as 'scales' package is available and will be used. [1] "springgreen3" [1] "darkturquoise" [1] "springgreen3" [1] "darkturquoise" Saving _problems/test-vcf-import-266.R Saving _problems/test-vcf-import-270.R [ FAIL 2 | WARN 87 | SKIP 0 | PASS 653 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-vcf-import.R:263:9'): import.vcf accurately imports INFO fields ── Expected `ncol(select.info.test.vcf$dat)` to equal `ncol.select`. Differences: `actual`: 19.0 `expected`: 18.0 ── Failure ('test-vcf-import.R:267:9'): import.vcf accurately imports INFO fields ── Expected `ncol(all.info.test.vcf$dat)` to equal `ncol.all`. Differences: `actual`: 32.0 `expected`: 31.0 [ FAIL 2 | WARN 87 | SKIP 0 | PASS 653 ] Error: ! Test failures. Execution halted Flavor: r-oldrel-windows-x86_64

Package bedr

Current CRAN status: OK: 14

Package BoutrosLab.plotting.general

Current CRAN status: OK: 14

Package OmicsQC

Current CRAN status: OK: 14

Package OutSeekR

Current CRAN status: NOTE: 2, OK: 12

Version: 1.1.0
Check: dependencies in R code
Result: NOTE Namespaces in Imports field not imported from: ‘future’ ‘truncnorm’ All declared Imports should be used. Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Package SeqKat

Current CRAN status: NOTE: 1, OK: 13

Version: 0.0.9
Check: package dependencies
Result: NOTE Package suggested but not available for checking: 'doMC' Flavor: r-oldrel-windows-x86_64

Package VennDiagram

Current CRAN status: OK: 14

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