gaawr2

Genetic Association Analysis

v0.0.5 · Jan 30, 2026 · MIT + file LICENSE

Description

This is a companion to Henry-Stewart talk by Zhao (2026, <doi:10.69645/FRFQ9519>), which gathers information, metadata and scripts to showcase modern genetic analysis -- ranging from testing of polymorphic variant(s) for Hardy-Weinberg equilibrium, association with traits using genetic and statistical models, Bayesian implementation, power calculation in study design, and genetic annotation. It also covers R integration with the Linux environment, GitHub, package creation and web applications. The earlier version by Zhao (2009, <doi:10.69645/DCRY5578>) provides an brief introduction to these topics.

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CRAN Check Status

5 ERROR

9 OK

Show all 14 flavors

Flavor	Status	Time
r-devel-linux-x86_64-debian-clang	ERROR	171.5s
r-devel-linux-x86_64-debian-gcc	OK	154.6s
r-devel-linux-x86_64-fedora-clang	OK	367.7s
r-devel-linux-x86_64-fedora-gcc	OK	349.9s
r-devel-macos-arm64	OK	67s
r-devel-windows-x86_64	OK	222s
r-oldrel-macos-arm64	ERROR	72s
r-oldrel-macos-x86_64	ERROR	206s
r-oldrel-windows-x86_64	OK	273s
r-patched-linux-x86_64	OK	207.7s
r-release-linux-x86_64	OK	203.7s
r-release-macos-arm64	ERROR	67s
r-release-macos-x86_64	ERROR	200s
r-release-windows-x86_64	OK	213s

Check details (16 non-OK)

ERROR r-devel-linux-x86_64-debian-clang

re-building of vignette outputs

Error(s) in re-building vignettes:
  ...
--- re-building ‘gaawr2.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'EnsDb.Hsapiens.v75''
Failed with error:  'there is no package called 'ensembldb''
Failed with error:  'there is no package called 'biomaRt''
running: bash  -c "export message=\"Hello, world!\"
echo \"print('\$message')\" > hello.R
R CMD BATCH hello.R
R --no-save -q < hello.R
R --no-save -q <<END
message <- Sys.getenv(\"message\"); print(message)
source(\"hello.R\")
END
echo \${message} | \\
Rscript -e '
message <- scan(\"stdin\", what=\"\", sep=\"\\n\", quiet=TRUE);
write.table(message, col.names=FALSE, row.names=FALSE,
            quote=FALSE)
' | \\
cat
rm hello.*"

Quitting from gaawr2.Rmd:415-421 [ensdb]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `loadNamespace()`:
! there is no package called 'ensembldb'
---
Backtrace:
    ▆
 1. └─base::loadNamespace(x)
 2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
 3.     └─base (local) withOneRestart(expr, restarts[[1L]])
 4.       └─base (local) doWithOneRestart(return(expr), restart)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'gaawr2.Rmd' failed with diagnostics:
there is no package called 'ensembldb'
--- failed re-building ‘gaawr2.Rmd’

--- re-building ‘web.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'Rsamtools''
[WARNING] Citeproc: citation tsv not found
--- finished re-building ‘web.Rmd’

SUMMARY: processing the following file failed:
  ‘gaawr2.Rmd’

Error: Vignette re-building failed.
Execution halted

OK r-devel-linux-x86_64-debian-gcc

OK r-devel-linux-x86_64-fedora-clang

OK r-devel-linux-x86_64-fedora-gcc

OK r-devel-macos-arm64

OK r-devel-windows-x86_64

NOTE r-oldrel-macos-arm64

package dependencies

Package suggested but not available for checking: ‘EnsDb.Hsapiens.v75’

ERROR r-oldrel-macos-arm64

re-building of vignette outputs

Error(s) in re-building vignettes:
--- re-building ‘gaawr2.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'EnsDb.Hsapiens.v75''
running: bash  -c "export message=\"Hello, world!\"
echo \"print('\$message')\" > hello.R
R CMD BATCH hello.R
R --no-save -q < hello.R
R --no-save -q <<END
message <- Sys.getenv(\"message\"); print(message)
source(\"hello.R\")
END
echo \${message} | \\
Rscript -e '
message <- scan(\"stdin\", what=\"\", sep=\"\\n\", quiet=TRUE);
write.table(message, col.names=FALSE, row.names=FALSE,
            quote=FALSE)
' | \\
cat
rm hello.*"

Quitting from gaawr2.Rmd:415-421 [ensdb]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'x' in selecting a method for function 'metadata': object 'EnsDb.Hsapiens.v75' not found
---
Backtrace:
    ▆
 1. ├─ensembldb::metadata(EnsDb.Hsapiens.v75)
 2. └─base::.handleSimpleError(...)
 3.   └─base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'gaawr2.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'metadata': object 'EnsDb.Hsapiens.v75' not found
--- failed re-building ‘gaawr2.Rmd’

--- re-building ‘web.Rmd’ using rmarkdown
[WARNING] Citeproc: citation tsv not found
--- finished re-building ‘web.Rmd’

SUMMARY: processing the following file failed:
  ‘gaawr2.Rmd’

Error: Vignette re-building failed.
Execution halted

NOTE r-oldrel-macos-x86_64

package dependencies

Package suggested but not available for checking: ‘EnsDb.Hsapiens.v75’

ERROR r-oldrel-macos-x86_64

re-building of vignette outputs

Error(s) in re-building vignettes:
--- re-building ‘gaawr2.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'EnsDb.Hsapiens.v75''
running: bash  -c "export message=\"Hello, world!\"
echo \"print('\$message')\" > hello.R
R CMD BATCH hello.R
R --no-save -q < hello.R
R --no-save -q <<END
message <- Sys.getenv(\"message\"); print(message)
source(\"hello.R\")
END
echo \${message} | \\
Rscript -e '
message <- scan(\"stdin\", what=\"\", sep=\"\\n\", quiet=TRUE);
write.table(message, col.names=FALSE, row.names=FALSE,
            quote=FALSE)
' | \\
cat
rm hello.*"

Quitting from gaawr2.Rmd:415-421 [ensdb]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'x' in selecting a method for function 'metadata': object 'EnsDb.Hsapiens.v75' not found
---
Backtrace:
    ▆
 1. ├─ensembldb::metadata(EnsDb.Hsapiens.v75)
 2. └─base::.handleSimpleError(...)
 3.   └─base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'gaawr2.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'metadata': object 'EnsDb.Hsapiens.v75' not found
--- failed re-building ‘gaawr2.Rmd’

--- re-building ‘web.Rmd’ using rmarkdown
[WARNING] Citeproc: citation tsv not found
--- finished re-building ‘web.Rmd’

SUMMARY: processing the following file failed:
  ‘gaawr2.Rmd’

Error: Vignette re-building failed.
Execution halted

OK r-oldrel-windows-x86_64

OK r-patched-linux-x86_64

OK r-release-linux-x86_64

ERROR r-release-macos-arm64

re-building of vignette outputs

Error(s) in re-building vignettes:
--- re-building ‘gaawr2.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'EnsDb.Hsapiens.v75''
running: bash  -c "export message=\"Hello, world!\"
echo \"print('\$message')\" > hello.R
R CMD BATCH hello.R
R --no-save -q < hello.R
R --no-save -q <<END
message <- Sys.getenv(\"message\"); print(message)
source(\"hello.R\")
END
echo \${message} | \\
Rscript -e '
message <- scan(\"stdin\", what=\"\", sep=\"\\n\", quiet=TRUE);
write.table(message, col.names=FALSE, row.names=FALSE,
            quote=FALSE)
' | \\
cat
rm hello.*"

Quitting from gaawr2.Rmd:415-421 [ensdb]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'x' in selecting a method for function 'metadata': object 'EnsDb.Hsapiens.v75' not found
---
Backtrace:
    ▆
 1. ├─ensembldb::metadata(EnsDb.Hsapiens.v75)
 2. └─base::.handleSimpleError(...)
 3.   └─base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'gaawr2.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'metadata': object 'EnsDb.Hsapiens.v75' not found
--- failed re-building ‘gaawr2.Rmd’

--- re-building ‘web.Rmd’ using rmarkdown
[WARNING] Citeproc: citation tsv not found
--- finished re-building ‘web.Rmd’

SUMMARY: processing the following file failed:
  ‘gaawr2.Rmd’

Error: Vignette re-building failed.
Execution halted

ERROR r-release-macos-x86_64

re-building of vignette outputs

Error(s) in re-building vignettes:
--- re-building ‘gaawr2.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'EnsDb.Hsapiens.v75''
running: bash  -c "export message=\"Hello, world!\"
echo \"print('\$message')\" > hello.R
R CMD BATCH hello.R
R --no-save -q < hello.R
R --no-save -q <<END
message <- Sys.getenv(\"message\"); print(message)
source(\"hello.R\")
END
echo \${message} | \\
Rscript -e '
message <- scan(\"stdin\", what=\"\", sep=\"\\n\", quiet=TRUE);
write.table(message, col.names=FALSE, row.names=FALSE,
            quote=FALSE)
' | \\
cat
rm hello.*"

Quitting from gaawr2.Rmd:415-421 [ensdb]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'x' in selecting a method for function 'metadata': object 'EnsDb.Hsapiens.v75' not found
---
Backtrace:
    ▆
 1. ├─ensembldb::metadata(EnsDb.Hsapiens.v75)
 2. └─base::.handleSimpleError(...)
 3.   └─base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'gaawr2.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'metadata': object 'EnsDb.Hsapiens.v75' not found
--- failed re-building ‘gaawr2.Rmd’

--- re-building ‘web.Rmd’ using rmarkdown
[WARNING] Citeproc: citation tsv not found
--- finished re-building ‘web.Rmd’

SUMMARY: processing the following file failed:
  ‘gaawr2.Rmd’

Error: Vignette re-building failed.
Execution halted

OK r-release-windows-x86_64

Additional Issues

noSuggests Details →

Check History

ERROR 9 OK · 0 NOTE · 0 WARNING · 5 ERROR · 0 FAILURE Mar 9, 2026

ERROR r-devel-linux-x86_64-debian-clang

re-building of vignette outputs

Error(s) in re-building vignettes:
  ...
--- re-building ‘gaawr2.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'EnsDb.Hsapiens.v75''
Failed with error:  'there is no package called 'ensembldb''
Failed with error:  'there is no package called 'biomaRt''
running: bash  -c "export message=\"Hello, world!\"
echo \"print('\$message')\" > hello.R
R CMD BATCH hello.R
R --no-save -q < hello.R
R --no-save -q <<END
message <- Sys.getenv(\"message\"); print(message)
source(\"hello.R\

ERROR r-release-macos-arm64

re-building of vignette outputs

Error(s) in re-building vignettes:
--- re-building ‘gaawr2.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'EnsDb.Hsapiens.v75''
running: bash  -c "export message=\"Hello, world!\"
echo \"print('\$message')\" > hello.R
R CMD BATCH hello.R
R --no-save -q < hello.R
R --no-save -q <<END
message <- Sys.getenv(\"message\"); print(message)
source(\"hello.R\")
END
echo \${message} | \\
Rscript -e '
message <- scan(\"stdin\", what=\"\", sep=\"\\n\", quiet=TRUE);
write.table(message,

ERROR r-release-macos-x86_64

re-building of vignette outputs

Error(s) in re-building vignettes:
--- re-building ‘gaawr2.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'EnsDb.Hsapiens.v75''
running: bash  -c "export message=\"Hello, world!\"
echo \"print('\$message')\" > hello.R
R CMD BATCH hello.R
R --no-save -q < hello.R
R --no-save -q <<END
message <- Sys.getenv(\"message\"); print(message)
source(\"hello.R\")
END
echo \${message} | \\
Rscript -e '
message <- scan(\"stdin\", what=\"\", sep=\"\\n\", quiet=TRUE);
write.table(message,

ERROR r-oldrel-macos-arm64

package dependencies

Package suggested but not available for checking: ‘EnsDb.Hsapiens.v75’

ERROR r-oldrel-macos-x86_64

package dependencies

Package suggested but not available for checking: ‘EnsDb.Hsapiens.v75’

Dependency Network

Version History

new 0.0.5 Mar 9, 2026