cran-comments.md
In rmsharp/nprcgenekeepr: Genetic Tools for Colony Management
Resubmission
This is a resubmission. In this version I have:
- Responded to each request provided by the reviewer
- Requests from 20250419:
- Used ::: in documentation:
man/fillGroupMembersWithSexRatio.Rd:
groupMembers <- nprcgenekeepr:::makeGroupMembers(numGp,
currentGroups, candidates, ped, harem = harem, minAge = minAge)
man/fillGroupMembersWithSexRatio.Rd:
grpNum <- nprcgenekeepr:::makeGrpNum(numGp)
Please omit one colon.
- I have exported both makeGroupMembers() and makeGrpNum() to remove the
use of ::: in the documentation.
- Use suppressable messages to the console.
- I have changed the use of cat() to message() in R/createPedOne.R and
R/makeSimPed.R
- Please do not set a seed to a specific number within a function.
-> R/createPedOne.R; R/createPedSix.R
- These two functions are dynamically generating pedigrees with functions
that use psuedo-random number generators. The purpose of these functions
is to generate the same pedigrees each time for testing and instructional
purposes. Thus, I continue to set the seed to a specific number within
these functions.
- Request from 20250415: Please reduce each example to less than 5 sec.
I have dramatically shortened the example code run time for
makeRelationClassesTable and fillGroupMembersWithSexRatio by truncating
the pedigrees used. I have added a comment to the user to comment out the
truncation code to see a more genetically realistic example.
- Request: please write 'Shiny' as 'shiny', as package names are
case-sensitive.
- I have not changed the capitalization of
Shiny in the description
section of the DESCRIPTION file as it is the name of the type of
application and is not being used as the name of the package. The use
of the capitalization is consistent with the capitalization used within
the documentation for the shiny package (?shiny, See the Details
section, first sentence where it is used as the type of tutorial.)
and all documentation and tutorials provided by the author and RStudio
where it is capitalized everywhere except when referring to the package.
- Request: It seems like you have too many spaces in your description field.
Probably because linebreaks count as spaces too. Please remove unecassary
ones.
- I have removed the extra spaces from the description field in the
DESCRIPTION file, which occurred at the end of some of the lines. The
remaining occurrences of multiple consecutive spaces are at the
beginning of lines, which are required for their mandatory indentation.
- Request: Please add \value to .Rd files regarding exported methods and
explain the functions results in the documentation. Please write about the
structure of the output (class) and also what the output means. (If a
function does not return a value, please document that too, e.g.,
\value{No return value, called for side effects} or similar).
- I have provided \value elements to all functions except the following,
which are documentation elements:
- data.R
- nprcgenekeeper.R
- nprcgenekeepr-package.R
- Running checkhelper::find_missing_tags() found there is no missing or
empty return value for exported functions and no missing
@export or
@noRd in the documentation
- Request: Please unwrap the examples if they are executable in < 5 sec, or
replace dontrun{} with \donttest{}.
\dontrun{} should only be used if the example really cannot be executed
(e.g. because of missing additional software, missing API keys, ...) by the
user. That's why wrapping examples in \dontrun{} adds the comment
("# Not run:") as a warning for the user. Does not seem necessary.
Please replace \dontrun with \donttest.
- I have removed all instances of \dontrun.
- I have replaced \dontrun with wrapping with if (interactive()) {} for
its use in the example for runGeneKeepR() because Shiny apps don't run
in R CMD check.
-
Request: Please do not set a seed to a specific number within a function.
For more details: https://contributor.r-project.org/cran-cookbook/code_issues.html#setting-a-specific-seed
- I have not made any changes based on this request as I have restricted
the use of setting a seed to those situations where each function's
purpose is to dynamically create a data set for instructional or unit
testing purposes. In both cases, producing identical results each time
is critical to the purpose of the function.
-
I have incremented the version from 1.0.6 to 1.0.7, updated NEWS to reflect
the changes, and updated all documentation to reflect the version change.
Test environments
- Rhub environments on 2025-04-21
- success with R Under development (2025-04-19):
- atlas on Fedora Linux 38 (r88162)
- c23 on Ubuntu 22.04.5 (r88161)
- clang-asan on Ubuntu 22.04.5 (r88162)
- clang-ubsan on Ubuntu 22.04.5 (r88162)
- clang16 on Ubuntu 22.04.5 (r88161)
- clang17 on Ubuntu 22.04.5 (r88161)
- clang18 on Ubuntu 22.04.5 (r88161)
- clang19 on Ubuntu 22.04.5 (r88161)
- clang20 on Ubuntu 22.04.5 (r88161)
- donttest on Ubuntu 22.04.5 (r88161)
- gcc-asan on Fedora Linux 40 (r88162)
- gcc13 on Fedora Linux 38 (r88162)
- gcc14 on Fedora Linux 40 (r88162)
- intel on Fedora Linux 38 (r88162)
- mkl on Fedora Linux 38 (r88162)
- nold on Ubuntu 22.04.5 (r88162)
- noremap on Ubuntu 22.04.5 (r88161)
- valgrind on Fedora Linux 38 (r88162)
- success on Ubuntu 22.04.5
- ubuntu-gcc12 [r-devel-linux-x86_64-debian-gcc]
- ubuntu-next [r-next, r-patched, r-patched-linux-x86_64]
- ubuntu-release [r-release, r-release-linux-x86_64, ubuntu] R version 4.4.3 (2025-02-28)
- success windows R Under development (unstable) (2025-04-11 r88138 ucrt)
- failure with R-devel (2025-04-15 r88147) Fedora Linux 42
- gcc15 on Fedora Linux 42 error in pak subprocess
Caused by error in
file(con, "rb"): ! cannot open the connection
- nosuggests R-devel (2025-04-19 r88162) Fedora Linux 38
Error in
library(dplyr): there is no package called 'dplyr'
- failure with rchk on Ubuntu 22.04.5 I was unable to understand the output
Warning: No files were found with the provided path: check.
No artifacts will be uploaded.
- failure with ubuntu-clang R-devel (2025-04-19 r88162) Ubuntu 22.04.5 LTS
error in pak subprocess
Caused by error in
file(con, "rb"): ! cannot open the connection
- failure m1-san and macos-arm64 (R-devel) ERROR: compilation failed for package ‘httpuv’
- devtools::check_mac_release() 2025-04-21
- macOS builder results Build system: r-release-macosx-arm64|4.4.2|macosx|
macOS 13.3.1 (22E261)|Mac mini|Apple M1||en_US.UTF-8|macOS 11.3|
clang-1403.0.22.14.1|GNU Fortran (GCC) 14.2.0
Status OK
- devtools::check_win_devel() and devtools::check_win_release() 2025-04-21
both had the same note about possible misspelled words is addressed below.
R CMD check results
── R CMD check results ─────────────────────────────────────── nprcgenekeepr 1.0.7 ────
Duration: 1m 51.5s
0 errors ✔ | 0 warnings ✔ | 0 notes ✔
- Words identified as possible misspellings in DESCRIPTION: EHR, Raboin, and
kinships are all correctly spelled.
Reverse dependencies
revdepcheck results
We checked 0 reverse dependencies, comparing R CMD check results across CRAN
and dev versions of this package.
- We saw 0 new problems
- We failed to check 0 packages
rmsharp/nprcgenekeepr documentation built on June 13, 2025, 9:16 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Resubmission
This is a resubmission. In this version I have:
- Responded to each request provided by the reviewer
- Requests from 20250419:
- Used ::: in documentation: man/fillGroupMembersWithSexRatio.Rd: groupMembers <- nprcgenekeepr:::makeGroupMembers(numGp, currentGroups, candidates, ped, harem = harem, minAge = minAge) man/fillGroupMembersWithSexRatio.Rd: grpNum <- nprcgenekeepr:::makeGrpNum(numGp) Please omit one colon.
- I have exported both makeGroupMembers() and makeGrpNum() to remove the use of ::: in the documentation.
- Use suppressable messages to the console.
- I have changed the use of cat() to message() in R/createPedOne.R and R/makeSimPed.R
- Please do not set a seed to a specific number within a function.
-> R/createPedOne.R; R/createPedSix.R
- These two functions are dynamically generating pedigrees with functions that use psuedo-random number generators. The purpose of these functions is to generate the same pedigrees each time for testing and instructional purposes. Thus, I continue to set the seed to a specific number within these functions.
- Request from 20250415: Please reduce each example to less than 5 sec. I have dramatically shortened the example code run time for makeRelationClassesTable and fillGroupMembersWithSexRatio by truncating the pedigrees used. I have added a comment to the user to comment out the truncation code to see a more genetically realistic example.
- Request: please write 'Shiny' as 'shiny', as package names are
case-sensitive.
- I have not changed the capitalization of
Shinyin the description section of the DESCRIPTION file as it is the name of the type of application and is not being used as the name of the package. The use of the capitalization is consistent with the capitalization used within the documentation for theshinypackage (?shiny, See the Details section, first sentence where it is used as the type of tutorial.) and all documentation and tutorials provided by the author and RStudio where it is capitalized everywhere except when referring to the package.
- I have not changed the capitalization of
- Request: It seems like you have too many spaces in your description field.
Probably because linebreaks count as spaces too. Please remove unecassary
ones.
- I have removed the extra spaces from the description field in the DESCRIPTION file, which occurred at the end of some of the lines. The remaining occurrences of multiple consecutive spaces are at the beginning of lines, which are required for their mandatory indentation.
- Request: Please add \value to .Rd files regarding exported methods and
explain the functions results in the documentation. Please write about the
structure of the output (class) and also what the output means. (If a
function does not return a value, please document that too, e.g.,
\value{No return value, called for side effects} or similar).
- I have provided \value elements to all functions except the following, which are documentation elements:
- data.R
- nprcgenekeeper.R
- nprcgenekeepr-package.R
- Running checkhelper::find_missing_tags() found there is no missing or
empty return value for exported functions and no missing
@exportor@noRdin the documentation
- Request: Please unwrap the examples if they are executable in < 5 sec, or
replace dontrun{} with \donttest{}.
\dontrun{} should only be used if the example really cannot be executed
(e.g. because of missing additional software, missing API keys, ...) by the
user. That's why wrapping examples in \dontrun{} adds the comment
("# Not run:") as a warning for the user. Does not seem necessary.
Please replace \dontrun with \donttest.
- I have removed all instances of \dontrun.
- I have replaced \dontrun with wrapping with if (interactive()) {} for its use in the example for runGeneKeepR() because Shiny apps don't run in R CMD check.
-
Request: Please do not set a seed to a specific number within a function. For more details: https://contributor.r-project.org/cran-cookbook/code_issues.html#setting-a-specific-seed
- I have not made any changes based on this request as I have restricted the use of setting a seed to those situations where each function's purpose is to dynamically create a data set for instructional or unit testing purposes. In both cases, producing identical results each time is critical to the purpose of the function.
-
I have incremented the version from 1.0.6 to 1.0.7, updated NEWS to reflect the changes, and updated all documentation to reflect the version change.
Test environments
- Rhub environments on 2025-04-21
- success with R Under development (2025-04-19):
- atlas on Fedora Linux 38 (r88162)
- c23 on Ubuntu 22.04.5 (r88161)
- clang-asan on Ubuntu 22.04.5 (r88162)
- clang-ubsan on Ubuntu 22.04.5 (r88162)
- clang16 on Ubuntu 22.04.5 (r88161)
- clang17 on Ubuntu 22.04.5 (r88161)
- clang18 on Ubuntu 22.04.5 (r88161)
- clang19 on Ubuntu 22.04.5 (r88161)
- clang20 on Ubuntu 22.04.5 (r88161)
- donttest on Ubuntu 22.04.5 (r88161)
- gcc-asan on Fedora Linux 40 (r88162)
- gcc13 on Fedora Linux 38 (r88162)
- gcc14 on Fedora Linux 40 (r88162)
- intel on Fedora Linux 38 (r88162)
- mkl on Fedora Linux 38 (r88162)
- nold on Ubuntu 22.04.5 (r88162)
- noremap on Ubuntu 22.04.5 (r88161)
- valgrind on Fedora Linux 38 (r88162)
- success on Ubuntu 22.04.5
- ubuntu-gcc12 [r-devel-linux-x86_64-debian-gcc]
- ubuntu-next [r-next, r-patched, r-patched-linux-x86_64]
- ubuntu-release [r-release, r-release-linux-x86_64, ubuntu] R version 4.4.3 (2025-02-28)
- success windows R Under development (unstable) (2025-04-11 r88138 ucrt)
- failure with R-devel (2025-04-15 r88147) Fedora Linux 42
- gcc15 on Fedora Linux 42 error in pak subprocess
Caused by error in
file(con, "rb"): ! cannot open the connection - nosuggests R-devel (2025-04-19 r88162) Fedora Linux 38
Error in
library(dplyr): there is no package called 'dplyr'
- gcc15 on Fedora Linux 42 error in pak subprocess
Caused by error in
- failure with rchk on Ubuntu 22.04.5 I was unable to understand the output Warning: No files were found with the provided path: check. No artifacts will be uploaded.
- failure with ubuntu-clang R-devel (2025-04-19 r88162) Ubuntu 22.04.5 LTS
error in pak subprocess
Caused by error in
file(con, "rb"): ! cannot open the connection - failure m1-san and macos-arm64 (R-devel) ERROR: compilation failed for package ‘httpuv’
- devtools::check_mac_release() 2025-04-21
- macOS builder results Build system: r-release-macosx-arm64|4.4.2|macosx| macOS 13.3.1 (22E261)|Mac mini|Apple M1||en_US.UTF-8|macOS 11.3| clang-1403.0.22.14.1|GNU Fortran (GCC) 14.2.0 Status OK
- devtools::check_win_devel() and devtools::check_win_release() 2025-04-21 both had the same note about possible misspelled words is addressed below.
R CMD check results
── R CMD check results ─────────────────────────────────────── nprcgenekeepr 1.0.7 ──── Duration: 1m 51.5s
0 errors ✔ | 0 warnings ✔ | 0 notes ✔
- Words identified as possible misspellings in DESCRIPTION: EHR, Raboin, and kinships are all correctly spelled.
Reverse dependencies
revdepcheck results
We checked 0 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
- We saw 0 new problems
- We failed to check 0 packages
R Package Documentation
Browse R Packages
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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