cran-comments.md

In psoerensen/qgg: Statistical Tools for Quantitative Genetic Analyses

Submission

This is a new submission:

• Fixed issue with depencies on C11 has been removed
• Major revision of documentation
• Fixed notes related to unused arguments
• Added new finemapping function gmap
• Removed qgg/man/qgg-package.Rd to avoid issues with redundant package info

Resubmission

This is a revised version of the package where we have:

• fixed a potential lto issue (fread/fwrite argument value type mismatch, was: c_int now: c_size_t in bigreml.f90) spotted by a CRAN member
• the fix was checked locally on linux/window machines) using: gfortran -g -c -O2 -flto -Wall -pedantic bigreml.f90 and no mismatch was detected
• used R version 4.2.1 (2022-06-23 ucrt), Rtools 4.2, GNU Fortran (GCC) 10.3.0

Resubmission

This is a revised version of the package where we have:

• fixed lto issue (fread/fwrite return value type mismatch, was: c_int now: c_size_t in bigreml.f90) detected on fedora-clang-devel
• the fix was check locally using: gfortran -g -c -O2 -mtune=native -Wall -pedantic bigreml.f90 -flto -o bigreml.o and no mismatch was detected
• used R version 4.2.1 (2022-06-23 ucrt) and Rtools 4.2

Resubmission

This is a revised version of the package where we have:

• fixed lto issue (fread/fwrite return value type mismatch, was: c_int now: c_size_t) found on fedora-clang-devel
• fixed c++ warnings with "variable nbytes_read set but not used"

Resubmission

This is a new version of the package where we have:

• added Bayesian linear regression models fitted using individual level data
• added Bayesian linear regression models fitted using marker summary statistics and sparse LD data
• added LDSC regression for estimation heritabily and correlation

• added functions for processing and quality control of marker summary statistics

• Check for CRAN was OK except for two Notes Note 1: "Found the following files/directories: lastMiKTeXException" Comment on Note 1: I believe Note 1 is a temporary error. Note 2: "checking installed package size ... NOTE. Installed size is 5.8Mb". Comment on Note 2: Our package contain c++ code and depends on the Rcpp package. According to the maintainer of Rcpp package this is a common Note among packages that depends on c++.

Results for check_for_cran(): https://builder.r-hub.io/status/qgg_1.1.0.tar.gz-ab24a1a0ba5741968f2753ee6148d97a https://builder.r-hub.io/status/qgg_1.1.0.tar.gz-2f695732d2004a3db81d1db54ea7ad95 https://builder.r-hub.io/status/qgg_1.1.0.tar.gz-065d908365274c2899cd39b618bae20b https://builder.r-hub.io/status/qgg_1.1.0.tar.gz-7094b2e6c8824b34b258f2b7633f7c39

Submission

This is a new submission where:

• Fixed issue with module name multiple defined detected on solaris
• Check for CRAN was OK except for the window build related to data.table not available but assume this is a temporary error.
• Check on solaris was OK.

Results for check_on_solaris: https://builder.r-hub.io/status/qgg_1.0.4.tar.gz-032fd7d9e906414cb679bc79d54e66f7

Results for check_for_cran(): https://builder.r-hub.io/status/qgg_1.0.4.tar.gz-23b75abdfecd459ea0141e9e58c65887 https://builder.r-hub.io/status/qgg_1.0.4.tar.gz-6a5bbd67917c468d802420182af4ce7d https://builder.r-hub.io/status/qgg_1.0.4.tar.gz-187feeb12c2d45228f8b0c35317053e0 https://builder.r-hub.io/status/qgg_1.0.4.tar.gz-9be5d8e78be94214a5d8bc00ce476cf4

Submission

This is a new submission where:

• Fixed issue with LTO (in fortran 2 c interface) detected on solaris
• Added a few user requested features.
• Check for CRAN was OK except for the window build related to data.table not available but assume this is a temporary error.

Results for check_for_cran(): https://builder.r-hub.io/status/qgg_1.0.4.tar.gz-5c9f861803a94d4ab7bf4ed23efc2ec3 https://builder.r-hub.io/status/qgg_1.0.4.tar.gz-c3230d7bb1064c2b809cb31f08e3a067 https://builder.r-hub.io/status/qgg_1.0.4.tar.gz-b7914ccce695408a9dc01e3ec7682543 https://builder.r-hub.io/status/qgg_1.0.4.tar.gz-a31493d3a3f8461a90274493d12c78f9

Submission

This is a new submission where:

• Dependencies on openmp is removed as required by CRAN.
• There was a note about misspelling, but checked that spelling is correct.
• There was a note that package was archived on CRAN due to the issues with openmp not being corrected in time.

Results for check_for_cran():

https://builder.r-hub.io/status/qgg_1.0.3.tar.gz-bfc21379cb454b4891678639fe1de18c https://builder.r-hub.io/status/qgg_1.0.3.tar.gz-44c5b58cf6b145baac2708f2ccef234d https://builder.r-hub.io/status/qgg_1.0.3.tar.gz-6040ed0410ac47f2824f272a5caa67e6 https://builder.r-hub.io/status/qgg_1.0.3.tar.gz-b4c0e33aba66401fac860801337ae75e

Submission

This is a new submission where I have fixed the following issues encountered on CRAN checks:

• Fixed additional issues related to build errors on fedora and solaris.
• There was a note about misspelling, but checked that spelling is correct.
• There was a note that package was archived on CRAN due to "reported installation issued was ignored in update".
• Clearly last updates did not fix the installation issues.
• New updates appear to have fixed previous installation issued which can be verified in the check links provided below.

Results for check_for_cran(): https://builder.r-hub.io/status/qgg_1.0.2.tar.gz-1dcb3475744a4294b8114d6aa8936b98 https://builder.r-hub.io/status/qgg_1.0.2.tar.gz-057edb786f4a4d6dbb9f449d9492dc9d https://builder.r-hub.io/status/qgg_1.0.2.tar.gz-37b08a62e5474ce6be940589d6f0ca1b https://builder.r-hub.io/status/qgg_1.0.2.tar.gz-5fe973bab2564cf39172fbded9fc5cc7

Results for check_on_solaris(): https://builder.r-hub.io/status/qgg_1.0.2.tar.gz-6759129787ba448880e6aa81de6044dc

Results for check_on_fedora(): https://builder.r-hub.io/status/qgg_1.0.2.tar.gz-36362d7179774f43b766b48b5f2eb752

Submission

This is a new submission where I have fixed the following issues encountered on CRAN checks:

• Fixed issues related to using fortran modules when building in parallel.
• Removed unused variables in fortran code.
• Fixed issue with a type mismatch in fortran code (LTO).
• The revised version passes check_for_cran() checks on all platforms.
• There was a note about misspelling, but checked that spelling is correct.

Resubmission

This is a resubmission where I have:

• Changed maintainer email address.
• Fixed minor bugs related to multi-core processing of bed files.
• Removed knitr/rmarkdown from suggest.

Resubmission

This is a resubmission where I have:

• Corrected Date Field.

Resubmission

This is a resubmission where I have:

• Corrected description text.
• Removed print statements in functions.
• Ensured that functions do not write in users home filespace by default.

Resubmission

This is a resubmission where I have:

• Removed capital letters in description text.
• Added more details about the package functionality in the DESCRIPTION file including a reference.
• Unwrapped test examples and ensured they can be executed in less than 5 sec.
• Ensured that examples only use 1 core.
• Ensured that functions can use files not in working directory.
• Included a small data set in inst/extdata.

There was a note about:

Possibly mis-spelled words in DESCRIPTION: al (14:14) et (14:11) heritability (13:281) qgg (13:18) Rohde (14:5)

I believe these are not mis-spelled.

Resubmission

This is a resubmission.

There were two notes.

Note 1 relates to the package is a new submission which is correct

Note 2 was related to 'cran-comments.md' not being ignored.

This has now been fixed by adding '^cran-comments.md$' to the .Rbuildignore file.

Test Platform (using devtools::rhub_check)

• Windows Server 2008 R2 SP1, R-devel, 32/64 bit
• Ubuntu Linux 16.04 LTS, R-release, GCC
• Fedora Linux, R-devel, clang, gfortran
• Debian Linux, R-devel, GCC ASAN/UBSAN

https://builder.r-hub.io/status/qgg_1.0.0.tar.gz-6892dda9117e451c8040d51af6f1eceb https://builder.r-hub.io/status/qgg_1.0.0.tar.gz-a264ecf4dfa94a4d9457a479c08dfe4d https://builder.r-hub.io/status/qgg_1.0.0.tar.gz-8d880f8d18da448196a7d486e8a9759a https://builder.r-hub.io/status/qgg_1.0.0.tar.gz-8f009b45da004cd6abf269c662518f10

The qgg package provides an infrastructure for efficient processing of large-scale genetic and phenotypic data including core functions for:

• fitting linear mixed models
• construction of genomic relationship matrices
• estimating genetic parameters (heritability and correlation)
• genomic prediction
• single marker association analysis
• gene set enrichment analysis

qgg handles large-scale data by taking advantage of: multi-core processing using openMP multithreaded matrix operations implemented in BLAS libraries (e.g. OpenBLAS, ATLAS or MKL) * fast and memory-efficient batch processing of genotype data stored in binary files (e.g. PLINK bedfiles)

In addition to the examples included in the package submission we have prepared an extensive set of examples avaliable on our github repository:

http://psoerensen.github.io/qgg/index.html http://psoerensen.github.io/qgg/articles/qgg.html

R CMD check results

On Windows and Ubuntu linux the following note appeared:

• checking CRAN incoming feasibility ... NOTE Maintainer: 'Peter Soerensen [e-mail]'

New submission

On Windows only the following note appeared:

• checking for non-standard things in the check directory ... NOTE Found the following files/directories: 'examples_i386' 'examples_x64' 'qgg-Ex_i386.Rout' 'qgg-Ex_x64.Rout'

Notes 1 relates to new submission which is correct.

Notes 2 only appeared on Windows and seems to be related to the r-hub builder.

psoerensen/qgg documentation built on April 30, 2024, 3:47 a.m.