Bioconductor Single Package Builder - Build History

Snapshot Date: 
URL:  https://git.bioconductor.org/packages/GXwasR
Last Changed Rev:  / Revision: 
Last Changed Date: 

Hostname OS /Arch BUILD CHECK BUILD BIN POST-PROCESSING
nebbiolo1 Linux (Ubuntu 24.04.4 LTS)/x86_64   OK     OK     skipped     OK  

nebbiolo1 Summary

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Package: GXwasR
Version: 0.99.4
RVersion: 4.6
BiocVersion: 3.23
BuildCommand: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data GXwasR
BuildTime: 3 minutes 10.34 seconds
CheckCommand: BiocCheckGitClone('GXwasR') && /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3911/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3911/GXwasR_20260922105330/GXwasR.install-out.txt GXwasR_0.99.4.tar.gz && BiocCheck('GXwasR_0.99.4.tar.gz', `new-package`=TRUE)
CheckTime: 7 minutes 57.82 seconds
BuildBinCommand:
BuildBinTime:
PackageFileSize: 3104.54 KiB
BuildID:: GXwasR_20260922105330
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: GXwasR. Starting Build package. Starting Check package.
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 0.

nebbiolo1 BUILD SRC output

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===============================

 R CMD BUILD

===============================

* checking for file ‘GXwasR/DESCRIPTION’ ... OK
* preparing ‘GXwasR’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to process help pages)
* saving partial Rd database
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘GXwasR_0.99.4.tar.gz’

nebbiolo1 CHECK output

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===============================

 BiocCheckGitClone('GXwasR')

===============================

── Running Git clone checks on GXwasR ──────────────────────────────────────────
* Checking valid files...
* Checking for inst/doc folders...
* Checking DESCRIPTION readability...
* Checking for valid use of maintainer fields...




===============================

 R CMD CHECK

===============================

* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3911/GXwasR_20260922105330/GXwasR.Rcheck’
* using R version 4.6.1 (2026-06-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.5 LTS
* using session charset: UTF-8
* current time: 2026-09-22 14:58:27 UTC
* using option ‘--no-vignettes’
* checking for file ‘GXwasR/DESCRIPTION’ ... OK
* this is package ‘GXwasR’ version ‘0.99.4’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 28 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GXwasR’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [12s/12s] OK
* checking whether the package can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the package can be unloaded cleanly ... [12s/12s] OK
* checking whether the namespace can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the namespace can be unloaded cleanly ... [12s/12s] OK
* checking loading without being on the library search path ... [13s/12s] OK
* checking whether startup messages can be suppressed ... [12s/12s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [54s/53s] OK
* checking Rd files ... [1s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [110s/119s] OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
PvalComb       13.600  0.566  14.167
GXwas           7.581  0.858  20.742
SumstatGenCorr  7.501  0.175   7.676
GeneticCorrBT   4.548  2.847   8.824
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [69s/66s]
 [70s/66s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [5s/5s] OK
* DONE

Status: OK





===============================

 BiocCheck('GXwasR_0.99.4.tar.gz')

===============================

── Installing GXwasR ───────────────────────────────────────────────────────────
✔ Package installed successfully
── GXwasR session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR
→ BiocVersion: 3.23
→ Package: GXwasR
→ PackageVersion: 0.99.4
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3911/GXwasR_20260922105330/GXwasR.BiocCheck
→ BiocCheckVersion: 1.49.31
→ sourceDir: /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR
→ installDir: /tmp/RtmpGm2N2R/file2d0691680ecbb/lib
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on GXwasR ─────────────────────────────────────────────────
* Checking for deprecated package usage...


* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
i NOTE: Update R version dependency from 4.5.0 to 4.6.0
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
→ Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking if 'Package:' field matches directory / tarball...
* Checking for Version: field...
* Checking DESCRIPTION readability...
* Checking validity of DESCRIPTION fields...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for whitespace in DESCRIPTION field names...
* Checking for proper Description: field...
i NOTE: The Description field in the DESCRIPTION is made up of less than 3
sentences. Provide a more detailed description of the package.
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (23%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
i No 'fnd' role found in 'Authors@R'. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/AncestryCheck.Rd:35: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/AncestryCheck.Rd:36: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/AncestryCheck.Rd:57: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/AncestryCheck.Rd:128: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/ClumpLD.Rd:74: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/ClumpLD.Rd:97: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/ComputeGeneticPC.Rd:50: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/ComputeGeneticPC.Rd:73: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/DummyCovar.Rd:26: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/DummyCovar.Rd:43: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/EstimateHerit.Rd:94: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/EstimateHerit.Rd:104: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/EstimateHerit.Rd:127: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/EstimateHerit.Rd:168: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/EstimateHerit.Rd:169: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/EstimateHerit.Rd:223: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GeneticCorrBT.Rd:72: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GeneticCorrBT.Rd:103: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GeneticCorrBT.Rd:134: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GXwas.Rd:63: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GXwas.Rd:102: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GXwas.Rd:102: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GXwas.Rd:102: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GXwas.Rd:103: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GXwas.Rd:110: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GXwas.Rd:113: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GXwas.Rd:117: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GXwas.Rd:122: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GXwas.Rd:211: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/MetaGWAS.Rd:34: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/MetaGWAS.Rd:117: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/MetaGWAS.Rd:119: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/MetaGWAS.Rd:147: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/PvalComb.Rd:51: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/PvalComb.Rd:53: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/PvalComb.Rd:110: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/QCsnp.Rd:77: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/QCsnp.Rd:118: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/SexCheck.Rd:60: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/SexCheck.Rd:94: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/SumstatGenCorr.Rd:97: unknown macro '\insertRef'
* Checking for library/require of GXwasR...
* Checking coding practice...
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/GXwasR_helper_functions.R (line 1607, column 9)
    • ...
    • print() in R/GXwasR_helper_functions.R (line 1711, column 9)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/analysis.R (line 667, column 14)
    • ...
    • R/sex-differential_test.R (line 229, column 14)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 57 times)
  • suppressWarnings() in R/analysis.R (line 249, column 23)
  • ...
  • suppressWarnings() in R/GXwasR_main_functions.R (line 1242, column 31)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 76
functions greater than 50 lines.
  The longest 5 functions are:
    • HDL.rg.parallel() (R/GXwasR_helper_functions.R): 768 lines
    • ...
    • AncestryCheck() (R/pre-imputation_qc.R): 234 lines
* Checking man page documentation...
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/AncestryCheck.Rd:35: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/AncestryCheck.Rd:36: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/AncestryCheck.Rd:57: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/AncestryCheck.Rd:128: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/ClumpLD.Rd:74: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/ClumpLD.Rd:97: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/ComputeGeneticPC.Rd:50: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/ComputeGeneticPC.Rd:73: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/DummyCovar.Rd:26: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/DummyCovar.Rd:43: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/EstimateHerit.Rd:94: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/EstimateHerit.Rd:104: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/EstimateHerit.Rd:127: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/EstimateHerit.Rd:168: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/EstimateHerit.Rd:169: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/EstimateHerit.Rd:223: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GeneticCorrBT.Rd:72: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GeneticCorrBT.Rd:103: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GeneticCorrBT.Rd:134: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GXwas.Rd:63: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GXwas.Rd:102: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GXwas.Rd:102: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GXwas.Rd:102: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GXwas.Rd:103: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GXwas.Rd:110: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GXwas.Rd:113: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GXwas.Rd:117: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GXwas.Rd:122: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GXwas.Rd:211: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/MetaGWAS.Rd:34: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/MetaGWAS.Rd:117: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/MetaGWAS.Rd:119: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/MetaGWAS.Rd:147: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/PvalComb.Rd:51: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/PvalComb.Rd:53: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/PvalComb.Rd:110: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/QCsnp.Rd:77: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/QCsnp.Rd:118: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/SexCheck.Rd:60: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/SexCheck.Rd:94: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/SumstatGenCorr.Rd:97: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/AncestryCheck.Rd:35: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/AncestryCheck.Rd:36: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/AncestryCheck.Rd:57: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/AncestryCheck.Rd:128: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/ClumpLD.Rd:74: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/ClumpLD.Rd:97: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/ComputeGeneticPC.Rd:50: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/ComputeGeneticPC.Rd:73: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/DummyCovar.Rd:26: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/DummyCovar.Rd:43: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/EstimateHerit.Rd:94: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/EstimateHerit.Rd:104: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/EstimateHerit.Rd:127: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/EstimateHerit.Rd:168: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/EstimateHerit.Rd:169: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/EstimateHerit.Rd:223: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GeneticCorrBT.Rd:72: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GeneticCorrBT.Rd:103: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GeneticCorrBT.Rd:134: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GXwas.Rd:63: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GXwas.Rd:102: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GXwas.Rd:102: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GXwas.Rd:102: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GXwas.Rd:103: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GXwas.Rd:110: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GXwas.Rd:113: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GXwas.Rd:117: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GXwas.Rd:122: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GXwas.Rd:211: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/MetaGWAS.Rd:34: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/MetaGWAS.Rd:117: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/MetaGWAS.Rd:119: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/MetaGWAS.Rd:147: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/PvalComb.Rd:51: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/PvalComb.Rd:53: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/PvalComb.Rd:110: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/QCsnp.Rd:77: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/QCsnp.Rd:118: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/SexCheck.Rd:60: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/SexCheck.Rd:94: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/SumstatGenCorr.Rd:97: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/AncestryCheck.Rd:35: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/AncestryCheck.Rd:36: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/AncestryCheck.Rd:57: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/AncestryCheck.Rd:128: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/ClumpLD.Rd:74: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/ClumpLD.Rd:97: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/ComputeGeneticPC.Rd:50: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/ComputeGeneticPC.Rd:73: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/DummyCovar.Rd:26: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/DummyCovar.Rd:43: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/EstimateHerit.Rd:94: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/EstimateHerit.Rd:104: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/EstimateHerit.Rd:127: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/EstimateHerit.Rd:168: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/EstimateHerit.Rd:169: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/EstimateHerit.Rd:223: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GeneticCorrBT.Rd:72: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GeneticCorrBT.Rd:103: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GeneticCorrBT.Rd:134: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GXwas.Rd:63: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GXwas.Rd:102: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GXwas.Rd:102: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GXwas.Rd:102: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GXwas.Rd:103: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GXwas.Rd:110: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GXwas.Rd:113: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GXwas.Rd:117: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GXwas.Rd:122: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/GXwas.Rd:211: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/MetaGWAS.Rd:34: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/MetaGWAS.Rd:117: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/MetaGWAS.Rd:119: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/MetaGWAS.Rd:147: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/PvalComb.Rd:51: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/PvalComb.Rd:53: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/PvalComb.Rd:110: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/QCsnp.Rd:77: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/QCsnp.Rd:118: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/SexCheck.Rd:60: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/SexCheck.Rd:94: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGm2N2R/file2d069115afbd7/GXwasR/man/SumstatGenCorr.Rd:97: unknown macro '\insertRef'
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 3239 lines (16%) are > 80 characters long.
  First few lines:
    • R/analysis.R#L1 #' MetaGWAS: Combining summary-level res ...
    • ...
    • vignettes/GXwasR_in_action.Rmd#L780 ```{r vignetteBiblio, results =
    "asis", ...
i NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain tabs.
  First few lines:
    • vignettes/GXwasR_in_action.Rmd#L92 -**(D) Sex-specific QC at sample
    level: ...
i NOTE: Consider multiples of 4 spaces for line indents; 370 lines (2%) are
not.
  First few lines:
    • R/analysis.R#L513 DataDir, ResultDir = tempdir(), fi ...
    • ...
    • vignettes/GXwasR_in_action.Rmd#L167 ...
i See https://contributions.bioconductor.org/r-code.html
i See styler package: https://cran.r-project.org/package=styler as described in
the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
i Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
i Maintainer is registered at support site.
i 'gxwasr' is already in your 'Watched Tags' on the Support Site.
── BiocCheck v1.49.31 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 9 NOTES
i See the GXwasR.BiocCheck folder and run
  `browseVignettes(package = 'BiocCheck')`
  for details.

nebbiolo1 BUILD BIN output

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