Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-03-28 11:36:55 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1648/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RAIDS 1.1.0  (landing page)
Pascal Belleau
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/RAIDS
git_branch: devel
git_last_commit: e58671a
git_last_commit_date: 2023-10-24 11:51:36 -0400 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for RAIDS on nebbiolo1


To the developers/maintainers of the RAIDS package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RAIDS.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: RAIDS
Version: 1.1.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:RAIDS.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings RAIDS_1.1.0.tar.gz
StartedAt: 2024-03-28 01:48:30 -0400 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 01:55:55 -0400 (Thu, 28 Mar 2024)
EllapsedTime: 445.6 seconds
RetCode: 0
Status:   OK  
CheckDir: RAIDS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:RAIDS.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings RAIDS_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/RAIDS.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘RAIDS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RAIDS’ version ‘1.1.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘RAIDS’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) RAIDS-package.Rd:39-40: Lost braces
    39 | \item \code{\link{runExomeAncestry}} {This function runs most steps
       |                                      ^
checkRd: (-1) RAIDS-package.Rd:41-42: Lost braces
    41 | \item \code{\link{runExomeAncestry}} {This function runs most steps
       |                                      ^
checkRd: (-1) RAIDS-package.Rd:43-46: Lost braces
    43 | \item \code{\link{estimateAllelicFraction}} { This function estimates
       |                                             ^
checkRd: (-1) RAIDS-package.Rd:47-49: Lost braces
    47 | \item \code{\link{computeSyntheticROC}} { This function calculate the
       |                                         ^
checkRd: (-1) RAIDS-package.Rd:50-53: Lost braces
    50 | \item \code{\link{generateMapSnvSel}} {The function applies a cut-off
       |                                       ^
checkRd: (-1) calcAFMLRNA.Rd:16-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calcAFMLRNA.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calcAFMLRNA.Rd:20-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calcAFMLRNA.Rd:29-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcAFMLRNA.Rd:32-33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcAFMLRNA.Rd:34-35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcAFMLRNA.Rd:36-38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAllelicFractionDNA.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAllelicFractionDNA.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAllelicFractionDNA.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAllelicFractionDNA.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAllelicFractionDNA.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAllelicFractionDNA.Rd:75-76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAllelicFractionDNA.Rd:77-78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAllelicFractionDNA.Rd:79-80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAllelicFractionDNA.Rd:81: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAllelicFractionDNA.Rd:82: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAllelicFractionDNA.Rd:83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAllelicFractionDNA.Rd:84: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAllelicFractionDNA.Rd:85-86: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAllelicFractionDNA.Rd:87-89: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAllelicFractionRNA.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAllelicFractionRNA.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAllelicFractionRNA.Rd:76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAllelicFractionRNA.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAllelicFractionRNA.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAllelicFractionRNA.Rd:79-80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAllelicFractionRNA.Rd:81-82: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAllelicFractionRNA.Rd:83-84: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAllelicFractionRNA.Rd:85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAllelicFractionRNA.Rd:86: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAllelicFractionRNA.Rd:87: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAllelicFractionRNA.Rd:88-90: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAllelicFractionRNA.Rd:91-92: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAllelicFractionRNA.Rd:93: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAllelicFractionRNA.Rd:94-95: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAllelicFractionRNA.Rd:96-98: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAllelicFractionRNA.Rd:99-100: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAllelicImbDNAChr.Rd:15-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeAllelicImbDNAChr.Rd:17-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeAllelicImbDNAChr.Rd:19-20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeAllelicImbDNAChr.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeAllelicImbDNAChr.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeAllelicImbDNAChr.Rd:23-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeAllelicImbDNAChr.Rd:27-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeAllelicImbDNAChr.Rd:29-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeAllelicImbDNAChr.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeAllelicImbDNAChr.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeAllelicImbDNAChr.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeAllelicImbDNAChr.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeAllelicImbDNAChr.Rd:35-36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeAncestryFromSyntheticFile.Rd:99-110: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAncestryFromSyntheticFile.Rd:102-103: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAncestryFromSyntheticFile.Rd:104-105: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAncestryFromSyntheticFile.Rd:106-108: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAncestryFromSyntheticFile.Rd:112-183: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAncestryFromSyntheticFile.Rd:116-134: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAncestryFromSyntheticFile.Rd:120-121: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAncestryFromSyntheticFile.Rd:122-124: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAncestryFromSyntheticFile.Rd:125-127: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAncestryFromSyntheticFile.Rd:128-130: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAncestryFromSyntheticFile.Rd:131-132: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAncestryFromSyntheticFile.Rd:135-154: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAncestryFromSyntheticFile.Rd:140-141: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAncestryFromSyntheticFile.Rd:142-143: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAncestryFromSyntheticFile.Rd:144-146: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAncestryFromSyntheticFile.Rd:147-149: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAncestryFromSyntheticFile.Rd:150-152: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAncestryFromSyntheticFile.Rd:155-174: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAncestryFromSyntheticFile.Rd:159-160: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAncestryFromSyntheticFile.Rd:161-162: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAncestryFromSyntheticFile.Rd:163-164: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAncestryFromSyntheticFile.Rd:165-167: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAncestryFromSyntheticFile.Rd:168-169: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAncestryFromSyntheticFile.Rd:170-172: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAncestryFromSyntheticFile.Rd:175-176: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAncestryFromSyntheticFile.Rd:177-178: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAncestryFromSyntheticFile.Rd:179-181: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAncestryFromSyntheticFile.Rd:185-206: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAncestryFromSyntheticFile.Rd:189-190: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAncestryFromSyntheticFile.Rd:191-204: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAncestryFromSyntheticFile.Rd:195-196: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAncestryFromSyntheticFile.Rd:197-198: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAncestryFromSyntheticFile.Rd:199-200: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAncestryFromSyntheticFile.Rd:201-202: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAncestryFromSyntheticFile.Rd:208-221: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAncestryFromSyntheticFile.Rd:212-213: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAncestryFromSyntheticFile.Rd:214-215: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAncestryFromSyntheticFile.Rd:216-217: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeAncestryFromSyntheticFile.Rd:218-219: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeKNNRefSample.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeKNNRefSample.Rd:53-68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeKNNRefSample.Rd:59-60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeKNNRefSample.Rd:61-62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeKNNRefSample.Rd:63-64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeKNNRefSample.Rd:65-66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeKNNRefSynthetic.Rd:61-62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeKNNRefSynthetic.Rd:63-65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeKNNRefSynthetic.Rd:66-68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeKNNRefSynthetic.Rd:69-84: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeKNNRefSynthetic.Rd:75-76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeKNNRefSynthetic.Rd:77-78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeKNNRefSynthetic.Rd:79-80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeKNNRefSynthetic.Rd:81-82: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeLOHBlocksDNAChr.Rd:23-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeLOHBlocksDNAChr.Rd:25-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeLOHBlocksDNAChr.Rd:27-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeLOHBlocksDNAChr.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeLOHBlocksDNAChr.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeLOHBlocksDNAChr.Rd:31-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeLOHBlocksDNAChr.Rd:35-36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeLOHBlocksDNAChr.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeLOHBlocksDNAChr.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeLOHBlocksDNAChr.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeLOHBlocksDNAChr.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeLOHBlocksDNAChr.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeLOHBlocksDNAChr.Rd:56-58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeLOHBlocksDNAChr.Rd:59-61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeLOHBlocksDNAChr.Rd:62-66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeLOHBlocksDNAChr.Rd:67-69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeLOHBlocksDNAChr.Rd:70-71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeLOHBlocksDNAChr.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeLOHBlocksDNAChr.Rd:73-74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeLOHBlocksDNAChr.Rd:75-76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeLOHBlocksDNAChr.Rd:77-78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeLOHBlocksDNAChr.Rd:79-81: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computePCAMultiSynthetic.Rd:41-43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computePCAMultiSynthetic.Rd:44-45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computePCAMultiSynthetic.Rd:46-47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computePCARefRMMulti.Rd:57-58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computePCARefRMMulti.Rd:59-60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computePCARefSample.Rd:55-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computePCARefSample.Rd:57-58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computePCARefSample.Rd:59-60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computePoolSyntheticAncestryGr.Rd:92-93: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computePoolSyntheticAncestryGr.Rd:94-96: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computePoolSyntheticAncestryGr.Rd:97-99: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computePoolSyntheticAncestryGr.Rd:100-104: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeSyntheticConfMat.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeSyntheticConfMat.Rd:46-47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeSyntheticROC.Rd:48-49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeSyntheticROC.Rd:50-51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) computeSyntheticROC.Rd:52-53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) demoKnownSuperPop1KG.Rd:63-64: Lost braces
    63 | \item \code{\link{computeKNNRefSynthetic}} {for running a k-nearest
       |                                            ^
checkRd: (-1) demoKnownSuperPop1KG.Rd:65-67: Lost braces
    65 | \item \code{\link{computePoolSyntheticAncestryGr}} { for running a
       |                                                    ^
checkRd: (-1) demoPCA1KG.Rd:14-15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) demoPCA1KG.Rd:16-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) demoPCA1KG.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) demoPCA1KG.Rd:29-30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) demoPCASyntheticProfiles.Rd:13-14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) demoPCASyntheticProfiles.Rd:15-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) demoPCASyntheticProfiles.Rd:17-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) demoPCASyntheticProfiles.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) demoPCASyntheticProfiles.Rd:32-33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) demoPCASyntheticProfiles.Rd:34-36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) demoPCASyntheticProfiles.Rd:83-84: Lost braces
    83 | \item \code{\link{computeKNNRefSynthetic}} {for running a k-nearest
       |                                            ^
checkRd: (-1) demoPedigreeEx1.Rd:11-12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) demoPedigreeEx1.Rd:13-14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) demoPedigreeEx1.Rd:15-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) demoPedigreeEx1.Rd:17-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) demoPedigreeEx1.Rd:19-20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) demoPedigreeEx1.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) demoPedigreeEx1.Rd:32-33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) demoPedigreeEx1.Rd:34-35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) demoPedigreeEx1.Rd:36-37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) demoPedigreeEx1.Rd:38-39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) demoPedigreeEx1.Rd:133-135: Lost braces
   133 | \item \code{\link{runExomeAncestry}} {for running runs most
       |                                      ^
checkRd: (-1) generateGeneBlock.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generateGeneBlock.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generateGeneBlock.Rd:26-27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generateGeneBlock.Rd:28-29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generateGeneBlock.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generateGeneBlock.Rd:32-33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generateGeneBlock.Rd:34-35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generateMapSnvSel.Rd:40-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) generateMapSnvSel.Rd:42-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) generateMapSnvSel.Rd:44-45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) generateMapSnvSel.Rd:46-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) generateMapSnvSel.Rd:48-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) generateMapSnvSel.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) generateMapSnvSel.Rd:52-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) generateMapSnvSel.Rd:54-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getTableSNV.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getTableSNV.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getTableSNV.Rd:53-54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getTableSNV.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getTableSNV.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getTableSNV.Rd:57-60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getTableSNV.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getTableSNV.Rd:62-63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getTableSNV.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getTableSNV.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getTableSNV.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) matKNNSynthetic.Rd:12-13: Lost braces
    12 | \item \code{sample.id} {a \code{character} string representing the unique
       |                        ^
checkRd: (-1) matKNNSynthetic.Rd:14-15: Lost braces
    14 | \item \code{D} {a \code{numeric} representing the number of dimensions used
       |                ^
checkRd: (-1) matKNNSynthetic.Rd:16-17: Lost braces
    16 | \item \code{K} {a \code{numeric} representing the number of neighbors used
       |                ^
checkRd: (-1) matKNNSynthetic.Rd:18-19: Lost braces
    18 | \item \code{SuperPop} {a \code{character} string representing the
       |                       ^
checkRd: (-1) matKNNSynthetic.Rd:29-30: Lost braces
    29 | \item \code{sample.id} {a \code{character} string representing the unique
       |                        ^
checkRd: (-1) matKNNSynthetic.Rd:31-32: Lost braces
    31 | \item \code{D} {a \code{numeric} representing the number of dimensions used
       |                ^
checkRd: (-1) matKNNSynthetic.Rd:33-34: Lost braces
    33 | \item \code{K} {a \code{numeric} representing the number of neighbors used
       |                ^
checkRd: (-1) matKNNSynthetic.Rd:35-36: Lost braces
    35 | \item \code{SuperPop} {a \code{character} string representing the
       |                       ^
checkRd: (-1) matKNNSynthetic.Rd:74-76: Lost braces
    74 | \item \code{\link{computeSyntheticROC}} {for calculating the AUROC of
       |                                         ^
checkRd: (-1) pedSynthetic.Rd:15-16: Lost braces
    15 | \item \code{data.id} {a \code{character} string representing the unique
       |                      ^
checkRd: (-1) pedSynthetic.Rd:17-18: Lost braces
    17 | \item \code{case.id} {a \code{character} string representing the unique
       |                      ^
checkRd: (-1) pedSynthetic.Rd:19-20: Lost braces
    19 | \item \code{sample.type} {a \code{character} string representing the type
       |                          ^
checkRd: (-1) pedSynthetic.Rd:21-22: Lost braces
    21 | \item \code{diagnosis} {a \code{character} string representing the
       |                        ^
checkRd: (-1) pedSynthetic.Rd:23-24: Lost braces
    23 | \item \code{source} {a \code{character} string representing the
       |                     ^
checkRd: (-1) pedSynthetic.Rd:25-26: Lost braces
    25 | \item \code{study.id} {a \code{character} string representing the
       |                       ^
checkRd: (-1) pedSynthetic.Rd:27-29: Lost braces
    27 | \item \code{superPop} {a \code{character} string representing the
       |                       ^
checkRd: (-1) pedSynthetic.Rd:41-42: Lost braces
    41 | \item \code{data.id} {a \code{character} string representing the unique
       |                      ^
checkRd: (-1) pedSynthetic.Rd:43-44: Lost braces
    43 | \item \code{case.id} {a \code{character} string representing the unique
       |                      ^
checkRd: (-1) pedSynthetic.Rd:45-46: Lost braces
    45 | \item \code{sample.type} {a \code{character} string representing the type
       |                          ^
checkRd: (-1) pedSynthetic.Rd:47-48: Lost braces
    47 | \item \code{diagnosis} {a \code{character} string representing the
       |                        ^
checkRd: (-1) pedSynthetic.Rd:49-50: Lost braces
    49 | \item \code{source} {a \code{character} string representing the
       |                     ^
checkRd: (-1) pedSynthetic.Rd:51-52: Lost braces
    51 | \item \code{study.id} {a \code{character} string representing the
       |                       ^
checkRd: (-1) pedSynthetic.Rd:53-55: Lost braces
    53 | \item \code{superPop} {a \code{character} string representing the
       |                       ^
checkRd: (-1) pedSynthetic.Rd:94-96: Lost braces
    94 | \item \code{\link{computeSyntheticROC}} {for calculating the AUROC of
       |                                         ^
checkRd: (-1) prepPed1KG.Rd:32-33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) prepPed1KG.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) prepPed1KG.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) prepPed1KG.Rd:36-37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) prepPed1KG.Rd:38-39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) prepPed1KG.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readSNVFileGeneric.Rd:24-25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readSNVFileGeneric.Rd:26-27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readSNVFileGeneric.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readSNVFileGeneric.Rd:29-30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readSNVFileGeneric.Rd:31-32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readSNVFileGeneric.Rd:33-34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readSNVFileGeneric.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readSNVPileupFile.Rd:24-25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readSNVPileupFile.Rd:26-27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readSNVPileupFile.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readSNVPileupFile.Rd:29-30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readSNVPileupFile.Rd:31-32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readSNVPileupFile.Rd:33-34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readSNVPileupFile.Rd:35-36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readSNVPileupFile.Rd:37-38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readSNVPileupFile.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readSNVVCF.Rd:24-25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readSNVVCF.Rd:26-27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readSNVVCF.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readSNVVCF.Rd:29-30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readSNVVCF.Rd:31-32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readSNVVCF.Rd:33-34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readSNVVCF.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) runExomeAncestry.Rd:67-68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runExomeAncestry.Rd:69-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runExomeAncestry.Rd:71-72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runExomeAncestry.Rd:106-107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runExomeAncestry.Rd:108-109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runExomeAncestry.Rd:110-111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runIBDKING.Rd:33-34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) runIBDKING.Rd:35-36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) runIBDKING.Rd:37-38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) runIBDKING.Rd:39-40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) runIBDKING.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) runIBDKING.Rd:42-43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) runProfileAncestry.Rd:56-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runProfileAncestry.Rd:58-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runProfileAncestry.Rd:60-61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runProfileAncestry.Rd:102-103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runProfileAncestry.Rd:104-105: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runProfileAncestry.Rd:106-107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runRNAAncestry.Rd:68-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runRNAAncestry.Rd:70-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runRNAAncestry.Rd:72-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runRNAAncestry.Rd:111-112: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runRNAAncestry.Rd:113-114: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runRNAAncestry.Rd:115-116: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runWrapperAncestry.Rd:68-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runWrapperAncestry.Rd:70-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runWrapperAncestry.Rd:72-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runWrapperAncestry.Rd:115-116: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runWrapperAncestry.Rd:117-118: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runWrapperAncestry.Rd:119-120: Lost braces in \itemize; meant \describe ?
checkRd: (-1) selParaPCAUpQuartile.Rd:56-74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) selParaPCAUpQuartile.Rd:60-61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) selParaPCAUpQuartile.Rd:62-64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) selParaPCAUpQuartile.Rd:65-67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) selParaPCAUpQuartile.Rd:68-70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) selParaPCAUpQuartile.Rd:71-72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) selParaPCAUpQuartile.Rd:75-94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) selParaPCAUpQuartile.Rd:80-81: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) selParaPCAUpQuartile.Rd:82-83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) selParaPCAUpQuartile.Rd:84-86: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) selParaPCAUpQuartile.Rd:87-89: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) selParaPCAUpQuartile.Rd:90-92: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) selParaPCAUpQuartile.Rd:95-96: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) selParaPCAUpQuartile.Rd:97-98: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) selParaPCAUpQuartile.Rd:99-101: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) select1KGPop.Rd:25-26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) select1KGPop.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) select1KGPop.Rd:29-30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) snpPositionDemo.Rd:12-13: Lost braces
    12 | \item \code{cnt.tot} {a \code{integer} representing the number of reads at
       |                      ^
checkRd: (-1) snpPositionDemo.Rd:14-15: Lost braces
    14 | \item \code{cnt.ref} {a \code{integer} representing the number of reads
       |                      ^
checkRd: (-1) snpPositionDemo.Rd:16-17: Lost braces
    16 | \item \code{cnt.alt} {a \code{integer} representing the number of reads
       |                      ^
checkRd: (-1) snpPositionDemo.Rd:18-19: Lost braces
    18 | \item \code{snp.pos} {a \code{integer} representing the position of the
       |                      ^
checkRd: (-1) snpPositionDemo.Rd:20-21: Lost braces
    20 | \item \code{snp.chr} {a \code{integer} representing the chromosome on which
       |                      ^
checkRd: (-1) snpPositionDemo.Rd:22-23: Lost braces
    22 | \item \code{normal.geno} {a \code{integer} representing the genotype
       |                          ^
checkRd: (-1) snpPositionDemo.Rd:24: Lost braces
    24 | \item \code{pruned} {a \code{logical} indicated if the SNV is pruned.}
       |                     ^
checkRd: (-1) snpPositionDemo.Rd:25-26: Lost braces
    25 | \item \code{snp.index} {a \code{integer} representing the index of the
       |                        ^
checkRd: (-1) snpPositionDemo.Rd:27-28: Lost braces
    27 | \item \code{keep} {a \code{logical} indicated if the genotype
       |                   ^
checkRd: (-1) snpPositionDemo.Rd:29: Lost braces
    29 | \item \code{hetero} {a \code{logical} indicated if the SNV is heterozygote.}
       |                     ^
checkRd: (-1) snpPositionDemo.Rd:30: Lost braces
    30 | \item \code{homo} {a \code{logical} indicated if the SNV is homozygote.}
       |                   ^
checkRd: (-1) snpPositionDemo.Rd:31-32: Lost braces
    31 | \item \code{block.id} {a \code{integer} representing the block identifier
       |                       ^
checkRd: (-1) snpPositionDemo.Rd:33-34: Lost braces
    33 | \item \code{phase} {a \code{integer} representing the block identifier
       |                    ^
checkRd: (-1) snpPositionDemo.Rd:35: Lost braces
    35 | \item \code{lap} {a \code{numeric} representing the lower allelic fraction.}
       |                  ^
checkRd: (-1) snpPositionDemo.Rd:36-37: Lost braces
    36 | \item \code{LOH} {a \code{integer} indicating if the SNV is in an LOH region
       |                  ^
checkRd: (-1) snpPositionDemo.Rd:38-40: Lost braces
    38 | \item \code{imbAR} {a \code{integer} indicating if the SNV is in an
       |                    ^
checkRd: (-1) snpPositionDemo.Rd:41-42: Lost braces
    41 | \item \code{freq} {a \code{numeric} representing the frequency of the
       |                   ^
checkRd: (-1) snpPositionDemo.Rd:52-53: Lost braces
    52 | \item \code{cnt.tot} {a \code{integer} representing the number of reads at
       |                      ^
checkRd: (-1) snpPositionDemo.Rd:54-55: Lost braces
    54 | \item \code{cnt.ref} {a \code{integer} representing the number of reads
       |                      ^
checkRd: (-1) snpPositionDemo.Rd:56-57: Lost braces
    56 | \item \code{cnt.alt} {a \code{integer} representing the number of reads
       |                      ^
checkRd: (-1) snpPositionDemo.Rd:58-59: Lost braces
    58 | \item \code{snp.pos} {a \code{integer} representing the position of the
       |                      ^
checkRd: (-1) snpPositionDemo.Rd:60-61: Lost braces
    60 | \item \code{snp.chr} {a \code{integer} representing the chromosome on which
       |                      ^
checkRd: (-1) snpPositionDemo.Rd:62-63: Lost braces
    62 | \item \code{normal.geno} {a \code{integer} representing the genotype
       |                          ^
checkRd: (-1) snpPositionDemo.Rd:64: Lost braces
    64 | \item \code{pruned} {a \code{logical} indicated if the SNV is pruned.}
       |                     ^
checkRd: (-1) snpPositionDemo.Rd:65-66: Lost braces
    65 | \item \code{snp.index} {a \code{integer} representing the index of the
       |                        ^
checkRd: (-1) snpPositionDemo.Rd:67-68: Lost braces
    67 | \item \code{keep} {a \code{logical} indicated if the genotype
       |                   ^
checkRd: (-1) snpPositionDemo.Rd:69: Lost braces
    69 | \item \code{hetero} {a \code{logical} indicated if the SNV is heterozygote.}
       |                     ^
checkRd: (-1) snpPositionDemo.Rd:70: Lost braces
    70 | \item \code{homo} {a \code{logical} indicated if the SNV is homozygote.}
       |                   ^
checkRd: (-1) snpPositionDemo.Rd:71-72: Lost braces
    71 | \item \code{block.id} {a \code{integer} representing the block identifier
       |                       ^
checkRd: (-1) snpPositionDemo.Rd:73-74: Lost braces
    73 | \item \code{phase} {a \code{integer} representing the block identifier
       |                    ^
checkRd: (-1) snpPositionDemo.Rd:75: Lost braces
    75 | \item \code{lap} {a \code{numeric} representing the lower allelic fraction.}
       |                  ^
checkRd: (-1) snpPositionDemo.Rd:76-77: Lost braces
    76 | \item \code{LOH} {a \code{integer} indicating if the SNV is in an LOH region
       |                  ^
checkRd: (-1) snpPositionDemo.Rd:78-80: Lost braces
    78 | \item \code{imbAR} {a \code{integer} indicating if the SNV is in an
       |                    ^
checkRd: (-1) snpPositionDemo.Rd:81-82: Lost braces
    81 | \item \code{freq} {a \code{numeric} representing the frequency of the
       |                   ^
checkRd: (-1) splitSelectByPop.Rd:13-14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) splitSelectByPop.Rd:15-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) splitSelectByPop.Rd:17-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tableBlockAF.Rd:20-21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tableBlockAF.Rd:22-23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tableBlockAF.Rd:24-25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tableBlockAF.Rd:26-27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tableBlockAF.Rd:28-29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tableBlockAF.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tableBlockAF.Rd:32-33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tableBlockAF.Rd:34-35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tableBlockAF.Rd:36-37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tableBlockAF.Rd:38-39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tableBlockAF.Rd:40-41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tableBlockAF.Rd:42-43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) tableBlockAF.Rd:44-45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testAlleleFractionChange.Rd:15-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) testAlleleFractionChange.Rd:17-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) testAlleleFractionChange.Rd:33-36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testAlleleFractionChange.Rd:37-38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testAlleleFractionChange.Rd:39-40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testAlleleFractionChange.Rd:41-42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testEmptyBox.Rd:15-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) testEmptyBox.Rd:17-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) testEmptyBox.Rd:28-30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testEmptyBox.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testEmptyBox.Rd:32-33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testEmptyBox.Rd:34-35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) validateRunExomeOrRNAAncestry.Rd:61-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) validateRunExomeOrRNAAncestry.Rd:63-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) validateRunExomeOrRNAAncestry.Rd:65-66: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
Documented arguments not in \usage in Rd file 'appendGDSSampleOnly.Rd':
  ‘listSample’

Documented arguments not in \usage in Rd file 'appendGDSgenotype.Rd':
  ‘listSamples’

Documented arguments not in \usage in Rd file 'validateProfileGDSExist.Rd':
  ‘currentProfile’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                  user system elapsed
computeAncestryFromSyntheticFile 6.081  0.276   6.358
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/RAIDS.Rcheck/00check.log’
for details.


Installation output

RAIDS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL RAIDS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘RAIDS’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RAIDS)

Tests output

RAIDS.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(RAIDS)
Loading required package: gdsfmt
Loading required package: SNPRelate
SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)
Loading required package: GENESIS
> 
> ## Run all unit tests
> test_check("RAIDS")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 432 ]
> 
> proc.time()
   user  system elapsed 
 27.187   1.386  28.563 

Example timings

RAIDS.Rcheck/RAIDS-Ex.timings

nameusersystemelapsed
add1KG2SampleGDS0.0380.0280.073
addBlockInGDSAnnot0.0080.0040.013
addGDSRef0.0040.0000.004
addGDSStudyPruning0.0010.0010.002
addGeneBlockGDSRefAnnot0.7940.1540.949
addRef2GDS1KG0.0010.0050.006
addStudy1Kg0.0030.0060.010
addStudyGDSSample0.0060.0000.006
addUpdateLap0.0010.0010.002
addUpdateSegment0.0000.0020.001
appendGDSRefSample0.0050.0010.006
appendGDSSampleOnly0.0010.0000.001
appendGDSgenotype0.0190.0040.023
appendGDSgenotypeMat0.0000.0030.003
calcAFMLRNA0.0060.0010.007
computeAlleleFraction0.0040.0000.005
computeAllelicFractionDNA0.1720.0320.204
computeAllelicFractionRNA0.2130.0080.221
computeAllelicImbDNAChr0.0070.0000.007
computeAncestryFromSyntheticFile6.0810.2766.358
computeKNNRefSample0.0180.0000.018
computeKNNRefSynthetic1.4300.0461.476
computeLOHBlocksDNAChr0.0080.0010.009
computePCAMultiSynthetic0.0050.0050.009
computePCARefRMMulti0.1480.0140.162
computePCARefSample0.1880.0000.189
computePoolSyntheticAncestryGr0.4640.0040.468
computeSyntheticConfMat0.0150.0000.014
computeSyntheticROC0.0360.0030.039
createStudy2GDS1KG0.0480.0040.052
demoKnownSuperPop1KG1.4370.0041.441
demoPCA1KG0.0040.0050.009
demoPCASyntheticProfiles1.4470.0221.469
demoPedigreeEx10.0140.0040.018
estimateAllelicFraction0.1000.0040.104
generateGDS1KG0.0130.0000.013
generateGDS1KGgenotypeFromSNPPileup0.0400.0030.042
generateGDSRefSample0.0010.0040.005
generateGDSSNPinfo0.0050.0000.004
generateGDSgenotype0.0130.0000.013
generateGeneBlock0.0020.0000.002
generateMapSnvSel0.0030.0000.003
generatePhase1KG2GDS0.0090.0040.013
getBlockIDs0.0020.0000.002
getRef1KGPop0.0030.0000.004
getTableSNV0.0080.0040.012
groupChr1KGSNV0.0470.0080.055
identifyRelative0.0100.0040.014
matKNNSynthetic0.0370.0040.042
pedSynthetic0.0350.0060.041
prepPed1KG0.0040.0010.005
prepPedSynthetic1KG0.0060.0000.006
prepSynthetic0.0100.0000.011
pruning1KGbyChr0.0040.0000.004
pruningSample0.0310.0120.043
readSNVFileGeneric0.0040.0000.004
readSNVPileupFile0.0320.0000.032
readSNVVCF4.7570.1484.906
runExomeAncestry0.0150.0000.015
runIBDKING0.0550.0000.057
runLDPruning0.0170.0080.025
runProfileAncestry0.0130.0040.018
runRNAAncestry0.0150.0000.015
runWrapperAncestry0.0160.0000.016
selParaPCAUpQuartile4.6280.0284.656
select1KGPop0.0010.0040.005
snpPositionDemo0.0030.0000.002
snvListVCF0.0010.0040.004
splitSelectByPop0.0010.0000.001
syntheticGeno0.0250.0040.029
tableBlockAF0.020.000.02
testAlleleFractionChange0.0020.0000.001
testEmptyBox0.0020.0000.001
validateAdd1KG2SampleGDS0.0020.0000.002
validateAddStudy1Kg0.0020.0000.002
validateCharacterString0.0010.0000.000
validateComputeAncestryFromSyntheticFile0.0020.0000.003
validateComputeKNNRefSample0.0000.0040.004
validateComputeKNNRefSynthetic0.0060.0000.005
validateComputePCAMultiSynthetic0.0050.0000.004
validateComputePCARefSample0.0020.0000.002
validateComputePoolSyntheticAncestryGr0.0020.0000.002
validateComputeSyntheticRoc0.0110.0000.011
validateCreateStudy2GDS1KG0.0020.0000.002
validateDataRefSynParameter0.0000.0000.001
validateEstimateAllelicFraction0.0010.0030.004
validateGDSClass0.0010.0000.002
validateGenerateGDS1KG0.0010.0000.001
validateLogical0.0010.0000.000
validatePEDStudyParameter0.0000.0010.001
validatePepSynthetic0.0000.0020.001
validatePositiveIntegerVector000
validatePrepPed1KG0.0010.0000.001
validateProfileGDSExist0.0200.0080.027
validatePruningSample0.0020.0000.002
validateRunExomeOrRNAAncestry0.0040.0000.005
validateSingleRatio000
validateStudyDataFrameParameter0.0010.0000.000
validateSyntheticGeno0.0020.0010.002