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 11:38:18 -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 palomino3


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: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RAIDS.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings RAIDS_1.1.0.tar.gz
StartedAt: 2024-03-28 05:36:11 -0400 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 05:44:07 -0400 (Thu, 28 Mar 2024)
EllapsedTime: 476.2 seconds
RetCode: 0
Status:   OK  
CheckDir: RAIDS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RAIDS.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings RAIDS_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/RAIDS.Rcheck'
* using R Under development (unstable) (2024-03-16 r86144 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* 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 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 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 8.72   0.23    8.97
readSNVVCF                       7.08   0.10    7.19
selParaPCAUpQuartile             6.00   0.24    6.23
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

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


Installation output

RAIDS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL RAIDS
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 
  33.96    3.01   37.79 

Example timings

RAIDS.Rcheck/RAIDS-Ex.timings

nameusersystemelapsed
add1KG2SampleGDS0.220.050.75
addBlockInGDSAnnot0.000.010.02
addGDSRef0.010.000.02
addGDSStudyPruning000
addGeneBlockGDSRefAnnot1.030.131.15
addRef2GDS1KG0.020.000.05
addStudy1Kg0.020.000.05
addStudyGDSSample0.000.000.01
addUpdateLap000
addUpdateSegment000
appendGDSRefSample0.000.010.05
appendGDSSampleOnly000
appendGDSgenotype0.030.000.05
appendGDSgenotypeMat000
calcAFMLRNA000
computeAlleleFraction0.010.000.02
computeAllelicFractionDNA0.190.030.28
computeAllelicFractionRNA0.300.010.33
computeAllelicImbDNAChr000
computeAncestryFromSyntheticFile8.720.238.97
computeKNNRefSample0.010.040.05
computeKNNRefSynthetic2.080.102.21
computeLOHBlocksDNAChr0.010.000.01
computePCAMultiSynthetic0.000.020.02
computePCARefRMMulti0.290.050.33
computePCARefSample0.390.010.40
computePoolSyntheticAncestryGr0.540.070.61
computeSyntheticConfMat0.020.010.03
computeSyntheticROC0.060.020.08
createStudy2GDS1KG0.080.040.13
demoKnownSuperPop1KG1.750.131.87
demoPCA1KG0.000.010.02
demoPCASyntheticProfiles1.920.051.97
demoPedigreeEx10.020.020.03
estimateAllelicFraction0.090.030.15
generateGDS1KG0.020.000.04
generateGDS1KGgenotypeFromSNPPileup0.070.010.10
generateGDSRefSample0.000.000.02
generateGDSSNPinfo000
generateGDSgenotype0.020.000.01
generateGeneBlock000
generateMapSnvSel0.000.020.02
generatePhase1KG2GDS0.000.010.04
getBlockIDs000
getRef1KGPop000
getTableSNV0.010.020.04
groupChr1KGSNV0.050.051.07
identifyRelative0.050.000.05
matKNNSynthetic0.030.010.05
pedSynthetic0.040.000.04
prepPed1KG0.020.000.02
prepPedSynthetic1KG0.000.020.02
prepSynthetic0.010.000.04
pruning1KGbyChr0.000.010.02
pruningSample0.050.020.09
readSNVFileGeneric0.000.020.02
readSNVPileupFile0.060.000.06
readSNVVCF7.080.107.19
runExomeAncestry0.020.020.03
runIBDKING0.030.000.50
runLDPruning0.030.000.04
runProfileAncestry0.020.010.03
runRNAAncestry0.010.020.03
runWrapperAncestry0.020.000.01
selParaPCAUpQuartile6.000.246.23
select1KGPop0.010.000.02
snpPositionDemo0.000.010.01
snvListVCF0.000.000.02
splitSelectByPop000
syntheticGeno0.030.030.08
tableBlockAF0.040.000.03
testAlleleFractionChange000
testEmptyBox000
validateAdd1KG2SampleGDS000
validateAddStudy1Kg0.000.000.02
validateCharacterString000
validateComputeAncestryFromSyntheticFile000
validateComputeKNNRefSample0.000.020.01
validateComputeKNNRefSynthetic0.000.030.03
validateComputePCAMultiSynthetic0.000.020.02
validateComputePCARefSample000
validateComputePoolSyntheticAncestryGr000
validateComputeSyntheticRoc0.010.010.03
validateCreateStudy2GDS1KG000
validateDataRefSynParameter000
validateEstimateAllelicFraction0.020.000.01
validateGDSClass000
validateGenerateGDS1KG000
validateLogical0.010.000.02
validatePEDStudyParameter000
validatePepSynthetic000
validatePositiveIntegerVector000
validatePrepPed1KG000
validateProfileGDSExist000
validatePruningSample0.000.020.02
validateRunExomeOrRNAAncestry000
validateSingleRatio000
validateStudyDataFrameParameter000
validateSyntheticGeno0.000.010.01