Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-16 11:41 -0400 (Tue, 16 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4677 |
palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4416 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4393 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4373 |
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 1622/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
RAIDS 1.3.0 (landing page) Pascal Belleau
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
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. |
Package: RAIDS |
Version: 1.3.0 |
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RAIDS.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings RAIDS_1.3.0.tar.gz |
StartedAt: 2024-07-16 03:04:30 -0400 (Tue, 16 Jul 2024) |
EndedAt: 2024-07-16 03:11:36 -0400 (Tue, 16 Jul 2024) |
EllapsedTime: 426.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: RAIDS.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RAIDS.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings RAIDS_1.3.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/RAIDS.Rcheck' * using R version 4.4.1 (2024-06-14 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 '1.3.0' * 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 6.64 0.26 6.95 selParaPCAUpQuartile 5.14 0.08 5.50 * 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 'C:/Users/biocbuild/bbs-3.20-bioc/meat/RAIDS.Rcheck/00check.log' for details.
RAIDS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL RAIDS ### ############################################################################## ############################################################################## * installing to library 'C:/Users/biocbuild/bbs-3.20-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)
RAIDS.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 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 31.92 3.12 37.89
RAIDS.Rcheck/RAIDS-Ex.timings
name | user | system | elapsed | |
add1KG2SampleGDS | 0.03 | 0.05 | 0.09 | |
addBlockInGDSAnnot | 0.01 | 0.00 | 0.01 | |
addGDSRef | 0 | 0 | 0 | |
addGDSStudyPruning | 0 | 0 | 0 | |
addGeneBlockGDSRefAnnot | 0.78 | 0.14 | 0.92 | |
addRef2GDS1KG | 0.00 | 0.00 | 0.03 | |
addStudy1Kg | 0.02 | 0.02 | 0.03 | |
addStudyGDSSample | 0.00 | 0.01 | 0.02 | |
addUpdateLap | 0 | 0 | 0 | |
addUpdateSegment | 0 | 0 | 0 | |
appendGDSRefSample | 0.00 | 0.02 | 0.01 | |
appendGDSSampleOnly | 0 | 0 | 0 | |
appendGDSgenotype | 0.01 | 0.00 | 0.02 | |
appendGDSgenotypeMat | 0.00 | 0.01 | 0.02 | |
calcAFMLRNA | 0 | 0 | 0 | |
computeAlleleFraction | 0.02 | 0.00 | 0.01 | |
computeAllelicFractionDNA | 0.12 | 0.02 | 0.16 | |
computeAllelicFractionRNA | 0.20 | 0.00 | 0.22 | |
computeAllelicImbDNAChr | 0.02 | 0.00 | 0.02 | |
computeAncestryFromSyntheticFile | 6.64 | 0.26 | 6.95 | |
computeKNNRefSample | 0.00 | 0.04 | 0.03 | |
computeKNNRefSynthetic | 2.73 | 0.03 | 2.94 | |
computeLOHBlocksDNAChr | 0.02 | 0.00 | 0.02 | |
computePCAMultiSynthetic | 0.01 | 0.00 | 0.01 | |
computePCARefRMMulti | 0.21 | 0.00 | 0.20 | |
computePCARefSample | 0.18 | 0.01 | 0.21 | |
computePoolSyntheticAncestryGr | 0.39 | 0.07 | 0.45 | |
computeSyntheticConfMat | 0.02 | 0.01 | 0.03 | |
computeSyntheticROC | 0.03 | 0.02 | 0.05 | |
createStudy2GDS1KG | 0.05 | 0.01 | 0.06 | |
demoKnownSuperPop1KG | 1.25 | 0.08 | 1.33 | |
demoPCA1KG | 0.00 | 0.02 | 0.01 | |
demoPCASyntheticProfiles | 1.20 | 0.15 | 1.35 | |
demoPedigreeEx1 | 0.02 | 0.00 | 0.01 | |
estimateAllelicFraction | 0.07 | 0.02 | 0.10 | |
generateGDS1KG | 0.02 | 0.00 | 0.01 | |
generateGDS1KGgenotypeFromSNPPileup | 0.05 | 0.03 | 0.08 | |
generateGDSRefSample | 0.00 | 0.00 | 0.02 | |
generateGDSSNPinfo | 0.00 | 0.01 | 0.01 | |
generateGDSgenotype | 0.00 | 0.02 | 0.02 | |
generateGeneBlock | 0 | 0 | 0 | |
generateMapSnvSel | 0.01 | 0.00 | 0.03 | |
generatePhase1KG2GDS | 0.02 | 0.00 | 0.03 | |
getBlockIDs | 0.00 | 0.02 | 0.02 | |
getRef1KGPop | 0 | 0 | 0 | |
getTableSNV | 0.01 | 0.00 | 0.03 | |
groupChr1KGSNV | 0.74 | 0.03 | 1.81 | |
identifyRelative | 0.01 | 0.01 | 0.03 | |
matKNNSynthetic | 0.04 | 0.00 | 0.03 | |
pedSynthetic | 0.03 | 0.00 | 0.03 | |
prepPed1KG | 0.00 | 0.02 | 0.02 | |
prepPedSynthetic1KG | 0 | 0 | 0 | |
prepSynthetic | 0.02 | 0.01 | 0.04 | |
pruning1KGbyChr | 0.00 | 0.00 | 0.02 | |
pruningSample | 0.04 | 0.00 | 0.06 | |
readSNVFileGeneric | 0 | 0 | 0 | |
readSNVPileupFile | 0.05 | 0.00 | 0.05 | |
readSNVVCF | 4.53 | 0.16 | 4.70 | |
runExomeAncestry | 0.02 | 0.00 | 0.02 | |
runIBDKING | 0.03 | 0.02 | 0.04 | |
runLDPruning | 0.03 | 0.03 | 0.07 | |
runProfileAncestry | 0.02 | 0.01 | 0.03 | |
runRNAAncestry | 0.01 | 0.00 | 0.01 | |
runWrapperAncestry | 0.02 | 0.00 | 0.03 | |
selParaPCAUpQuartile | 5.14 | 0.08 | 5.50 | |
select1KGPop | 0.01 | 0.00 | 0.02 | |
snpPositionDemo | 0 | 0 | 0 | |
snvListVCF | 0.02 | 0.00 | 0.01 | |
splitSelectByPop | 0 | 0 | 0 | |
syntheticGeno | 0.02 | 0.00 | 0.07 | |
tableBlockAF | 0.01 | 0.00 | 0.01 | |
testAlleleFractionChange | 0.02 | 0.00 | 0.02 | |
testEmptyBox | 0 | 0 | 0 | |
validateAdd1KG2SampleGDS | 0 | 0 | 0 | |
validateAddStudy1Kg | 0 | 0 | 0 | |
validateCharacterString | 0 | 0 | 0 | |
validateComputeAncestryFromSyntheticFile | 0.00 | 0.02 | 0.01 | |
validateComputeKNNRefSample | 0 | 0 | 0 | |
validateComputeKNNRefSynthetic | 0.01 | 0.00 | 0.02 | |
validateComputePCAMultiSynthetic | 0.00 | 0.00 | 0.02 | |
validateComputePCARefSample | 0 | 0 | 0 | |
validateComputePoolSyntheticAncestryGr | 0 | 0 | 0 | |
validateComputeSyntheticRoc | 0.02 | 0.01 | 0.03 | |
validateCreateStudy2GDS1KG | 0 | 0 | 0 | |
validateDataRefSynParameter | 0 | 0 | 0 | |
validateEstimateAllelicFraction | 0.00 | 0.02 | 0.01 | |
validateGDSClass | 0 | 0 | 0 | |
validateGenerateGDS1KG | 0 | 0 | 0 | |
validateLogical | 0 | 0 | 0 | |
validatePEDStudyParameter | 0 | 0 | 0 | |
validatePepSynthetic | 0 | 0 | 0 | |
validatePositiveIntegerVector | 0 | 0 | 0 | |
validatePrepPed1KG | 0 | 0 | 0 | |
validateProfileGDSExist | 0 | 0 | 0 | |
validatePruningSample | 0 | 0 | 0 | |
validateRunExomeOrRNAAncestry | 0.01 | 0.00 | 0.01 | |
validateSingleRatio | 0 | 0 | 0 | |
validateStudyDataFrameParameter | 0 | 0 | 0 | |
validateSyntheticGeno | 0 | 0 | 0 | |