Pascal Belleau
| Snapshot Date: 2024-05-29 14:00:10 -0400 (Wed, 29 May 2024) |
| git_url: https://git.bioconductor.org/packages/RAIDS |
| git_branch: RELEASE_3_19 |
| git_last_commit: a9ec943 |
| git_last_commit_date: 2024-04-30 11:51:55 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-30 11:35:50 -0400 (Thu, 30 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4518 |
| 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 1669/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RAIDS 1.2.0 (landing page) Pascal Belleau
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 1.2.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RAIDS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RAIDS_1.2.0.tar.gz |
| StartedAt: 2024-05-29 23:06:14 -0400 (Wed, 29 May 2024) |
| EndedAt: 2024-05-29 23:14:19 -0400 (Wed, 29 May 2024) |
| EllapsedTime: 484.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RAIDS.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RAIDS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RAIDS_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/RAIDS.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RAIDS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RAIDS’ version ‘1.2.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RAIDS’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 ?
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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
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checkRd: (-1) computeLOHBlocksDNAChr.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
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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
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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
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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
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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 ?
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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 7.573 0.188 7.825
readSNVVCF 6.609 0.103 6.765
selParaPCAUpQuartile 6.537 0.068 6.658
* 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
‘/Users/biocbuild/bbs-3.19-bioc/meat/RAIDS.Rcheck/00check.log’
for details.
RAIDS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RAIDS ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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
36.791 2.675 40.016
RAIDS.Rcheck/RAIDS-Ex.timings
| name | user | system | elapsed | |
| add1KG2SampleGDS | 0.113 | 0.027 | 0.152 | |
| addBlockInGDSAnnot | 0.006 | 0.005 | 0.012 | |
| addGDSRef | 0.003 | 0.003 | 0.007 | |
| addGDSStudyPruning | 0.001 | 0.002 | 0.004 | |
| addGeneBlockGDSRefAnnot | 1.108 | 0.119 | 1.256 | |
| addRef2GDS1KG | 0.006 | 0.005 | 0.012 | |
| addStudy1Kg | 0.013 | 0.012 | 0.028 | |
| addStudyGDSSample | 0.009 | 0.006 | 0.016 | |
| addUpdateLap | 0.001 | 0.002 | 0.004 | |
| addUpdateSegment | 0.001 | 0.002 | 0.004 | |
| appendGDSRefSample | 0.007 | 0.005 | 0.014 | |
| appendGDSSampleOnly | 0.001 | 0.002 | 0.004 | |
| appendGDSgenotype | 0.019 | 0.016 | 0.040 | |
| appendGDSgenotypeMat | 0.002 | 0.003 | 0.004 | |
| calcAFMLRNA | 0.005 | 0.002 | 0.007 | |
| computeAlleleFraction | 0.002 | 0.000 | 0.003 | |
| computeAllelicFractionDNA | 0.177 | 0.012 | 0.193 | |
| computeAllelicFractionRNA | 0.294 | 0.017 | 0.315 | |
| computeAllelicImbDNAChr | 0.008 | 0.002 | 0.010 | |
| computeAncestryFromSyntheticFile | 7.573 | 0.188 | 7.825 | |
| computeKNNRefSample | 1.213 | 0.017 | 1.241 | |
| computeKNNRefSynthetic | 1.877 | 0.085 | 1.981 | |
| computeLOHBlocksDNAChr | 0.013 | 0.002 | 0.015 | |
| computePCAMultiSynthetic | 0.009 | 0.004 | 0.013 | |
| computePCARefRMMulti | 0.402 | 0.009 | 0.415 | |
| computePCARefSample | 0.406 | 0.006 | 0.416 | |
| computePoolSyntheticAncestryGr | 0.747 | 0.021 | 0.773 | |
| computeSyntheticConfMat | 0.017 | 0.004 | 0.021 | |
| computeSyntheticROC | 0.046 | 0.005 | 0.052 | |
| createStudy2GDS1KG | 0.078 | 0.018 | 0.100 | |
| demoKnownSuperPop1KG | 1.853 | 0.046 | 1.914 | |
| demoPCA1KG | 0.008 | 0.004 | 0.012 | |
| demoPCASyntheticProfiles | 2.011 | 0.039 | 2.067 | |
| demoPedigreeEx1 | 0.019 | 0.003 | 0.023 | |
| estimateAllelicFraction | 0.104 | 0.006 | 0.113 | |
| generateGDS1KG | 0.016 | 0.014 | 0.031 | |
| generateGDS1KGgenotypeFromSNPPileup | 0.068 | 0.017 | 0.087 | |
| generateGDSRefSample | 0.005 | 0.003 | 0.010 | |
| generateGDSSNPinfo | 0.005 | 0.005 | 0.012 | |
| generateGDSgenotype | 0.017 | 0.012 | 0.031 | |
| generateGeneBlock | 0.001 | 0.001 | 0.002 | |
| generateMapSnvSel | 0.004 | 0.003 | 0.007 | |
| generatePhase1KG2GDS | 0.016 | 0.014 | 0.034 | |
| getBlockIDs | 0.003 | 0.001 | 0.004 | |
| getRef1KGPop | 0.003 | 0.002 | 0.004 | |
| getTableSNV | 0.014 | 0.003 | 0.018 | |
| groupChr1KGSNV | 0.066 | 0.107 | 0.212 | |
| identifyRelative | 0.018 | 0.006 | 0.025 | |
| matKNNSynthetic | 0.051 | 0.004 | 0.055 | |
| pedSynthetic | 0.048 | 0.005 | 0.053 | |
| prepPed1KG | 0.006 | 0.003 | 0.009 | |
| prepPedSynthetic1KG | 0.005 | 0.002 | 0.007 | |
| prepSynthetic | 0.012 | 0.006 | 0.019 | |
| pruning1KGbyChr | 0.005 | 0.003 | 0.007 | |
| pruningSample | 0.047 | 0.012 | 0.061 | |
| readSNVFileGeneric | 0.004 | 0.002 | 0.006 | |
| readSNVPileupFile | 0.049 | 0.002 | 0.051 | |
| readSNVVCF | 6.609 | 0.103 | 6.765 | |
| runExomeAncestry | 0.021 | 0.003 | 0.024 | |
| runIBDKING | 0.049 | 0.005 | 0.058 | |
| runLDPruning | 0.026 | 0.013 | 0.040 | |
| runProfileAncestry | 0.024 | 0.004 | 0.028 | |
| runRNAAncestry | 0.020 | 0.004 | 0.022 | |
| runWrapperAncestry | 0.023 | 0.004 | 0.027 | |
| selParaPCAUpQuartile | 6.537 | 0.068 | 6.658 | |
| select1KGPop | 0.006 | 0.001 | 0.007 | |
| snpPositionDemo | 0.003 | 0.001 | 0.004 | |
| snvListVCF | 0.004 | 0.002 | 0.007 | |
| splitSelectByPop | 0.001 | 0.000 | 0.001 | |
| syntheticGeno | 0.030 | 0.006 | 0.037 | |
| tableBlockAF | 0.021 | 0.002 | 0.023 | |
| testAlleleFractionChange | 0.002 | 0.001 | 0.002 | |
| testEmptyBox | 0.002 | 0.001 | 0.003 | |
| validateAdd1KG2SampleGDS | 0.001 | 0.001 | 0.003 | |
| validateAddStudy1Kg | 0.002 | 0.001 | 0.003 | |
| validateCharacterString | 0 | 0 | 0 | |
| validateComputeAncestryFromSyntheticFile | 0.002 | 0.001 | 0.003 | |
| validateComputeKNNRefSample | 0.004 | 0.003 | 0.008 | |
| validateComputeKNNRefSynthetic | 0.006 | 0.003 | 0.010 | |
| validateComputePCAMultiSynthetic | 0.004 | 0.003 | 0.008 | |
| validateComputePCARefSample | 0.002 | 0.001 | 0.004 | |
| validateComputePoolSyntheticAncestryGr | 0.002 | 0.001 | 0.003 | |
| validateComputeSyntheticRoc | 0.016 | 0.003 | 0.019 | |
| validateCreateStudy2GDS1KG | 0.003 | 0.001 | 0.003 | |
| validateDataRefSynParameter | 0.001 | 0.001 | 0.001 | |
| validateEstimateAllelicFraction | 0.005 | 0.002 | 0.007 | |
| validateGDSClass | 0.001 | 0.001 | 0.003 | |
| validateGenerateGDS1KG | 0.001 | 0.001 | 0.002 | |
| validateLogical | 0 | 0 | 0 | |
| validatePEDStudyParameter | 0.001 | 0.001 | 0.001 | |
| validatePepSynthetic | 0.002 | 0.001 | 0.003 | |
| validatePositiveIntegerVector | 0.000 | 0.001 | 0.000 | |
| validatePrepPed1KG | 0.001 | 0.001 | 0.002 | |
| validateProfileGDSExist | 0.001 | 0.001 | 0.002 | |
| validatePruningSample | 0.002 | 0.002 | 0.003 | |
| validateRunExomeOrRNAAncestry | 0.005 | 0.001 | 0.006 | |
| validateSingleRatio | 0.001 | 0.000 | 0.000 | |
| validateStudyDataFrameParameter | 0.001 | 0.001 | 0.001 | |
| validateSyntheticGeno | 0.002 | 0.001 | 0.003 | |