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This page was generated on 2023-01-29 16:33:52 -0000 (Sun, 29 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch64R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" 4021
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

CHECK results for GWASTools on kunpeng1


To the developers/maintainers of the GWASTools package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GWASTools.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 871/2162HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GWASTools 1.45.0  (landing page)
Stephanie M. Gogarten
Snapshot Date: 2023-01-27 13:09:27 -0000 (Fri, 27 Jan 2023)
git_url: https://git.bioconductor.org/packages/GWASTools
git_branch: master
git_last_commit: 0127e8c
git_last_commit_date: 2022-11-01 15:06:22 -0000 (Tue, 01 Nov 2022)
kunpeng1Linux (Ubuntu 22.04.1 LTS) / aarch64  OK    OK    ERROR  

Summary

Package: GWASTools
Version: 1.45.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GWASTools.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings GWASTools_1.45.0.tar.gz
StartedAt: 2023-01-29 00:38:55 -0000 (Sun, 29 Jan 2023)
EndedAt: 2023-01-29 00:44:53 -0000 (Sun, 29 Jan 2023)
EllapsedTime: 357.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: GWASTools.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GWASTools.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings GWASTools_1.45.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/GWASTools.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘GWASTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GWASTools’ version ‘1.45.0’
* 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 ‘GWASTools’ can be installed ... 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 ... WARNING
Invalid citation information in ‘inst/CITATION’:
  Warning message:
  In utils::packageDescription(basename(dir), dirname(dir)) :
    no package 'GWASTools' was found
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... WARNING
Error in library(GWASTools, lib.loc = "/home/biocbuild/bbs-3.17-bioc/R/library") : 
  there is no package called ‘GWASTools’
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘S4Vectors:::make_zero_col_DataFrame’
  See the note in ?`:::` about the use of this operator.
* 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 ... WARNING
checkRd: (5) GdsGenotypeReader-class.Rd:36-67: \item in \describe must have non-empty label
checkRd: (5) GdsGenotypeReader-class.Rd:76-78: \item in \describe must have non-empty label
checkRd: (5) GdsGenotypeReader-class.Rd:79-81: \item in \describe must have non-empty label
checkRd: (5) GdsGenotypeReader-class.Rd:82-86: \item in \describe must have non-empty label
checkRd: (5) GdsGenotypeReader-class.Rd:87-95: \item in \describe must have non-empty label
checkRd: (5) GdsGenotypeReader-class.Rd:96-100: \item in \describe must have non-empty label
checkRd: (5) GdsGenotypeReader-class.Rd:101-105: \item in \describe must have non-empty label
checkRd: (5) GdsGenotypeReader-class.Rd:106-110: \item in \describe must have non-empty label
checkRd: (5) GdsGenotypeReader-class.Rd:111-115: \item in \describe must have non-empty label
checkRd: (5) GdsGenotypeReader-class.Rd:116-129: \item in \describe must have non-empty label
checkRd: (5) GdsGenotypeReader-class.Rd:130-141: \item in \describe must have non-empty label
checkRd: (5) GdsGenotypeReader-class.Rd:142-150: \item in \describe must have non-empty label
checkRd: (5) GdsGenotypeReader-class.Rd:151-154: \item in \describe must have non-empty label
checkRd: (5) GdsGenotypeReader-class.Rd:155-158: \item in \describe must have non-empty label
checkRd: (5) GdsGenotypeReader-class.Rd:159-162: \item in \describe must have non-empty label
checkRd: (5) GdsGenotypeReader-class.Rd:163-166: \item in \describe must have non-empty label
checkRd: (5) GdsIntensityReader-class.Rd:42-76: \item in \describe must have non-empty label
checkRd: (5) GdsIntensityReader-class.Rd:93-95: \item in \describe must have non-empty label
checkRd: (5) GdsIntensityReader-class.Rd:96-98: \item in \describe must have non-empty label
checkRd: (5) GdsIntensityReader-class.Rd:99-103: \item in \describe must have non-empty label
checkRd: (5) GdsIntensityReader-class.Rd:104-112: \item in \describe must have non-empty label
checkRd: (5) GdsIntensityReader-class.Rd:113-117: \item in \describe must have non-empty label
checkRd: (5) GdsIntensityReader-class.Rd:118-122: \item in \describe must have non-empty label
checkRd: (5) GdsIntensityReader-class.Rd:123-128: \item in \describe must have non-empty label
checkRd: (5) GdsIntensityReader-class.Rd:129-132: \item in \describe must have non-empty label
checkRd: (5) GdsIntensityReader-class.Rd:133-138: \item in \describe must have non-empty label
checkRd: (5) GdsIntensityReader-class.Rd:139-142: \item in \describe must have non-empty label
checkRd: (5) GdsIntensityReader-class.Rd:143-148: \item in \describe must have non-empty label
checkRd: (5) GdsIntensityReader-class.Rd:149-152: \item in \describe must have non-empty label
checkRd: (5) GdsIntensityReader-class.Rd:153-158: \item in \describe must have non-empty label
checkRd: (5) GdsIntensityReader-class.Rd:159-162: \item in \describe must have non-empty label
checkRd: (5) GdsIntensityReader-class.Rd:163-168: \item in \describe must have non-empty label
checkRd: (5) GdsIntensityReader-class.Rd:169-172: \item in \describe must have non-empty label
checkRd: (5) GdsIntensityReader-class.Rd:173-180: \item in \describe must have non-empty label
checkRd: (5) GdsIntensityReader-class.Rd:181-184: \item in \describe must have non-empty label
checkRd: (5) GdsIntensityReader-class.Rd:185-188: \item in \describe must have non-empty label
checkRd: (5) GdsIntensityReader-class.Rd:189-192: \item in \describe must have non-empty label
checkRd: (5) GdsIntensityReader-class.Rd:193-196: \item in \describe must have non-empty label
checkRd: (5) GdsIntensityReader-class.Rd:197-200: \item in \describe must have non-empty label
checkRd: (5) GdsReader-class.Rd:24-35: \item in \describe must have non-empty label
checkRd: (5) GdsReader-class.Rd:43-67: \item in \describe must have non-empty label
checkRd: (5) GdsReader-class.Rd:68-71: \item in \describe must have non-empty label
checkRd: (5) GdsReader-class.Rd:72-75: \item in \describe must have non-empty label
checkRd: (5) GdsReader-class.Rd:76-78: \item in \describe must have non-empty label
checkRd: (5) GdsReader-class.Rd:79-83: \item in \describe must have non-empty label
checkRd: (5) GdsReader-class.Rd:84-87: \item in \describe must have non-empty label
checkRd: (5) GdsReader-class.Rd:95-97: \item in \describe must have non-empty label
checkRd: (5) GdsReader-class.Rd:98-100: \item in \describe must have non-empty label
checkRd: (5) GdsReader-class.Rd:101-103: \item in \describe must have non-empty label
checkRd: (5) GenotypeData-class.Rd:60-74: \item in \describe must have non-empty label
checkRd: (5) GenotypeData-class.Rd:82-84: \item in \describe must have non-empty label
checkRd: (5) GenotypeData-class.Rd:85-87: \item in \describe must have non-empty label
checkRd: (5) GenotypeData-class.Rd:88-92: \item in \describe must have non-empty label
checkRd: (5) GenotypeData-class.Rd:93-100: \item in \describe must have non-empty label
checkRd: (5) GenotypeData-class.Rd:101-105: \item in \describe must have non-empty label
checkRd: (5) GenotypeData-class.Rd:106-110: \item in \describe must have non-empty label
checkRd: (5) GenotypeData-class.Rd:111-115: \item in \describe must have non-empty label
checkRd: (5) GenotypeData-class.Rd:116-120: \item in \describe must have non-empty label
checkRd: (5) GenotypeData-class.Rd:121-125: \item in \describe must have non-empty label
checkRd: (5) GenotypeData-class.Rd:126-129: \item in \describe must have non-empty label
checkRd: (5) GenotypeData-class.Rd:130-143: \item in \describe must have non-empty label
checkRd: (5) GenotypeData-class.Rd:144-155: \item in \describe must have non-empty label
checkRd: (5) GenotypeData-class.Rd:156-161: \item in \describe must have non-empty label
checkRd: (5) GenotypeData-class.Rd:162-165: \item in \describe must have non-empty label
checkRd: (5) GenotypeData-class.Rd:166-169: \item in \describe must have non-empty label
checkRd: (5) GenotypeData-class.Rd:170-175: \item in \describe must have non-empty label
checkRd: (5) GenotypeData-class.Rd:176-179: \item in \describe must have non-empty label
checkRd: (5) GenotypeData-class.Rd:180-183: \item in \describe must have non-empty label
checkRd: (5) GenotypeData-class.Rd:184-190: \item in \describe must have non-empty label
checkRd: (5) GenotypeData-class.Rd:191-194: \item in \describe must have non-empty label
checkRd: (5) GenotypeData-class.Rd:195-197: \item in \describe must have non-empty label
checkRd: (5) GenotypeData-class.Rd:198-201: \item in \describe must have non-empty label
checkRd: (5) GenotypeData-class.Rd:202-204: \item in \describe must have non-empty label
checkRd: (5) GenotypeData-class.Rd:205-208: \item in \describe must have non-empty label
checkRd: (5) GenotypeData-class.Rd:209-211: \item in \describe must have non-empty label
checkRd: (5) GenotypeData-class.Rd:212-214: \item in \describe must have non-empty label
checkRd: (5) GenotypeData-class.Rd:215-218: \item in \describe must have non-empty label
checkRd: (5) GenotypeData-class.Rd:219-222: \item in \describe must have non-empty label
checkRd: (5) GenotypeData-class.Rd:223-226: \item in \describe must have non-empty label
checkRd: (5) GenotypeData-class.Rd:227-230: \item in \describe must have non-empty label
checkRd: (5) GenotypeData-class.Rd:231-234: \item in \describe must have non-empty label
checkRd: (5) GenotypeIterator-class.Rd:42-50: \item in \describe must have non-empty label
checkRd: (5) GenotypeIterator-class.Rd:56-57: \item in \describe must have non-empty label
checkRd: (5) GenotypeIterator-class.Rd:58-59: \item in \describe must have non-empty label
checkRd: (5) GenotypeIterator-class.Rd:60-61: \item in \describe must have non-empty label
checkRd: (5) GenotypeIterator-class.Rd:62-63: \item in \describe must have non-empty label
checkRd: (5) GenotypeIterator-class.Rd:64-65: \item in \describe must have non-empty label
checkRd: (5) GenotypeIterator-class.Rd:66-69: \item in \describe must have non-empty label
checkRd: (5) GenotypeIterator-class.Rd:70-73: \item in \describe must have non-empty label
checkRd: (5) GenotypeIterator-class.Rd:74-77: \item in \describe must have non-empty label
checkRd: (5) GenotypeIterator-class.Rd:78-80: \item in \describe must have non-empty label
checkRd: (5) GenotypeIterator-class.Rd:81-83: \item in \describe must have non-empty label
checkRd: (5) GenotypeIterator-class.Rd:84-87: \item in \describe must have non-empty label
checkRd: (5) GenotypeIterator-class.Rd:88-91: \item in \describe must have non-empty label
checkRd: (5) IntensityData-class.Rd:64-78: \item in \describe must have non-empty label
checkRd: (5) IntensityData-class.Rd:93-95: \item in \describe must have non-empty label
checkRd: (5) IntensityData-class.Rd:96-98: \item in \describe must have non-empty label
checkRd: (5) IntensityData-class.Rd:99-103: \item in \describe must have non-empty label
checkRd: (5) IntensityData-class.Rd:104-111: \item in \describe must have non-empty label
checkRd: (5) IntensityData-class.Rd:112-116: \item in \describe must have non-empty label
checkRd: (5) IntensityData-class.Rd:117-121: \item in \describe must have non-empty label
checkRd: (5) IntensityData-class.Rd:122-126: \item in \describe must have non-empty label
checkRd: (5) IntensityData-class.Rd:127-130: \item in \describe must have non-empty label
checkRd: (5) IntensityData-class.Rd:131-136: \item in \describe must have non-empty label
checkRd: (5) IntensityData-class.Rd:137-142: \item in \describe must have non-empty label
checkRd: (5) IntensityData-class.Rd:143-148: \item in \describe must have non-empty label
checkRd: (5) IntensityData-class.Rd:149-155: \item in \describe must have non-empty label
checkRd: (5) IntensityData-class.Rd:156-161: \item in \describe must have non-empty label
checkRd: (5) IntensityData-class.Rd:162-167: \item in \describe must have non-empty label
checkRd: (5) IntensityData-class.Rd:168-171: \item in \describe must have non-empty label
checkRd: (5) IntensityData-class.Rd:172-175: \item in \describe must have non-empty label
checkRd: (5) IntensityData-class.Rd:176-181: \item in \describe must have non-empty label
checkRd: (5) IntensityData-class.Rd:182-185: \item in \describe must have non-empty label
checkRd: (5) IntensityData-class.Rd:186-189: \item in \describe must have non-empty label
checkRd: (5) IntensityData-class.Rd:190-196: \item in \describe must have non-empty label
checkRd: (5) IntensityData-class.Rd:197-200: \item in \describe must have non-empty label
checkRd: (5) IntensityData-class.Rd:201-204: \item in \describe must have non-empty label
checkRd: (5) IntensityData-class.Rd:205-208: \item in \describe must have non-empty label
checkRd: (5) IntensityData-class.Rd:209-211: \item in \describe must have non-empty label
checkRd: (5) IntensityData-class.Rd:212-214: \item in \describe must have non-empty label
checkRd: (5) IntensityData-class.Rd:215-218: \item in \describe must have non-empty label
checkRd: (5) IntensityData-class.Rd:219-222: \item in \describe must have non-empty label
checkRd: (5) IntensityData-class.Rd:223-226: \item in \describe must have non-empty label
checkRd: (5) IntensityData-class.Rd:227-230: \item in \describe must have non-empty label
checkRd: (5) IntensityData-class.Rd:231-234: \item in \describe must have non-empty label
checkRd: (5) MatrixGenotypeReader-class.Rd:30-46: \item in \describe must have non-empty label
checkRd: (5) MatrixGenotypeReader-class.Rd:57-59: \item in \describe must have non-empty label
checkRd: (5) MatrixGenotypeReader-class.Rd:60-62: \item in \describe must have non-empty label
checkRd: (5) MatrixGenotypeReader-class.Rd:63-67: \item in \describe must have non-empty label
checkRd: (5) MatrixGenotypeReader-class.Rd:68-76: \item in \describe must have non-empty label
checkRd: (5) MatrixGenotypeReader-class.Rd:77-81: \item in \describe must have non-empty label
checkRd: (5) MatrixGenotypeReader-class.Rd:82-86: \item in \describe must have non-empty label
checkRd: (5) MatrixGenotypeReader-class.Rd:87-98: \item in \describe must have non-empty label
checkRd: (5) MatrixGenotypeReader-class.Rd:99-109: \item in \describe must have non-empty label
checkRd: (5) MatrixGenotypeReader-class.Rd:110-113: \item in \describe must have non-empty label
checkRd: (5) MatrixGenotypeReader-class.Rd:114-117: \item in \describe must have non-empty label
checkRd: (5) MatrixGenotypeReader-class.Rd:118-121: \item in \describe must have non-empty label
checkRd: (5) MatrixGenotypeReader-class.Rd:122-125: \item in \describe must have non-empty label
checkRd: (5) MatrixGenotypeReader-class.Rd:126-129: \item in \describe must have non-empty label
checkRd: (5) NcdfGenotypeReader-class.Rd:33-57: \item in \describe must have non-empty label
checkRd: (5) NcdfGenotypeReader-class.Rd:67-69: \item in \describe must have non-empty label
checkRd: (5) NcdfGenotypeReader-class.Rd:70-72: \item in \describe must have non-empty label
checkRd: (5) NcdfGenotypeReader-class.Rd:73-77: \item in \describe must have non-empty label
checkRd: (5) NcdfGenotypeReader-class.Rd:78-86: \item in \describe must have non-empty label
checkRd: (5) NcdfGenotypeReader-class.Rd:87-91: \item in \describe must have non-empty label
checkRd: (5) NcdfGenotypeReader-class.Rd:92-96: \item in \describe must have non-empty label
checkRd: (5) NcdfGenotypeReader-class.Rd:97-108: \item in \describe must have non-empty label
checkRd: (5) NcdfGenotypeReader-class.Rd:109-113: \item in \describe must have non-empty label
checkRd: (5) NcdfGenotypeReader-class.Rd:114-117: \item in \describe must have non-empty label
checkRd: (5) NcdfGenotypeReader-class.Rd:118-121: \item in \describe must have non-empty label
checkRd: (5) NcdfGenotypeReader-class.Rd:122-125: \item in \describe must have non-empty label
checkRd: (5) NcdfGenotypeReader-class.Rd:126-129: \item in \describe must have non-empty label
checkRd: (5) NcdfGenotypeReader-class.Rd:130-133: \item in \describe must have non-empty label
checkRd: (5) NcdfIntensityReader-class.Rd:42-73: \item in \describe must have non-empty label
checkRd: (5) NcdfIntensityReader-class.Rd:91-93: \item in \describe must have non-empty label
checkRd: (5) NcdfIntensityReader-class.Rd:94-96: \item in \describe must have non-empty label
checkRd: (5) NcdfIntensityReader-class.Rd:97-101: \item in \describe must have non-empty label
checkRd: (5) NcdfIntensityReader-class.Rd:102-110: \item in \describe must have non-empty label
checkRd: (5) NcdfIntensityReader-class.Rd:111-115: \item in \describe must have non-empty label
checkRd: (5) NcdfIntensityReader-class.Rd:116-120: \item in \describe must have non-empty label
checkRd: (5) NcdfIntensityReader-class.Rd:121-126: \item in \describe must have non-empty label
checkRd: (5) NcdfIntensityReader-class.Rd:127-130: \item in \describe must have non-empty label
checkRd: (5) NcdfIntensityReader-class.Rd:131-136: \item in \describe must have non-empty label
checkRd: (5) NcdfIntensityReader-class.Rd:137-140: \item in \describe must have non-empty label
checkRd: (5) NcdfIntensityReader-class.Rd:141-146: \item in \describe must have non-empty label
checkRd: (5) NcdfIntensityReader-class.Rd:147-150: \item in \describe must have non-empty label
checkRd: (5) NcdfIntensityReader-class.Rd:151-156: \item in \describe must have non-empty label
checkRd: (5) NcdfIntensityReader-class.Rd:157-160: \item in \describe must have non-empty label
checkRd: (5) NcdfIntensityReader-class.Rd:161-166: \item in \describe must have non-empty label
checkRd: (5) NcdfIntensityReader-class.Rd:167-170: \item in \describe must have non-empty label
checkRd: (5) NcdfIntensityReader-class.Rd:171-178: \item in \describe must have non-empty label
checkRd: (5) NcdfIntensityReader-class.Rd:179-182: \item in \describe must have non-empty label
checkRd: (5) NcdfIntensityReader-class.Rd:183-186: \item in \describe must have non-empty label
checkRd: (5) NcdfIntensityReader-class.Rd:187-190: \item in \describe must have non-empty label
checkRd: (5) NcdfIntensityReader-class.Rd:191-194: \item in \describe must have non-empty label
checkRd: (5) NcdfIntensityReader-class.Rd:195-198: \item in \describe must have non-empty label
checkRd: (5) NcdfReader-class.Rd:28-35: \item in \describe must have non-empty label
checkRd: (5) NcdfReader-class.Rd:43-66: \item in \describe must have non-empty label
checkRd: (5) NcdfReader-class.Rd:67-70: \item in \describe must have non-empty label
checkRd: (5) NcdfReader-class.Rd:71-74: \item in \describe must have non-empty label
checkRd: (5) NcdfReader-class.Rd:75-79: \item in \describe must have non-empty label
checkRd: (5) NcdfReader-class.Rd:80-85: \item in \describe must have non-empty label
checkRd: (5) NcdfReader-class.Rd:86-90: \item in \describe must have non-empty label
checkRd: (5) NcdfReader-class.Rd:91-95: \item in \describe must have non-empty label
checkRd: (5) NcdfReader-class.Rd:103-105: \item in \describe must have non-empty label
checkRd: (5) NcdfReader-class.Rd:106-108: \item in \describe must have non-empty label
checkRd: (5) NcdfReader-class.Rd:109-111: \item in \describe must have non-empty label
checkRd: (5) ScanAnnotationDataFrame-class.Rd:30-50: \item in \describe must have non-empty label
checkRd: (5) ScanAnnotationDataFrame-class.Rd:59-63: \item in \describe must have non-empty label
checkRd: (5) ScanAnnotationDataFrame-class.Rd:64-68: \item in \describe must have non-empty label
checkRd: (5) ScanAnnotationDataFrame-class.Rd:69-72: \item in \describe must have non-empty label
checkRd: (5) ScanAnnotationDataFrame-class.Rd:73-80: \item in \describe must have non-empty label
checkRd: (5) ScanAnnotationDataFrame-class.Rd:81-84: \item in \describe must have non-empty label
checkRd: (5) ScanAnnotationDataFrame-class.Rd:85-88: \item in \describe must have non-empty label
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checkRd: (5) ScanAnnotationSQLite-class.Rd:31-56: \item in \describe must have non-empty label
checkRd: (5) ScanAnnotationSQLite-class.Rd:65-67: \item in \describe must have non-empty label
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checkRd: (5) ScanAnnotationSQLite-class.Rd:92-100: \item in \describe must have non-empty label
checkRd: (5) ScanAnnotationSQLite-class.Rd:101-104: \item in \describe must have non-empty label
checkRd: (5) ScanAnnotationSQLite-class.Rd:105-108: \item in \describe must have non-empty label
checkRd: (5) ScanAnnotationSQLite-class.Rd:109-112: \item in \describe must have non-empty label
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checkRd: (5) ScanAnnotationSQLite-class.Rd:117-120: \item in \describe must have non-empty label
checkRd: (5) ScanAnnotationSQLite-class.Rd:121-125: \item in \describe must have non-empty label
checkRd: (5) ScanAnnotationSQLite-class.Rd:126-131: \item in \describe must have non-empty label
checkRd: (5) SnpAnnotationDataFrame-class.Rd:36-58: \item in \describe must have non-empty label
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checkRd: (5) SnpAnnotationDataFrame-class.Rd:91-95: \item in \describe must have non-empty label
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checkRd: (5) SnpAnnotationDataFrame-class.Rd:145-148: \item in \describe must have non-empty label
checkRd: (5) SnpAnnotationDataFrame-class.Rd:149-152: \item in \describe must have non-empty label
checkRd: (5) SnpAnnotationDataFrame-class.Rd:153-156: \item in \describe must have non-empty label
checkRd: (5) SnpAnnotationDataFrame-class.Rd:157-160: \item in \describe must have non-empty label
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checkRd: (5) SnpAnnotationSQLite-class.Rd:75-77: \item in \describe must have non-empty label
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checkRd: (5) SnpAnnotationSQLite-class.Rd:91-101: \item in \describe must have non-empty label
checkRd: (5) SnpAnnotationSQLite-class.Rd:102-108: \item in \describe must have non-empty label
checkRd: (5) SnpAnnotationSQLite-class.Rd:109-114: \item in \describe must have non-empty label
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checkRd: (5) SnpAnnotationSQLite-class.Rd:121-129: \item in \describe must have non-empty label
checkRd: (5) SnpAnnotationSQLite-class.Rd:130-133: \item in \describe must have non-empty label
checkRd: (5) SnpAnnotationSQLite-class.Rd:134-137: \item in \describe must have non-empty label
checkRd: (5) SnpAnnotationSQLite-class.Rd:138-141: \item in \describe must have non-empty label
checkRd: (5) SnpAnnotationSQLite-class.Rd:142-145: \item in \describe must have non-empty label
checkRd: (5) SnpAnnotationSQLite-class.Rd:146-149: \item in \describe must have non-empty label
checkRd: (5) SnpAnnotationSQLite-class.Rd:150-155: \item in \describe must have non-empty label
checkRd: (5) SnpAnnotationSQLite-class.Rd:156-161: \item in \describe must have non-empty label
checkRd: (5) SnpAnnotationSQLite-class.Rd:162-165: \item in \describe must have non-empty label
checkRd: (5) SnpAnnotationSQLite-class.Rd:166-169: \item in \describe must have non-empty label
checkRd: (5) SnpAnnotationSQLite-class.Rd:170-173: \item in \describe must have non-empty label
checkRd: (5) SnpAnnotationSQLite-class.Rd:174-177: \item in \describe must have non-empty label
checkRd: (5) SnpAnnotationSQLite-class.Rd:178-181: \item in \describe must have non-empty label
checkRd: (-1) chromIntensityPlot.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) meanIntensityByScanChrom.Rd:3: Escaped LaTeX specials: \&
* 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 ... OK
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’
 ERROR
Running the tests in ‘tests/test.R’ failed.
Last 13 lines of output:
  Reading genotype file...
  Block 1 of 1
  Determining number of SNPs and samples...
  Reading SNP files...
  Reading genotype file...
  Block 1 of 1
  Determining number of SNPs and samples...
  Reading SNP files...
  Reading genotype file...
  Block 1 of 1
  Determining number of SNPs and samples...
  Reading SNP files...
  Reading genotype file...
  Block 1 of 1
  Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘Affymetrix.Rnw’ using ‘UTF-8’... OK
  ‘DataCleaning.Rnw’ using ‘UTF-8’... OK
  ‘Formats.Rnw’ using ‘UTF-8’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/GWASTools.Rcheck/00check.log’
for details.

Installation output

GWASTools.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL GWASTools
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘GWASTools’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (GWASTools)

Tests output

GWASTools.Rcheck/tests/test.Rout.fail


R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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(GWASdata)
Loading required package: GWASTools
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> library(ncdf4)
> library(gdsfmt)
> BiocGenerics:::testPackage("GWASTools", pattern=".*_test\\.R$")
block 1 of 1
adding variables: quality, X, Y
Clean up the fragments of GDS file:
    open the file '/tmp/RtmpPSFDx5/file2ede30785efff9' (67.1K)
    # of fragments: 35
    save to '/tmp/RtmpPSFDx5/file2ede30785efff9.tmp'
    rename '/tmp/RtmpPSFDx5/file2ede30785efff9.tmp' (66.9K, reduced: 216B)
    # of fragments: 17
adding variables: quality, X, Y
Clean up the fragments of GDS file:
    open the file '/tmp/RtmpPSFDx5/file2ede30697b0dea' (67.1K)
    # of fragments: 35
    save to '/tmp/RtmpPSFDx5/file2ede30697b0dea.tmp'
    rename '/tmp/RtmpPSFDx5/file2ede30697b0dea.tmp' (66.9K, reduced: 216B)
    # of fragments: 17
Analyzing: X280 
Analyzing: X281 
Analyzing: X280 
Analyzing: X281 
Analyzing: X280 
Analyzing: X281 
Sun Jan 29 00:42:15 2023 Chromosome 1
Sun Jan 29 00:42:15 2023 Chromosome 2
Sun Jan 29 00:42:15 2023 Chromosome 3
Sun Jan 29 00:42:15 2023 Chromosome 4
Sun Jan 29 00:42:15 2023 Chromosome 5
Sun Jan 29 00:42:15 2023 Chromosome 6
Sun Jan 29 00:42:15 2023 Chromosome 7
Sun Jan 29 00:42:15 2023 Chromosome 8
Sun Jan 29 00:42:15 2023 Chromosome 9
Sun Jan 29 00:42:15 2023 Chromosome 10
Sun Jan 29 00:42:15 2023 Chromosome 11
Sun Jan 29 00:42:15 2023 Chromosome 12
Sun Jan 29 00:42:15 2023 Chromosome 13
Sun Jan 29 00:42:15 2023 Chromosome 14
Sun Jan 29 00:42:15 2023 Chromosome 15
Sun Jan 29 00:42:15 2023 Chromosome 16
Sun Jan 29 00:42:15 2023 Chromosome 17
Sun Jan 29 00:42:15 2023 Chromosome 18
Sun Jan 29 00:42:15 2023 Chromosome 19
Sun Jan 29 00:42:15 2023 Chromosome 20
Sun Jan 29 00:42:15 2023 Chromosome 21
Sun Jan 29 00:42:15 2023 Chromosome 22
Sun Jan 29 00:42:15 2023 Chromosome 23
Sun Jan 29 00:42:15 2023 Chromosome 24
Sun Jan 29 00:42:15 2023 Chromosome 25
Sun Jan 29 00:42:15 2023 Chromosome 26
Sun Jan 29 00:42:15 2023 Total # of SNPs selected: 7
Sun Jan 29 00:42:15 2023 Chromosome 1
Sun Jan 29 00:42:15 2023 Chromosome 2
Sun Jan 29 00:42:15 2023 Chromosome 3
Sun Jan 29 00:42:15 2023 Chromosome 4
Sun Jan 29 00:42:15 2023 Chromosome 5
Sun Jan 29 00:42:15 2023 Chromosome 6
Sun Jan 29 00:42:15 2023 Chromosome 7
Sun Jan 29 00:42:15 2023 Chromosome 8
Sun Jan 29 00:42:15 2023 Chromosome 9
Sun Jan 29 00:42:15 2023 Chromosome 10
Sun Jan 29 00:42:15 2023 Chromosome 11
Sun Jan 29 00:42:15 2023 Chromosome 12
Sun Jan 29 00:42:15 2023 Chromosome 13
Sun Jan 29 00:42:15 2023 Chromosome 14
Sun Jan 29 00:42:15 2023 Chromosome 15
Sun Jan 29 00:42:15 2023 Chromosome 16
Sun Jan 29 00:42:15 2023 Chromosome 17
Sun Jan 29 00:42:15 2023 Chromosome 18
Sun Jan 29 00:42:15 2023 Chromosome 19
Sun Jan 29 00:42:15 2023 Chromosome 20
Sun Jan 29 00:42:15 2023 Chromosome 21
Sun Jan 29 00:42:15 2023 Chromosome 22
Sun Jan 29 00:42:15 2023 Chromosome 23
Sun Jan 29 00:42:15 2023 Chromosome 24
Sun Jan 29 00:42:15 2023 Chromosome 25
Sun Jan 29 00:42:15 2023 Chromosome 26
Sun Jan 29 00:42:15 2023 Total # of SNPs selected: 9
Loading required package: VariantAnnotation
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

The following object is masked from 'package:Biobase':

    rowMedians

Loading required package: GenomeInfoDb
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit


Attaching package: 'VariantAnnotation'

The following object is masked from 'package:base':

    tabulate

Loading required package: SNPRelate
SNPRelate
Reading in Phenotype and Covariate Data...
Running analysis with 40 Samples
Beginning Calculations...
Block 1 of 1 Completed - 0.6905 secs
Reading in Phenotype and Covariate Data...
Running analysis with 50 Samples
Beginning Calculations...
[1] "hi"
   LR.Stat    LR.pval 
8.55400428 0.03584773 
[1] "hi"
  LR.Stat   LR.pval 
1.6733633 0.6428719 
[1] "hi"
    LR.Stat     LR.pval 
11.30391026  0.01019107 
[1] "hi"
  LR.Stat   LR.pval 
3.5479450 0.3145968 
[1] "hi"
   LR.Stat    LR.pval 
8.85703394 0.03125334 
[1] "hi"
  LR.Stat   LR.pval 
4.5360542 0.2090968 
[1] "hi"
  LR.Stat   LR.pval 
5.2442899 0.1547585 
[1] "hi"
  LR.Stat   LR.pval 
2.6576472 0.4474727 
[1] "hi"
    LR.Stat     LR.pval 
15.67110354  0.00132434 
[1] "hi"
  LR.Stat   LR.pval 
1.7737546 0.6206628 
[1] "hi"
  LR.Stat   LR.pval 
2.7135101 0.4379363 
[1] "hi"
  LR.Stat   LR.pval 
2.4907942 0.4769571 
[1] "hi"
    LR.Stat     LR.pval 
10.06391337  0.01803059 
[1] "hi"
 LR.Stat  LR.pval 
4.834600 0.184317 
[1] "hi"
   LR.Stat    LR.pval 
6.85119755 0.07679492 
[1] "hi"
     LR.Stat      LR.pval 
12.410321031  0.006101951 
[1] "hi"
  LR.Stat   LR.pval 
5.9806637 0.1125548 
[1] "hi"
  LR.Stat   LR.pval 
4.5674714 0.2063504 
[1] "hi"
    LR.Stat     LR.pval 
10.29919824  0.01618679 
[1] "hi"
     LR.Stat      LR.pval 
12.161441314  0.006850104 
[1] "hi"
   LR.Stat    LR.pval 
8.85117856 0.03133641 
[1] "hi"
  LR.Stat   LR.pval 
4.6736748 0.1973122 
Block 1 of 1 Completed - 2.049 secs
Reading in Phenotype and Covariate Data...
Running analysis with 50 Samples
Beginning Calculations...
[1] "hi"
     LR.Stat      LR.pval 
1.567110e+01 7.536688e-05 
[1] "hi"
  LR.Stat   LR.pval 
1.6624991 0.1972662 
[1] "hi"
   LR.Stat    LR.pval 
8.38393977 0.00378551 
Block 1 of 1 Completed - 1.359 secs
Reading in Phenotype and Covariate Data...
Running analysis with 50 Samples
Beginning Calculations...
Block 1 of 1 Completed - 0.583 secs
Reading in Phenotype and Covariate Data...
Running analysis with 500 Samples
Beginning Calculations...
Block 1 of 1 Completed - 0.778 secs
Reading in Phenotype and Covariate Data...
Running analysis with 50 Samples
Beginning Calculations...
Block 1 of 1 Completed - 0.8407 secs
Reading in Phenotype and Covariate Data...
Running analysis with 50 Samples
Beginning Calculations...
Block 1 of 1 Completed - 0.3305 secs
Reading in Phenotype and Covariate Data...
Running analysis with 23 Samples
Beginning Calculations...
Block 1 of 1 Completed - 0.1824 secs
Reading in Phenotype and Covariate Data...
Running analysis with 23 Samples
Beginning Calculations...
Block 1 of 1 Completed - 0.1928 secs
Reading in Phenotype and Covariate Data...
Reading in Phenotype and Covariate Data...
Running analysis with 50 Samples
Beginning Calculations...
Block 1 of 1 Completed - 0.1945 secs
Reading in Phenotype and Covariate Data...
Running analysis with 50 Samples
Beginning Calculations...
Block 1 of 4 Completed - 0.06144 secs
Block 2 of 4 Completed - 0.06473 secs
Block 3 of 4 Completed - 0.06605 secs
Block 4 of 4 Completed - 0.002516 secs
Reading in Phenotype and Covariate Data...
Running analysis with 50 Samples
Beginning Calculations...
Block 1 of 1 Completed - 0.2945 secs
Reading in Phenotype and Covariate Data...
Running analysis with 50 Samples
Beginning Calculations...
Block 1 of 1 Completed - 0.2718 secs
Reading in Phenotype and Covariate Data...
Running analysis with 40 Samples
Beginning Calculations...
Block 1 of 1 Completed - 0.5332 secs
Reading in Phenotype and Covariate Data...
Running analysis with 40 Samples
Beginning Calculations...
Block 1 of 1 Completed - 0.2946 secs
Reading in Phenotype and Covariate Data...
Running analysis with 40 Samples
Beginning Calculations...
Block 1 of 1 Completed - 0.359 secs
Loading required package: zoo

Attaching package: 'zoo'

The following objects are masked from 'package:Rsamtools':

    index, index<-

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric

Reading in Phenotype and Covariate Data...
Running analysis with 40 Samples
Beginning Calculations...
Block 1 of 1 Completed - 0.4157 secs
Reading in Phenotype and Covariate Data...
Running analysis with 50 Samples
Beginning Calculations...
Block 1 of 1 Completed - 0.2163 secs
Reading in Phenotype and Covariate Data...
Running analysis with 50 Samples
Beginning Calculations...
Block 1 of 1 Completed - 0.09253 secs
Reading in Phenotype and Covariate Data...
Running analysis with 50 Samples
Beginning Calculations...
Block 1 of 1 Completed - 0.09464 secs
Sun Jan 29 00:42:45 2023	Load genotype dataset ...
Sun Jan 29 00:42:45 2023	1/2	batch1
Sun Jan 29 00:42:45 2023	Load genotype dataset ...
Sun Jan 29 00:42:45 2023	1/4	batch1
Sun Jan 29 00:42:45 2023	2/4	batch2
Sun Jan 29 00:42:45 2023	3/4	batch3
Sun Jan 29 00:42:45 2023	4/4	batch4
Sun Jan 29 00:42:45 2023	Load genotype dataset ...
Sun Jan 29 00:42:46 2023	1/4	batch1
Sun Jan 29 00:42:46 2023	2/4	batch2
Sun Jan 29 00:42:46 2023	3/4	batch3
Sun Jan 29 00:42:46 2023	4/4	batch4
Sun Jan 29 00:42:46 2023	Load genotype dataset ...
Sun Jan 29 00:42:46 2023	1/4	batch1
Sun Jan 29 00:42:46 2023	2/4	batch2
Sun Jan 29 00:42:46 2023	3/4	batch3
Sun Jan 29 00:42:46 2023	4/4	batch4
Sun Jan 29 00:42:46 2023	Load genotype dataset ...
Sun Jan 29 00:42:46 2023	1/4	batch1
Sun Jan 29 00:42:46 2023	2/4	batch2
Sun Jan 29 00:42:46 2023	3/4	batch3
Sun Jan 29 00:42:46 2023	4/4	batch4
Sun Jan 29 00:42:46 2023	Load genotype dataset ...
Sun Jan 29 00:42:46 2023	1/4	batch1
Sun Jan 29 00:42:46 2023	2/4	batch2
Sun Jan 29 00:42:46 2023	3/4	batch3
Sun Jan 29 00:42:46 2023	4/4	batch4
Sun Jan 29 00:42:46 2023	Load genotype dataset ...
Sun Jan 29 00:42:46 2023	1/4	batch1
Sun Jan 29 00:42:46 2023	2/4	batch2
Sun Jan 29 00:42:46 2023	3/4	batch3
Sun Jan 29 00:42:46 2023	4/4	batch4
Sun Jan 29 00:42:46 2023	Load genotype dataset ...
Sun Jan 29 00:42:46 2023	1/4	batch1
Sun Jan 29 00:42:46 2023	2/4	batch2
Sun Jan 29 00:42:46 2023	3/4	batch3
Sun Jan 29 00:42:46 2023	4/4	batch4
Sun Jan 29 00:42:46 2023	Load genotype dataset ...
Sun Jan 29 00:42:46 2023	1/4	batch1
Sun Jan 29 00:42:46 2023	2/4	batch2
Sun Jan 29 00:42:46 2023	3/4	batch3
Sun Jan 29 00:42:46 2023	4/4	batch4
Sun Jan 29 00:42:47 2023	Load genotype dataset ...
Sun Jan 29 00:42:47 2023	1/2	batch1
Sun Jan 29 00:42:47 2023	Load genotype dataset ...
Sun Jan 29 00:42:47 2023	1/4	batch1
Sun Jan 29 00:42:48 2023	2/4	batch2
Sun Jan 29 00:42:48 2023	3/4	batch3
Sun Jan 29 00:42:48 2023	4/4	batch4
Sun Jan 29 00:42:48 2023	Load genotype dataset ...
Sun Jan 29 00:42:48 2023	1/2	batch1
Sun Jan 29 00:42:48 2023	Load genotype dataset ...
Sun Jan 29 00:42:49 2023	1/2	batch1
Sun Jan 29 00:42:49 2023	Load genotype dataset ...
Sun Jan 29 00:42:49 2023	1/2	batch1
Sun Jan 29 00:42:49 2023	Load genotype dataset ...
Sun Jan 29 00:42:49 2023	1/2	batch1
Sun Jan 29 00:42:49 2023	Load genotype dataset ...
Sun Jan 29 00:42:49 2023	1/2	batch1
Sun Jan 29 00:42:49 2023	Load genotype dataset ...
Sun Jan 29 00:42:49 2023	1/2	batch1
Sun Jan 29 00:42:49 2023	Load genotype dataset ...
Sun Jan 29 00:42:49 2023	1/2	batch1
Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
Block 1 of 1
Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
Block 1 of 1
Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
Block 1 of 1
Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
Block 1 of 1
Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
Block 1 of 1
Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
Block 1 of 3
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Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
Block 1 of 2
Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
Block 1 of 2
Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
Block 1 of 2
Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP file...
Reading genotype file...
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Determining number of SNPs and samples...
Reading sample file...
Reading genotype file...
Block 1 of 1
Determining number of SNPs and samples...
Reading sample file...
Reading genotype file...
Block 1 of 1
Determining number of SNPs and samples...
Reading sample file...
Reading genotype file...
Block 1 of 4
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Determining number of SNPs and samples...
Reading sample file...
Reading genotype file...
Block 1 of 4
Determining number of SNPs and samples...
Reading sample file...
Reading genotype file...
Block 1 of 2
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Determining number of SNPs and samples...
Reading sample file...
Reading genotype file...
Block 1 of 2
Determining number of SNPs and samples...
Reading sample file...
Reading genotype file...
Block 1 of 1
Determining number of SNPs and samples...
Reading sample file...
Reading genotype file...
Block 1 of 1
Determining number of SNPs and samples...
Reading sample file...
Reading genotype file...
Block 1 of 4
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Determining number of SNPs and samples...
Reading sample file...
Reading genotype file...
Block 1 of 4
Block 2 of 4
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Determining number of SNPs and samples...
Reading sample file...
Reading genotype file...
Block 1 of 2
Block 2 of 2
Determining number of SNPs and samples...
Reading sample file...
Reading genotype file...
Block 1 of 2
Determining number of SNPs and samples...
Reading sample file...
Reading genotype file...
Block 1 of 1
Determining number of SNPs and samples...
Reading sample file...
Reading genotype file...
Block 1 of 4
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Block 3 of 4
Determining number of SNPs and samples...
Reading sample file...
Reading genotype file...
Block 1 of 2
Determining number of SNPs and samples...
Reading sample file...
Reading genotype file...
Block 1 of 33
Block 2 of 33
Determining number of SNPs and samples...
Reading SNP files...
Reading genotype file...
Block 1 of 1
Determining number of SNPs and samples...
Reading SNP files...
Reading genotype file...
Block 1 of 1
Determining number of SNPs and samples...
Reading SNP files...
Reading genotype file...
Block 1 of 1
Determining number of SNPs and samples...
Reading SNP files...
Reading genotype file...
Block 1 of 1
Determining number of SNPs and samples...
Reading SNP files...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP files...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP files...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP files...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP files...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP files...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP files...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP files...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP files...
Reading genotype file...
Block 1 of 1
Determining number of SNPs and samples...
Reading SNP files...
Reading genotype file...
Block 1 of 1
Determining number of SNPs and samples...
Reading SNP files...
Reading genotype file...
Block 1 of 1
Determining number of SNPs and samples...
Reading SNP files...
Reading genotype file...
Block 1 of 1
Determining number of SNPs and samples...
Reading SNP files...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP files...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP files...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP files...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP files...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP files...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP files...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP files...
Reading genotype file...
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Determining number of SNPs and samples...
Reading SNP files...
Reading genotype file...
Block 1 of 1
Determining number of SNPs and samples...
Reading SNP files...
Reading genotype file...
Block 1 of 1
Determining number of SNPs and samples...
Reading SNP files...
Reading genotype file...
Block 1 of 1
Determining number of SNPs and samples...
Reading SNP files...
Reading genotype file...
Block 1 of 1
Determining number of SNPs and samples...
Reading SNP files...
Reading genotype file...
Block 1 of 1
Determining number of SNPs and samples...
Reading SNP files...
Reading genotype file...
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Killed

Example timings