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This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 770/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GBScleanR 2.0.2  (landing page)
Tomoyuki Furuta
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/GBScleanR
git_branch: RELEASE_3_20
git_last_commit: c18bfaa
git_last_commit_date: 2024-10-31 20:21:40 -0500 (Thu, 31 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for GBScleanR on lconway

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

raw results


Summary

Package: GBScleanR
Version: 2.0.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GBScleanR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GBScleanR_2.0.2.tar.gz
StartedAt: 2024-11-19 22:15:32 -0500 (Tue, 19 Nov 2024)
EndedAt: 2024-11-19 22:22:16 -0500 (Tue, 19 Nov 2024)
EllapsedTime: 404.1 seconds
RetCode: 0
Status:   OK  
CheckDir: GBScleanR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GBScleanR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GBScleanR_2.0.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/GBScleanR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GBScleanR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GBScleanR’ version ‘2.0.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘GBScleanR’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* 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 ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/GBScleanR/libs/GBScleanR.so’:
  Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
estGeno      2.082  9.734  12.013
setParents   1.973  9.319  11.443
getHaplotype 1.975  8.870  10.972
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/GBScleanR.Rcheck/00check.log’
for details.


Installation output

GBScleanR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GBScleanR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘GBScleanR’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c gbsrCalcProb.cpp -o gbsrCalcProb.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c gbsrFB.cpp -o gbsrFB.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c gbsrIPO.cpp -o gbsrIPO.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c gbsrStats.cpp -o gbsrStats.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c gbsrViterbi.cpp -o gbsrViterbi.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c gbsrutil.cpp -o gbsrutil.o
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o GBScleanR.so RcppExports.o gbsrCalcProb.o gbsrFB.o gbsrIPO.o gbsrStats.o gbsrViterbi.o gbsrutil.o -L/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/lib -ltbb -ltbbmalloc -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-GBScleanR/00new/GBScleanR/libs
** R
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GBScleanR)

Tests output

GBScleanR.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
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(GBScleanR)
Loading required package: SeqArray
Loading required package: gdsfmt
> 
> test_check("GBScleanR")
Loading GDS file.
Working on 'genotype' ...
Working on 'phase' ...
Working on 'annotation/format/AD' ...
Clean up the fragments of GDS file:
    open the file '/private/tmp/RtmpHZj0RC/sample120f41e100a63.gds' (95.5K)
    # of fragments: 69
    save to '/private/tmp/RtmpHZj0RC/sample120f41e100a63.gds.tmp'
    rename '/private/tmp/RtmpHZj0RC/sample120f41e100a63.gds.tmp' (95.4K, reduced: 108B)
    # of fragments: 60
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
Working on 'genotype' ...
Working on 'phase' ...
Working on 'annotation/format/AD' ...
Clean up the fragments of GDS file:
    open the file '/private/tmp/RtmpHZj0RC/sample120f436eb1cbd.gds' (95.5K)
    # of fragments: 69
    save to '/private/tmp/RtmpHZj0RC/sample120f436eb1cbd.gds.tmp'
    rename '/private/tmp/RtmpHZj0RC/sample120f436eb1cbd.gds.tmp' (95.4K, reduced: 108B)
    # of fragments: 60
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
Overwrite the previous parents information.
The connection to the GDS file was closed.
Loading GDS file.
Overwrite the previous parents information.
Overwrite the previous parents information.
The connection to the GDS file was closed.
Loading GDS file.
Overwrite the previous parents information.
Overwrite the previous parents information.
The connection to the GDS file was closed.
Loading GDS file.
Overwrite the previous parents information.
The connection to the GDS file was closed.
Loading GDS file.
Working on 'genotype' ...
Working on 'phase' ...
Working on 'annotation/format/AD' ...
Clean up the fragments of GDS file:
    open the file '/private/tmp/RtmpHZj0RC/sample120f42e7917.gds' (95.5K)
    # of fragments: 69
    save to '/private/tmp/RtmpHZj0RC/sample120f42e7917.gds.tmp'
    rename '/private/tmp/RtmpHZj0RC/sample120f42e7917.gds.tmp' (95.4K, reduced: 108B)
    # of fragments: 60
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Tue Nov 19 22:21:48 2024
Variant Call Format (VCF) Import:
    file:
        sample.vcf (210.3K)
    file format: VCFv4.2
    genome reference: <unknown>
    # of sets of chromosomes (ploidy): 2
    # of samples: 102
    genotype field: GT
    genotype storage: bit2
    compression method: customized
    # of samples: 102
    INFO:
    FORMAT: AD
Output:
    /tmp/RtmpHZj0RC/sample120f41abc1df.gds
    [Progress Info: sample120f41abc1df.gds.progress]
Parsing 'sample.vcf':
+ genotype/data   { Bit2 2x102x242 ZIP_ra, 16B }
Digests:
    sample.id  [md5: 338086c89cac9760256e9d1ec0a77327]
    variant.id  [md5: 6f6b771cc6816e18766cd7b202765193]
    position  [md5: f3033fec247b8ec6980e81005e257bd8]
    chromosome  [md5: 891ee7d299e1dba9146b8ae33476741c]
    allele  [md5: 9fc3f097ae98a7ebff52fac77379926e]
    genotype  [md5: b83af5eb9818d83c2ccaa40d494f15a8]
    phase  [md5: 9d686e01959b61df5fdc1a4684bd72b3]
    annotation/id  [md5: 021994c12424cab1e907740e364c7c24]
    annotation/qual  [md5: 5a566f4332739a2b28d23b215163b70a]
    annotation/filter  [md5: cb74cdb22966d99a9290a2c804a10580]
    annotation/format/AD  [md5: f8b130e5e4e497ee162cf32b15b0ac3a]
Done.
Tue Nov 19 22:21:48 2024
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file '/tmp/RtmpHZj0RC/sample120f41abc1df.gds' (53.4K)
    # of fragments: 108
    save to '/tmp/RtmpHZj0RC/sample120f41abc1df.gds.tmp'
    rename '/tmp/RtmpHZj0RC/sample120f41abc1df.gds.tmp' (52.8K, reduced: 648B)
    # of fragments: 54
Tue Nov 19 22:21:48 2024
Loading GDS file.
Working on 'genotype' ...
Working on 'phase' ...
Working on 'annotation/format/AD' ...
Clean up the fragments of GDS file:
    open the file '/private/tmp/RtmpHZj0RC/sample120f41abc1df.gds' (95.5K)
    # of fragments: 69
    save to '/private/tmp/RtmpHZj0RC/sample120f41abc1df.gds.tmp'
    rename '/private/tmp/RtmpHZj0RC/sample120f41abc1df.gds.tmp' (95.4K, reduced: 108B)
    # of fragments: 60
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
Working on 'genotype' ...
Working on 'phase' ...
Working on 'annotation/format/AD' ...
Clean up the fragments of GDS file:
    open the file '/private/tmp/RtmpHZj0RC/sample120f42661c8ae.gds' (95.5K)
    # of fragments: 69
    save to '/private/tmp/RtmpHZj0RC/sample120f42661c8ae.gds.tmp'
    rename '/private/tmp/RtmpHZj0RC/sample120f42661c8ae.gds.tmp' (95.4K, reduced: 108B)
    # of fragments: 60
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
Reformatting FGT
The connection to the GDS file was closed.
Loading GDS file.
Reformatting FGT
The connection to the GDS file was closed.
Tue Nov 19 22:21:56 2024
Variant Call Format (VCF) Import:
    file:
        sample.vcf (210.3K)
    file format: VCFv4.2
    genome reference: <unknown>
    # of sets of chromosomes (ploidy): 2
    # of samples: 102
    genotype field: GT
    genotype storage: bit2
    compression method: customized
    # of samples: 102
    INFO:
    FORMAT: AD
Output:
    /tmp/RtmpHZj0RC/sample120f4555e560c.gds
    [Progress Info: sample120f4555e560c.gds.progress]
Parsing 'sample.vcf':
+ genotype/data   { Bit2 2x102x242 ZIP_ra, 16B }
Digests:
    sample.id  [md5: 338086c89cac9760256e9d1ec0a77327]
    variant.id  [md5: 6f6b771cc6816e18766cd7b202765193]
    position  [md5: f3033fec247b8ec6980e81005e257bd8]
    chromosome  [md5: 891ee7d299e1dba9146b8ae33476741c]
    allele  [md5: 9fc3f097ae98a7ebff52fac77379926e]
    genotype  [md5: b83af5eb9818d83c2ccaa40d494f15a8]
    phase  [md5: 9d686e01959b61df5fdc1a4684bd72b3]
    annotation/id  [md5: 021994c12424cab1e907740e364c7c24]
    annotation/qual  [md5: 5a566f4332739a2b28d23b215163b70a]
    annotation/filter  [md5: cb74cdb22966d99a9290a2c804a10580]
    annotation/format/AD  [md5: f8b130e5e4e497ee162cf32b15b0ac3a]
Done.
Tue Nov 19 22:21:56 2024
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file '/tmp/RtmpHZj0RC/sample120f4555e560c.gds' (53.4K)
    # of fragments: 108
    save to '/tmp/RtmpHZj0RC/sample120f4555e560c.gds.tmp'
    rename '/tmp/RtmpHZj0RC/sample120f4555e560c.gds.tmp' (52.8K, reduced: 648B)
    # of fragments: 54
Tue Nov 19 22:21:56 2024
Loading GDS file.
Working on 'genotype' ...
Working on 'phase' ...
Working on 'annotation/format/AD' ...
Clean up the fragments of GDS file:
    open the file '/private/tmp/RtmpHZj0RC/sample120f4555e560c.gds' (95.5K)
    # of fragments: 69
    save to '/private/tmp/RtmpHZj0RC/sample120f4555e560c.gds.tmp'
    rename '/private/tmp/RtmpHZj0RC/sample120f4555e560c.gds.tmp' (95.4K, reduced: 108B)
    # of fragments: 60
No parents info.
Tue Nov 19 22:21:56 2024
Variant Call Format (VCF) Import:
    file:
        out120f476906514.vcf (70.0K)
    file format: VCFv4.2
    genome reference: <unknown>
    # of sets of chromosomes (ploidy): 2
    # of samples: 64
    genotype field: GT
    genotype storage: bit2
    compression method: customized
    # of samples: 64
    INFO:
    FORMAT: AD
Output:
    /tmp/RtmpHZj0RC/newgds120f423262c78.gds
    [Progress Info: newgds120f423262c78.gds.progress]
Parsing 'out120f476906514.vcf':
+ genotype/data   { Bit2 2x64x124 ZIP_ra, 16B }
Digests:
    sample.id  [md5: f4f513988a8b9d9c95d52e466cd1c193]
    variant.id  [md5: 43796264d31bd83842b0aa403fce0906]
    position  [md5: 159055a67b4e5136a05e1348dec898f4]
    chromosome  [md5: 60b3fe36b6edd92bcd04f5335c4a669b]
    allele  [md5: b290087c2705520ea96fec04c277499e]
    genotype  [md5: b0214f362e1160db87bc76fd674f8c9c]
    phase  [md5: 53d6f426ab629db0fda0e25cbca87b63]
    annotation/id  [md5: 9b0c828c9bb271fc95cf18a3d62b9fb3]
    annotation/qual  [md5: 6cc8f26d6552e7eaab7c984d5ff4b83c]
    annotation/filter  [md5: aa5bfe55f7fbf2b12c60e9c055da37bf]
    annotation/format/AD  [md5: 78db53c715d110b4ea0aacfef78bf03e]
Done.
Tue Nov 19 22:21:56 2024
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file '/tmp/RtmpHZj0RC/newgds120f423262c78.gds' (22.9K)
    # of fragments: 107
    save to '/tmp/RtmpHZj0RC/newgds120f423262c78.gds.tmp'
    rename '/tmp/RtmpHZj0RC/newgds120f423262c78.gds.tmp' (22.2K, reduced: 636B)
    # of fragments: 54
Tue Nov 19 22:21:56 2024
Loading GDS file.
Working on 'genotype' ...
Working on 'phase' ...
Working on 'annotation/format/AD' ...
Clean up the fragments of GDS file:
    open the file '/private/tmp/RtmpHZj0RC/newgds120f423262c78.gds' (36.5K)
    # of fragments: 69
    save to '/private/tmp/RtmpHZj0RC/newgds120f423262c78.gds.tmp'
    rename '/private/tmp/RtmpHZj0RC/newgds120f423262c78.gds.tmp' (36.4K, reduced: 108B)
    # of fragments: 60
No parents info.
Tue Nov 19 22:21:57 2024
Variant Call Format (VCF) Import:
    file:
        out120f45ccded47.vcf (133.6K)
    file format: VCFv4.2
    genome reference: <unknown>
    # of sets of chromosomes (ploidy): 2
    # of samples: 64
    genotype field: GT
    genotype storage: bit2
    compression method: customized
    # of samples: 64
    INFO:
    FORMAT: AD,FAD,FGT
Output:
    /tmp/RtmpHZj0RC/newgds120f45b2d8684.gds
    [Progress Info: newgds120f45b2d8684.gds.progress]
Parsing 'out120f45ccded47.vcf':
+ genotype/data   { Bit2 2x64x124 ZIP_ra, 16B }
Digests:
    sample.id  [md5: f4f513988a8b9d9c95d52e466cd1c193]
    variant.id  [md5: 43796264d31bd83842b0aa403fce0906]
    position  [md5: 159055a67b4e5136a05e1348dec898f4]
    chromosome  [md5: 60b3fe36b6edd92bcd04f5335c4a669b]
    allele  [md5: b290087c2705520ea96fec04c277499e]
    genotype  [md5: b0214f362e1160db87bc76fd674f8c9c]
    phase  [md5: 53d6f426ab629db0fda0e25cbca87b63]
    annotation/id  [md5: 9b0c828c9bb271fc95cf18a3d62b9fb3]
    annotation/qual  [md5: 6cc8f26d6552e7eaab7c984d5ff4b83c]
    annotation/filter  [md5: aa5bfe55f7fbf2b12c60e9c055da37bf]
    annotation/format/AD  [md5: 78db53c715d110b4ea0aacfef78bf03e]
    annotation/format/FAD  [md5: ae2209ed8295f04ab941eb16992a7cf8]
    annotation/format/FGT  [md5: 749de24d71df19f5999d9dcef149c44d]
Done.
Tue Nov 19 22:21:57 2024
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file '/tmp/RtmpHZj0RC/newgds120f45b2d8684.gds' (33.8K)
    # of fragments: 129
    save to '/tmp/RtmpHZj0RC/newgds120f45b2d8684.gds.tmp'
    rename '/tmp/RtmpHZj0RC/newgds120f45b2d8684.gds.tmp' (33.0K, reduced: 780B)
    # of fragments: 64
Tue Nov 19 22:21:57 2024
Loading GDS file.
Reformatting FGT
Working on 'genotype' ...
Working on 'phase' ...
Working on 'annotation/format/AD' ...
Working on 'annotation/format/FAD' ...
Working on 'annotation/format/FGT' ...
Clean up the fragments of GDS file:
    open the file '/private/tmp/RtmpHZj0RC/newgds120f45b2d8684.gds' (59.9K)
    # of fragments: 86
    save to '/private/tmp/RtmpHZj0RC/newgds120f45b2d8684.gds.tmp'
    rename '/private/tmp/RtmpHZj0RC/newgds120f45b2d8684.gds.tmp' (58.2K, reduced: 1.7K)
    # of fragments: 74
The connection to the GDS file was closed.
The connection to the GDS file was closed.
Loading GDS file.
Working on 'genotype' ...
Working on 'phase' ...
Working on 'annotation/format/AD' ...
Clean up the fragments of GDS file:
    open the file '/private/tmp/RtmpHZj0RC/sample120f450f09244.gds' (95.5K)
    # of fragments: 69
    save to '/private/tmp/RtmpHZj0RC/sample120f450f09244.gds.tmp'
    rename '/private/tmp/RtmpHZj0RC/sample120f450f09244.gds.tmp' (95.4K, reduced: 108B)
    # of fragments: 60
As `mating` was not specified, set the following mating design.
     [,1]
[1,]    3
[2,]    3
Member IDs were not assigned to samples.
Assign 4 to all samples as member ID.
Set the number of threads: 1
Start cleaning...
Preparing genotype and haplotype pattern table...
Possible allele dosages: 0 1 2
Number of possible founder genotypes: 2
Member ID(s) to be processed: 4
Number of offspring haplotypes: 4

Now cleaning chr 1...

Cycle 1: 

Forward round of genotype estimation ...

Founder genotype probability calculation ...                                                                      
Founder genotype probability calculation at marker#: 10                                                                      
Founder genotype probability calculation at marker#: 20                                                                      
Founder genotype probability calculation at marker#: 30                                                                      
Founder genotype probability calculation at marker#: 40                                                                      
Founder genotype probability calculation at marker#: 50                                                                      
Founder genotype probability calculation at marker#: 60                                                                      
Founder genotype probability calculation at marker#: 70                                                                      
Founder genotype probability calculation at marker#: 80                                                                      
Founder genotype probability calculation at marker#: 90                                                                      
Founder genotype probability calculation at marker#: 100                                                                      
Founder genotype probability calculation at marker#: 110                                                                      
Founder genotype probability calculation at marker#: 120                                                                      
Founder genotype probability calculation at marker#: 130                                                                      
Founder genotype probability calculation at marker#: 140                                                                      
Founder genotype probability calculation at marker#: 150                                                                      
Founder genotype probability calculation at marker#: 160                                                                      
Founder genotype probability calculation at marker#: 170                                                                      
Founder genotype probability calculation at marker#: 180                                                                      
Founder genotype probability calculation at marker#: 190                                                                      
Founder genotype probability calculation at marker#: 200                                                                      
Founder genotype probability calculation at marker#: 210                                                                      
Founder genotype probability calculation at marker#: 220                                                                      
Founder genotype probability calculation at marker#: 230                                                                      
Founder genotype probability calculation at marker#: 240                                                                      
Backtracking best genotype sequences at marker#: 240                                                                      
Backtracking best genotype sequences at marker#: 230                                                                      
Backtracking best genotype sequences at marker#: 220                                                                      
Backtracking best genotype sequences at marker#: 210                                                                      
Backtracking best genotype sequences at marker#: 200                                                                      
Backtracking best genotype sequences at marker#: 190                                                                      
Backtracking best genotype sequences at marker#: 180                                                                      
Backtracking best genotype sequences at marker#: 170                                                                      
Backtracking best genotype sequences at marker#: 160                                                                      
Backtracking best genotype sequences at marker#: 150                                                                      
Backtracking best genotype sequences at marker#: 140                                                                      
Backtracking best genotype sequences at marker#: 130                                                                      
Backtracking best genotype sequences at marker#: 120                                                                      
Backtracking best genotype sequences at marker#: 110                                                                      
Backtracking best genotype sequences at marker#: 100                                                                      
Backtracking best genotype sequences at marker#: 90                                                                      
Backtracking best genotype sequences at marker#: 80                                                                      
Backtracking best genotype sequences at marker#: 70                                                                      
Backtracking best genotype sequences at marker#: 60                                                                      
Backtracking best genotype sequences at marker#: 50                                                                      
Backtracking best genotype sequences at marker#: 40                                                                      
Backtracking best genotype sequences at marker#: 30                                                                      
Backtracking best genotype sequences at marker#: 20                                                                      
Backtracking best genotype sequences at marker#: 10                                                                      
Backtracking best genotype sequences: Done!                                                                      
Offspring genotype probability calculation ...                                                                      
                                                                      
Backward round of genotype estimation  ...

Founder genotype probability calculation ...                                                                      
Founder genotype probability calculation at marker#: 10                                                                      
Founder genotype probability calculation at marker#: 20                                                                      
Founder genotype probability calculation at marker#: 30                                                                      
Founder genotype probability calculation at marker#: 40                                                                      
Founder genotype probability calculation at marker#: 50                                                                      
Founder genotype probability calculation at marker#: 60                                                                      
Founder genotype probability calculation at marker#: 70                                                                      
Founder genotype probability calculation at marker#: 80                                                                      
Founder genotype probability calculation at marker#: 90                                                                      
Founder genotype probability calculation at marker#: 100                                                                      
Founder genotype probability calculation at marker#: 110                                                                      
Founder genotype probability calculation at marker#: 120                                                                      
Founder genotype probability calculation at marker#: 130                                                                      
Founder genotype probability calculation at marker#: 140                                                                      
Founder genotype probability calculation at marker#: 150                                                                      
Founder genotype probability calculation at marker#: 160                                                                      
Founder genotype probability calculation at marker#: 170                                                                      
Founder genotype probability calculation at marker#: 180                                                                      
Founder genotype probability calculation at marker#: 190                                                                      
Founder genotype probability calculation at marker#: 200                                                                      
Founder genotype probability calculation at marker#: 210                                                                      
Founder genotype probability calculation at marker#: 220                                                                      
Founder genotype probability calculation at marker#: 230                                                                      
Founder genotype probability calculation at marker#: 240                                                                      
Backtracking best genotype sequences at marker#: 240                                                                      
Backtracking best genotype sequences at marker#: 230                                                                      
Backtracking best genotype sequences at marker#: 220                                                                      
Backtracking best genotype sequences at marker#: 210                                                                      
Backtracking best genotype sequences at marker#: 200                                                                      
Backtracking best genotype sequences at marker#: 190                                                                      
Backtracking best genotype sequences at marker#: 180                                                                      
Backtracking best genotype sequences at marker#: 170                                                                      
Backtracking best genotype sequences at marker#: 160                                                                      
Backtracking best genotype sequences at marker#: 150                                                                      
Backtracking best genotype sequences at marker#: 140                                                                      
Backtracking best genotype sequences at marker#: 130                                                                      
Backtracking best genotype sequences at marker#: 120                                                                      
Backtracking best genotype sequences at marker#: 110                                                                      
Backtracking best genotype sequences at marker#: 100                                                                      
Backtracking best genotype sequences at marker#: 90                                                                      
Backtracking best genotype sequences at marker#: 80                                                                      
Backtracking best genotype sequences at marker#: 70                                                                      
Backtracking best genotype sequences at marker#: 60                                                                      
Backtracking best genotype sequences at marker#: 50                                                                      
Backtracking best genotype sequences at marker#: 40                                                                      
Backtracking best genotype sequences at marker#: 30                                                                      
Backtracking best genotype sequences at marker#: 20                                                                      
Backtracking best genotype sequences at marker#: 10                                                                      
Backtracking best genotype sequences: Done!                                                                      
Offspring genotype probability calculation ...                                                                      
                                                                      
Paramter optimization ...

Cycle 2: 

Forward round of genotype estimation ...

Founder genotype probability calculation ...                                                                      
Founder genotype probability calculation at marker#: 10                                                                      
Founder genotype probability calculation at marker#: 20                                                                      
Founder genotype probability calculation at marker#: 30                                                                      
Founder genotype probability calculation at marker#: 40                                                                      
Founder genotype probability calculation at marker#: 50                                                                      
Founder genotype probability calculation at marker#: 60                                                                      
Founder genotype probability calculation at marker#: 70                                                                      
Founder genotype probability calculation at marker#: 80                                                                      
Founder genotype probability calculation at marker#: 90                                                                      
Founder genotype probability calculation at marker#: 100                                                                      
Founder genotype probability calculation at marker#: 110                                                                      
Founder genotype probability calculation at marker#: 120                                                                      
Founder genotype probability calculation at marker#: 130                                                                      
Founder genotype probability calculation at marker#: 140                                                                      
Founder genotype probability calculation at marker#: 150                                                                      
Founder genotype probability calculation at marker#: 160                                                                      
Founder genotype probability calculation at marker#: 170                                                                      
Founder genotype probability calculation at marker#: 180                                                                      
Founder genotype probability calculation at marker#: 190                                                                      
Founder genotype probability calculation at marker#: 200                                                                      
Founder genotype probability calculation at marker#: 210                                                                      
Founder genotype probability calculation at marker#: 220                                                                      
Founder genotype probability calculation at marker#: 230                                                                      
Founder genotype probability calculation at marker#: 240                                                                      
Backtracking best genotype sequences at marker#: 240                                                                      
Backtracking best genotype sequences at marker#: 230                                                                      
Backtracking best genotype sequences at marker#: 220                                                                      
Backtracking best genotype sequences at marker#: 210                                                                      
Backtracking best genotype sequences at marker#: 200                                                                      
Backtracking best genotype sequences at marker#: 190                                                                      
Backtracking best genotype sequences at marker#: 180                                                                      
Backtracking best genotype sequences at marker#: 170                                                                      
Backtracking best genotype sequences at marker#: 160                                                                      
Backtracking best genotype sequences at marker#: 150                                                                      
Backtracking best genotype sequences at marker#: 140                                                                      
Backtracking best genotype sequences at marker#: 130                                                                      
Backtracking best genotype sequences at marker#: 120                                                                      
Backtracking best genotype sequences at marker#: 110                                                                      
Backtracking best genotype sequences at marker#: 100                                                                      
Backtracking best genotype sequences at marker#: 90                                                                      
Backtracking best genotype sequences at marker#: 80                                                                      
Backtracking best genotype sequences at marker#: 70                                                                      
Backtracking best genotype sequences at marker#: 60                                                                      
Backtracking best genotype sequences at marker#: 50                                                                      
Backtracking best genotype sequences at marker#: 40                                                                      
Backtracking best genotype sequences at marker#: 30                                                                      
Backtracking best genotype sequences at marker#: 20                                                                      
Backtracking best genotype sequences at marker#: 10                                                                      
Backtracking best genotype sequences: Done!                                                                      
Offspring genotype probability calculation ...                                                                      
                                                                      
Backward round of genotype estimation  ...

Founder genotype probability calculation ...                                                                      
Founder genotype probability calculation at marker#: 10                                                                      
Founder genotype probability calculation at marker#: 20                                                                      
Founder genotype probability calculation at marker#: 30                                                                      
Founder genotype probability calculation at marker#: 40                                                                      
Founder genotype probability calculation at marker#: 50                                                                      
Founder genotype probability calculation at marker#: 60                                                                      
Founder genotype probability calculation at marker#: 70                                                                      
Founder genotype probability calculation at marker#: 80                                                                      
Founder genotype probability calculation at marker#: 90                                                                      
Founder genotype probability calculation at marker#: 100                                                                      
Founder genotype probability calculation at marker#: 110                                                                      
Founder genotype probability calculation at marker#: 120                                                                      
Founder genotype probability calculation at marker#: 130                                                                      
Founder genotype probability calculation at marker#: 140                                                                      
Founder genotype probability calculation at marker#: 150                                                                      
Founder genotype probability calculation at marker#: 160                                                                      
Founder genotype probability calculation at marker#: 170                                                                      
Founder genotype probability calculation at marker#: 180                                                                      
Founder genotype probability calculation at marker#: 190                                                                      
Founder genotype probability calculation at marker#: 200                                                                      
Founder genotype probability calculation at marker#: 210                                                                      
Founder genotype probability calculation at marker#: 220                                                                      
Founder genotype probability calculation at marker#: 230                                                                      
Founder genotype probability calculation at marker#: 240                                                                      
Backtracking best genotype sequences at marker#: 240                                                                      
Backtracking best genotype sequences at marker#: 230                                                                      
Backtracking best genotype sequences at marker#: 220                                                                      
Backtracking best genotype sequences at marker#: 210                                                                      
Backtracking best genotype sequences at marker#: 200                                                                      
Backtracking best genotype sequences at marker#: 190                                                                      
Backtracking best genotype sequences at marker#: 180                                                                      
Backtracking best genotype sequences at marker#: 170                                                                      
Backtracking best genotype sequences at marker#: 160                                                                      
Backtracking best genotype sequences at marker#: 150                                                                      
Backtracking best genotype sequences at marker#: 140                                                                      
Backtracking best genotype sequences at marker#: 130                                                                      
Backtracking best genotype sequences at marker#: 120                                                                      
Backtracking best genotype sequences at marker#: 110                                                                      
Backtracking best genotype sequences at marker#: 100                                                                      
Backtracking best genotype sequences at marker#: 90                                                                      
Backtracking best genotype sequences at marker#: 80                                                                      
Backtracking best genotype sequences at marker#: 70                                                                      
Backtracking best genotype sequences at marker#: 60                                                                      
Backtracking best genotype sequences at marker#: 50                                                                      
Backtracking best genotype sequences at marker#: 40                                                                      
Backtracking best genotype sequences at marker#: 30                                                                      
Backtracking best genotype sequences at marker#: 20                                                                      
Backtracking best genotype sequences at marker#: 10                                                                      
Backtracking best genotype sequences: Done!                                                                      
Offspring genotype probability calculation ...                                                                      
                                                                      
Summarizing output ...

Done!
The connection to the GDS file was closed.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 271 ]
> 
> proc.time()
   user  system elapsed 
 22.141   9.380  31.869 

Example timings

GBScleanR.Rcheck/GBScleanR-Ex.timings

nameusersystemelapsed
GbsrGenotypeData-class0.0110.0040.023
GbsrScheme-class0.0090.0020.011
addScheme0.0080.0030.018
assignScheme0.0660.0040.070
boxplotGBSR0.6680.0240.696
closeGDS0.0040.0010.009
countGenotype0.5510.0050.559
countRead0.5750.0070.586
estGeno 2.082 9.73412.013
gbsrGDS2CSV0.0280.0020.030
gbsrGDS2VCF0.0040.0010.005
gbsrVCF2GDS0.0680.0310.106
getAllele0.0040.0020.007
getChromosome0.0040.0020.006
getCountAlleleAlt0.3430.0070.352
getCountAlleleMissing0.3420.0040.347
getCountAlleleRef0.3380.0030.342
getCountGenoAlt0.3340.0030.337
getCountGenoHet0.3410.0030.344
getCountGenoMissing0.3520.0030.357
getCountGenoRef0.3360.0050.344
getCountRead0.3520.0030.356
getCountReadAlt0.3550.0030.358
getCountReadRef0.3610.0040.365
getFixedBias0.0600.0290.096
getGenotype0.0230.0010.025
getHaplotype 1.975 8.87010.972
getInfo0.0040.0010.004
getMAC0.3330.0030.337
getMAF0.3490.0040.355
getMarID0.0040.0020.006
getMeanReadAlt0.3590.0040.364
getMeanReadRef0.3450.0040.348
getMedianReadAlt0.3730.0040.379
getMedianReadRef0.3590.0040.364
getParents0.0060.0010.008
getPosition0.0040.0020.007
getRead0.0060.0010.007
getReplicates0.0050.0010.006
getSDReadAlt0.3470.0040.353
getSDReadRef0.3420.0050.349
getSamID0.0040.0020.006
histGBSR0.5280.0050.534
initScheme0.0060.0010.008
isOpenGDS0.0050.0010.006
loadGDS0.0620.0290.096
makeScheme0.0070.0010.008
nmar0.0030.0010.004
nsam0.0030.0010.004
pairsGBSR0.4680.0040.474
plotDosage0.1820.0050.189
plotGBSR0.4830.0030.485
plotReadRatio0.1510.0030.154
reopenGDS0.0060.0020.007
resetCallFilter0.4560.0470.514
resetFilter1.1410.0471.203
resetMarFilter0.6750.0040.683
resetSamFilter0.7560.0310.796
setCallFilter0.7940.0480.855
setFixedBias0.0570.0300.113
setInfoFilter0.0040.0010.006
setMarFilter0.6700.0030.675
setParents 1.973 9.31911.443
setReplicates0.0050.0020.007
setSamFilter0.6710.0030.676
showScheme0.0050.0020.007
thinMarker0.3380.0010.339
validMar0.0040.0020.006
validSam0.0040.0010.005