Tomoyuki Furuta
| Snapshot Date: 2024-09-26 13:40 -0400 (Thu, 26 Sep 2024) |
| git_url: https://git.bioconductor.org/packages/GBScleanR |
| git_branch: devel |
| git_last_commit: 99bbef5 |
| git_last_commit_date: 2024-09-25 05:29:24 -0400 (Wed, 25 Sep 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-09-27 12:30 -0400 (Fri, 27 Sep 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4451 |
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4417 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4456 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4489 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4436 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4435 |
| 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 763/2262 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GBScleanR 1.99.17 (landing page) Tomoyuki Furuta
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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. |
| Package: GBScleanR |
| Version: 1.99.17 |
| 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_1.99.17.tar.gz |
| StartedAt: 2024-09-26 21:02:10 -0400 (Thu, 26 Sep 2024) |
| EndedAt: 2024-09-26 21:06:35 -0400 (Thu, 26 Sep 2024) |
| EllapsedTime: 264.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GBScleanR.Rcheck |
| Warnings: 2 |
##############################################################################
##############################################################################
###
### 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_1.99.17.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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GBScleanR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GBScleanR’ version ‘1.99.17’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘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 ... NOTE
.mateGametes: no visible global function definition for ‘combn’
Undefined global functions or variables:
combn
Consider adding
importFrom("utils", "combn")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘getFixedBias’ ‘setFixedBias’
Undocumented S4 methods:
generic 'getFixedBias' and siglist 'GbsrGenotypeData'
generic 'setFixedBias' and siglist 'GbsrGenotypeData'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in Rd file 'estGeno.Rd':
‘fix_bias’ ‘fix_mismap’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking 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
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
getHaplotype 2.625 12.785 15.550
estGeno 2.701 12.443 15.244
setParents 2.529 12.475 15.112
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 4 NOTEs
See
‘/Users/biocbuild/bbs-3.20-bioc/meat/GBScleanR.Rcheck/00check.log’
for details.
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)
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/Rtmp6y5siJ/sample2d89b4754fb.gds' (95.5K)
# of fragments: 69
save to '/private/tmp/Rtmp6y5siJ/sample2d89b4754fb.gds.tmp'
rename '/private/tmp/Rtmp6y5siJ/sample2d89b4754fb.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/Rtmp6y5siJ/sample2d8943a05063.gds' (95.5K)
# of fragments: 69
save to '/private/tmp/Rtmp6y5siJ/sample2d8943a05063.gds.tmp'
rename '/private/tmp/Rtmp6y5siJ/sample2d8943a05063.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/Rtmp6y5siJ/sample2d89fb4cbd2.gds' (95.5K)
# of fragments: 69
save to '/private/tmp/Rtmp6y5siJ/sample2d89fb4cbd2.gds.tmp'
rename '/private/tmp/Rtmp6y5siJ/sample2d89fb4cbd2.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.
Thu Sep 26 21:05:53 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/Rtmp6y5siJ/sample2d8935f2aac.gds
[Progress Info: sample2d8935f2aac.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.
Thu Sep 26 21:05:53 2024
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file '/tmp/Rtmp6y5siJ/sample2d8935f2aac.gds' (53.4K)
# of fragments: 108
save to '/tmp/Rtmp6y5siJ/sample2d8935f2aac.gds.tmp'
rename '/tmp/Rtmp6y5siJ/sample2d8935f2aac.gds.tmp' (52.8K, reduced: 648B)
# of fragments: 54
Thu Sep 26 21:05:53 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/Rtmp6y5siJ/sample2d8935f2aac.gds' (95.5K)
# of fragments: 69
save to '/private/tmp/Rtmp6y5siJ/sample2d8935f2aac.gds.tmp'
rename '/private/tmp/Rtmp6y5siJ/sample2d8935f2aac.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/Rtmp6y5siJ/sample2d89131e6ddd.gds' (95.5K)
# of fragments: 69
save to '/private/tmp/Rtmp6y5siJ/sample2d89131e6ddd.gds.tmp'
rename '/private/tmp/Rtmp6y5siJ/sample2d89131e6ddd.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.
Thu Sep 26 21:06:05 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/Rtmp6y5siJ/sample2d8931b0025c.gds
[Progress Info: sample2d8931b0025c.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.
Thu Sep 26 21:06:05 2024
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file '/tmp/Rtmp6y5siJ/sample2d8931b0025c.gds' (53.4K)
# of fragments: 108
save to '/tmp/Rtmp6y5siJ/sample2d8931b0025c.gds.tmp'
rename '/tmp/Rtmp6y5siJ/sample2d8931b0025c.gds.tmp' (52.8K, reduced: 648B)
# of fragments: 54
Thu Sep 26 21:06:05 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/Rtmp6y5siJ/sample2d8931b0025c.gds' (95.5K)
# of fragments: 69
save to '/private/tmp/Rtmp6y5siJ/sample2d8931b0025c.gds.tmp'
rename '/private/tmp/Rtmp6y5siJ/sample2d8931b0025c.gds.tmp' (95.4K, reduced: 108B)
# of fragments: 60
No parents info.
Thu Sep 26 21:06:05 2024
Variant Call Format (VCF) Import:
file:
out2d8966ac3a0c.vcf (57.8K)
file format: VCFv4.2
genome reference: <unknown>
# of sets of chromosomes (ploidy): 2
# of samples: 52
genotype field: GT
genotype storage: bit2
compression method: customized
# of samples: 52
INFO:
FORMAT: AD
Output:
/tmp/Rtmp6y5siJ/newgds2d89d2bbc6.gds
[Progress Info: newgds2d89d2bbc6.gds.progress]
Parsing 'out2d8966ac3a0c.vcf':
+ genotype/data { Bit2 2x52x123 ZIP_ra, 16B }
Digests:
sample.id [md5: 310f3dc3112879d60ca65d6f3f649357]
variant.id [md5: 5a4e8bfc1e37fcd1800d6ca6831cbd4e]
position [md5: cfe49103a74fe59fc3ff9a4d72dca1fa]
chromosome [md5: f6bfc37d611c76b81e9d7b504bb3162c]
allele [md5: 269a3ad7c2e0effc50a8587bb0020918]
genotype [md5: 764c546d2ecb36c5ff0af810b4c9d21f]
phase [md5: 836543e9013dd58a3aabc0cf99e5716e]
annotation/id [md5: 190ca9dc63f30b136e45d621a4326567]
annotation/qual [md5: aba5ad5b4581d374c611cfab79690308]
annotation/filter [md5: eb14a330fb0decef5fabef1ce0f58772]
annotation/format/AD [md5: c1f59636a42647e67698b136ca0b2605]
Done.
Thu Sep 26 21:06:05 2024
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file '/tmp/Rtmp6y5siJ/newgds2d89d2bbc6.gds' (20.5K)
# of fragments: 107
save to '/tmp/Rtmp6y5siJ/newgds2d89d2bbc6.gds.tmp'
rename '/tmp/Rtmp6y5siJ/newgds2d89d2bbc6.gds.tmp' (19.9K, reduced: 636B)
# of fragments: 54
Thu Sep 26 21:06:05 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/Rtmp6y5siJ/newgds2d89d2bbc6.gds' (32.0K)
# of fragments: 69
save to '/private/tmp/Rtmp6y5siJ/newgds2d89d2bbc6.gds.tmp'
rename '/private/tmp/Rtmp6y5siJ/newgds2d89d2bbc6.gds.tmp' (31.9K, reduced: 108B)
# of fragments: 60
No parents info.
Thu Sep 26 21:06:06 2024
Variant Call Format (VCF) Import:
file:
out2d89780fb902.vcf (109.4K)
file format: VCFv4.2
genome reference: <unknown>
# of sets of chromosomes (ploidy): 2
# of samples: 52
genotype field: GT
genotype storage: bit2
compression method: customized
# of samples: 52
INFO:
FORMAT: AD,FAD,FGT
Output:
/tmp/Rtmp6y5siJ/newgds2d896e2e8794.gds
[Progress Info: newgds2d896e2e8794.gds.progress]
Parsing 'out2d89780fb902.vcf':
+ genotype/data { Bit2 2x52x123 ZIP_ra, 16B }
Digests:
sample.id [md5: 310f3dc3112879d60ca65d6f3f649357]
variant.id [md5: 5a4e8bfc1e37fcd1800d6ca6831cbd4e]
position [md5: cfe49103a74fe59fc3ff9a4d72dca1fa]
chromosome [md5: f6bfc37d611c76b81e9d7b504bb3162c]
allele [md5: 269a3ad7c2e0effc50a8587bb0020918]
genotype [md5: 764c546d2ecb36c5ff0af810b4c9d21f]
phase [md5: 836543e9013dd58a3aabc0cf99e5716e]
annotation/id [md5: 190ca9dc63f30b136e45d621a4326567]
annotation/qual [md5: aba5ad5b4581d374c611cfab79690308]
annotation/filter [md5: eb14a330fb0decef5fabef1ce0f58772]
annotation/format/AD [md5: c1f59636a42647e67698b136ca0b2605]
annotation/format/FAD [md5: c293cb2c441b93169ce0b1d85d271ef8]
annotation/format/FGT [md5: c0da1944bbf1a1424648af07db9be911]
Done.
Thu Sep 26 21:06:06 2024
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file '/tmp/Rtmp6y5siJ/newgds2d896e2e8794.gds' (30.1K)
# of fragments: 129
save to '/tmp/Rtmp6y5siJ/newgds2d896e2e8794.gds.tmp'
rename '/tmp/Rtmp6y5siJ/newgds2d896e2e8794.gds.tmp' (29.3K, reduced: 780B)
# of fragments: 64
Thu Sep 26 21:06:06 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/Rtmp6y5siJ/newgds2d896e2e8794.gds' (52.0K)
# of fragments: 86
save to '/private/tmp/Rtmp6y5siJ/newgds2d896e2e8794.gds.tmp'
rename '/private/tmp/Rtmp6y5siJ/newgds2d896e2e8794.gds.tmp' (50.6K, reduced: 1.4K)
# 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/Rtmp6y5siJ/sample2d89a24a30f.gds' (95.5K)
# of fragments: 69
save to '/private/tmp/Rtmp6y5siJ/sample2d89a24a30f.gds.tmp'
rename '/private/tmp/Rtmp6y5siJ/sample2d89a24a30f.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
31.211 14.036 45.763
GBScleanR.Rcheck/GBScleanR-Ex.timings
| name | user | system | elapsed | |
| GbsrGenotypeData-class | 0.016 | 0.003 | 0.020 | |
| GbsrScheme-class | 0.014 | 0.002 | 0.016 | |
| addScheme | 0.011 | 0.003 | 0.015 | |
| assignScheme | 0.279 | 0.005 | 0.284 | |
| boxplotGBSR | 0.990 | 0.035 | 1.030 | |
| closeGDS | 0.004 | 0.002 | 0.005 | |
| countGenotype | 0.786 | 0.008 | 0.797 | |
| countRead | 0.877 | 0.008 | 0.889 | |
| estGeno | 2.701 | 12.443 | 15.244 | |
| gbsrGDS2CSV | 0.036 | 0.004 | 0.040 | |
| gbsrGDS2VCF | 0.006 | 0.002 | 0.008 | |
| gbsrVCF2GDS | 0.098 | 0.043 | 0.151 | |
| getAllele | 0.007 | 0.003 | 0.010 | |
| getChromosome | 0.006 | 0.002 | 0.008 | |
| getCountAlleleAlt | 0.458 | 0.006 | 0.467 | |
| getCountAlleleMissing | 0.486 | 0.005 | 0.495 | |
| getCountAlleleRef | 0.483 | 0.005 | 0.491 | |
| getCountGenoAlt | 0.464 | 0.005 | 0.472 | |
| getCountGenoHet | 0.462 | 0.006 | 0.471 | |
| getCountGenoMissing | 0.474 | 0.007 | 0.483 | |
| getCountGenoRef | 0.468 | 0.005 | 0.475 | |
| getCountRead | 0.511 | 0.006 | 0.519 | |
| getCountReadAlt | 0.466 | 0.006 | 0.474 | |
| getCountReadRef | 0.450 | 0.007 | 0.459 | |
| getGenotype | 0.034 | 0.002 | 0.036 | |
| getHaplotype | 2.625 | 12.785 | 15.550 | |
| getInfo | 0.005 | 0.002 | 0.007 | |
| getMAC | 0.427 | 0.007 | 0.437 | |
| getMAF | 0.412 | 0.006 | 0.421 | |
| getMarID | 0.005 | 0.004 | 0.010 | |
| getMeanReadAlt | 0.435 | 0.006 | 0.444 | |
| getMeanReadRef | 0.436 | 0.008 | 0.446 | |
| getMedianReadAlt | 0.447 | 0.007 | 0.459 | |
| getMedianReadRef | 0.434 | 0.007 | 0.444 | |
| getParents | 0.009 | 0.003 | 0.012 | |
| getPosition | 0.006 | 0.005 | 0.010 | |
| getRead | 0.009 | 0.002 | 0.010 | |
| getReplicates | 0.006 | 0.002 | 0.008 | |
| getSDReadAlt | 0.474 | 0.006 | 0.482 | |
| getSDReadRef | 0.458 | 0.006 | 0.467 | |
| getSamID | 0.006 | 0.002 | 0.008 | |
| histGBSR | 0.684 | 0.006 | 0.692 | |
| initScheme | 0.008 | 0.002 | 0.010 | |
| isOpenGDS | 0.006 | 0.002 | 0.008 | |
| loadGDS | 0.078 | 0.046 | 0.139 | |
| makeScheme | 0.006 | 0.002 | 0.008 | |
| nmar | 0.003 | 0.001 | 0.005 | |
| nsam | 0.003 | 0.002 | 0.004 | |
| pairsGBSR | 0.612 | 0.004 | 0.620 | |
| plotDosage | 0.234 | 0.004 | 0.240 | |
| plotGBSR | 0.627 | 0.005 | 0.635 | |
| plotReadRatio | 0.207 | 0.005 | 0.212 | |
| reopenGDS | 0.007 | 0.002 | 0.009 | |
| resetCallFilter | 0.588 | 0.069 | 0.678 | |
| resetFilter | 1.424 | 0.066 | 1.509 | |
| resetMarFilter | 0.884 | 0.006 | 0.894 | |
| resetSamFilter | 0.919 | 0.045 | 0.976 | |
| setCallFilter | 1.057 | 0.083 | 1.162 | |
| setInfoFilter | 0.006 | 0.002 | 0.008 | |
| setMarFilter | 0.921 | 0.007 | 0.932 | |
| setParents | 2.529 | 12.475 | 15.112 | |
| setReplicates | 0.005 | 0.002 | 0.009 | |
| setSamFilter | 0.923 | 0.007 | 0.932 | |
| showScheme | 0.007 | 0.003 | 0.010 | |
| thinMarker | 0.495 | 0.005 | 0.505 | |
| validMar | 0.007 | 0.005 | 0.012 | |
| validSam | 0.006 | 0.003 | 0.010 | |