Tomoyuki Furuta
| Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022) |
| git_url: https://git.bioconductor.org/packages/GBScleanR |
| git_branch: RELEASE_3_15 |
| git_last_commit: b95e1b2 |
| git_last_commit_date: 2022-10-17 11:01:34 -0400 (Mon, 17 Oct 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-10-19 13:22:58 -0400 (Wed, 19 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
| 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 | ||||
|
To the developers/maintainers of the GBScleanR package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 723/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GBScleanR 1.0.6 (landing page) Tomoyuki Furuta
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: GBScleanR |
| Version: 1.0.6 |
| 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_1.0.6.tar.gz |
| StartedAt: 2022-10-19 02:38:26 -0400 (Wed, 19 Oct 2022) |
| EndedAt: 2022-10-19 02:43:22 -0400 (Wed, 19 Oct 2022) |
| EllapsedTime: 295.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GBScleanR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.0.6.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/GBScleanR.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GBScleanR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GBScleanR’ version ‘1.0.6’
* 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
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
getHaplotype 2.697 4.527 7.234
estGeno 2.752 4.450 7.212
setParents 2.164 4.639 6.811
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.15-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/4.2/Resources/library’ * installing *source* package ‘GBScleanR’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c GBSR_HMM.cpp -o GBSR_HMM.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c GBSR_stats.cpp -o GBSR_stats.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o GBScleanR.so GBSR_HMM.o GBSR_stats.o RcppExports.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.2/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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(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/RtmpOr0L6U/sample3574472af96.gds' (95.5K)
# of fragments: 69
save to '/private/tmp/RtmpOr0L6U/sample3574472af96.gds.tmp'
rename '/private/tmp/RtmpOr0L6U/sample3574472af96.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/RtmpOr0L6U/sample3574565c3f5.gds' (95.5K)
# of fragments: 69
save to '/private/tmp/RtmpOr0L6U/sample3574565c3f5.gds.tmp'
rename '/private/tmp/RtmpOr0L6U/sample3574565c3f5.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.
Working on 'genotype' ...
Working on 'phase' ...
Working on 'annotation/format/AD' ...
Clean up the fragments of GDS file:
open the file '/private/tmp/RtmpOr0L6U/sample3571c242d6b.gds' (95.5K)
# of fragments: 69
save to '/private/tmp/RtmpOr0L6U/sample3571c242d6b.gds.tmp'
rename '/private/tmp/RtmpOr0L6U/sample3571c242d6b.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.
Wed Oct 19 02:42:54 2022
Variant Call Format (VCF) Import:
file(s):
sample.vcf (210.3K)
file format: VCFv4.2
genome reference: <unknown>
the number of sets of chromosomes (ploidy): 2
the number of samples: 102
genotype storage: bit2
compression method: customized
# of samples: 102
Output:
/tmp/RtmpOr0L6U/sample357b21da3c.gds
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.
Wed Oct 19 02:42:54 2022
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file '/tmp/RtmpOr0L6U/sample357b21da3c.gds' (53.4K)
# of fragments: 108
save to '/tmp/RtmpOr0L6U/sample357b21da3c.gds.tmp'
rename '/tmp/RtmpOr0L6U/sample357b21da3c.gds.tmp' (52.8K, reduced: 648B)
# of fragments: 54
Wed Oct 19 02:42:54 2022
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/RtmpOr0L6U/sample357b21da3c.gds' (95.5K)
# of fragments: 69
save to '/private/tmp/RtmpOr0L6U/sample357b21da3c.gds.tmp'
rename '/private/tmp/RtmpOr0L6U/sample357b21da3c.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/RtmpOr0L6U/sample3575b7e9ed9.gds' (95.5K)
# of fragments: 69
save to '/private/tmp/RtmpOr0L6U/sample3575b7e9ed9.gds.tmp'
rename '/private/tmp/RtmpOr0L6U/sample3575b7e9ed9.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.
<None> <None> <None> <None> <None> <None> <None> <None> <None> <None>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.
Wed Oct 19 02:43:01 2022
Variant Call Format (VCF) Import:
file(s):
sample.vcf (210.3K)
file format: VCFv4.2
genome reference: <unknown>
the number of sets of chromosomes (ploidy): 2
the number of samples: 102
genotype storage: bit2
compression method: customized
# of samples: 102
Output:
/tmp/RtmpOr0L6U/sample35755eee77c.gds
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.
Wed Oct 19 02:43:01 2022
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file '/tmp/RtmpOr0L6U/sample35755eee77c.gds' (53.4K)
# of fragments: 108
save to '/tmp/RtmpOr0L6U/sample35755eee77c.gds.tmp'
rename '/tmp/RtmpOr0L6U/sample35755eee77c.gds.tmp' (52.8K, reduced: 648B)
# of fragments: 54
Wed Oct 19 02:43:01 2022
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/RtmpOr0L6U/sample35755eee77c.gds' (95.5K)
# of fragments: 69
save to '/private/tmp/RtmpOr0L6U/sample35755eee77c.gds.tmp'
rename '/private/tmp/RtmpOr0L6U/sample35755eee77c.gds.tmp' (95.4K, reduced: 108B)
# of fragments: 60
Wed Oct 19 02:43:01 2022
Variant Call Format (VCF) Import:
file(s):
out357534fb3a8.vcf (60.4K)
file format: VCFv4.2
genome reference: <unknown>
the number of sets of chromosomes (ploidy): 2
the number of samples: 52
genotype storage: bit2
compression method: customized
# of samples: 52
Output:
/tmp/RtmpOr0L6U/newgds357159c0553.gds
Parsing 'out357534fb3a8.vcf':
+ genotype/data { Bit2 2x52x129 ZIP_ra, 16B }
Digests:
sample.id [md5: 325c97d910b7d51a8bb8998ae5e72de7]
variant.id [md5: d27f3dfcca74722c10aa5ded353317a2]
position [md5: a028712642ff9f4be7c9f0f41b7db27b]
chromosome [md5: e6a57ba68a5a38e24d43f1f8af75be50]
allele [md5: d20be0316e151a0dd22bffdbe6584651]
genotype [md5: 35dd467929ea6985735e8714a31ea131]
phase [md5: e4f6def95aef0a05ef147ff781eb2c45]
annotation/id [md5: 9bf988cac318a42585beccb09c6e38a2]
annotation/qual [md5: 3afbb3038e8c0ea713491f4572f079b5]
annotation/filter [md5: ffbd21f2b4f3dd2b02d58633647a5d58]
annotation/format/AD [md5: 1ba1cef5721d12fd5dc04624cb369125]
Done.
Wed Oct 19 02:43:01 2022
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file '/tmp/RtmpOr0L6U/newgds357159c0553.gds' (21.1K)
# of fragments: 107
save to '/tmp/RtmpOr0L6U/newgds357159c0553.gds.tmp'
rename '/tmp/RtmpOr0L6U/newgds357159c0553.gds.tmp' (20.5K, reduced: 636B)
# of fragments: 54
Wed Oct 19 02:43:01 2022
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/RtmpOr0L6U/newgds357159c0553.gds' (33.2K)
# of fragments: 69
save to '/private/tmp/RtmpOr0L6U/newgds357159c0553.gds.tmp'
rename '/private/tmp/RtmpOr0L6U/newgds357159c0553.gds.tmp' (33.1K, reduced: 108B)
# of fragments: 60
Wed Oct 19 02:43:02 2022
Variant Call Format (VCF) Import:
file(s):
out3573621973a.vcf (128.3K)
file format: VCFv4.2
genome reference: <unknown>
the number of sets of chromosomes (ploidy): 2
the number of samples: 52
genotype storage: bit2
compression method: customized
# of samples: 52
Output:
/tmp/RtmpOr0L6U/newgds357237d4d97.gds
Parsing 'out3573621973a.vcf':
+ genotype/data { Bit2 2x52x129 ZIP_ra, 16B }
Digests:
sample.id [md5: 325c97d910b7d51a8bb8998ae5e72de7]
variant.id [md5: d27f3dfcca74722c10aa5ded353317a2]
position [md5: a028712642ff9f4be7c9f0f41b7db27b]
chromosome [md5: e6a57ba68a5a38e24d43f1f8af75be50]
allele [md5: d20be0316e151a0dd22bffdbe6584651]
genotype [md5: 35dd467929ea6985735e8714a31ea131]
phase [md5: e4f6def95aef0a05ef147ff781eb2c45]
annotation/id [md5: 9bf988cac318a42585beccb09c6e38a2]
annotation/qual [md5: 3afbb3038e8c0ea713491f4572f079b5]
annotation/filter [md5: ffbd21f2b4f3dd2b02d58633647a5d58]
annotation/format/AD [md5: 1ba1cef5721d12fd5dc04624cb369125]
annotation/format/CFT [md5: d40d5af3e9d38058a24957fafa3bd424]
annotation/format/FAD [md5: abe5cab45deaa03453bde0817603cb1b]
annotation/format/FGT [md5: 5320b14b9a1d53d946ae472749d69b7d]
Done.
Wed Oct 19 02:43:02 2022
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file '/tmp/RtmpOr0L6U/newgds357237d4d97.gds' (32.3K)
# of fragments: 140
save to '/tmp/RtmpOr0L6U/newgds357237d4d97.gds.tmp'
rename '/tmp/RtmpOr0L6U/newgds357237d4d97.gds.tmp' (31.5K, reduced: 852B)
# of fragments: 69
Wed Oct 19 02:43:02 2022
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/RtmpOr0L6U/newgds357237d4d97.gds' (55.0K)
# of fragments: 91
save to '/private/tmp/RtmpOr0L6U/newgds357237d4d97.gds.tmp'
rename '/private/tmp/RtmpOr0L6U/newgds357237d4d97.gds.tmp' (53.6K, reduced: 1.4K)
# of fragments: 79
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/RtmpOr0L6U/sample357777106b4.gds' (95.5K)
# of fragments: 69
save to '/private/tmp/RtmpOr0L6U/sample357777106b4.gds.tmp'
rename '/private/tmp/RtmpOr0L6U/sample357777106b4.gds.tmp' (95.4K, reduced: 108B)
# of fragments: 60
Set the number of threads: 1
Start cleaning...
Now cleaning chr 1...
Cycle 1: Forward path...
Forward founder genotype probability calculation at marker#: 10
Forward founder genotype probability calculation at marker#: 20
Forward founder genotype probability calculation at marker#: 30
Forward founder genotype probability calculation at marker#: 40
Forward founder genotype probability calculation at marker#: 50
Forward founder genotype probability calculation at marker#: 60
Forward founder genotype probability calculation at marker#: 70
Forward founder genotype probability calculation at marker#: 80
Forward founder genotype probability calculation at marker#: 90
Forward founder genotype probability calculation at marker#: 100
Forward founder genotype probability calculation at marker#: 110
Forward founder genotype probability calculation at marker#: 120
Forward founder genotype probability calculation at marker#: 130
Forward founder genotype probability calculation at marker#: 140
Forward founder genotype probability calculation at marker#: 150
Forward founder genotype probability calculation at marker#: 160
Forward founder genotype probability calculation at marker#: 170
Forward founder genotype probability calculation at marker#: 180
Forward founder genotype probability calculation at marker#: 190
Forward founder genotype probability calculation at marker#: 200
Forward founder genotype probability calculation at marker#: 210
Forward founder genotype probability calculation at marker#: 220
Forward founder genotype probability calculation at marker#: 230
Forward founder genotype probability calculation at marker#: 240
Forward founder genotype probability calculation: Done!
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!
Cycle 1: Backward path...
Forward founder genotype probability calculation at marker#: 10
Forward founder genotype probability calculation at marker#: 20
Forward founder genotype probability calculation at marker#: 30
Forward founder genotype probability calculation at marker#: 40
Forward founder genotype probability calculation at marker#: 50
Forward founder genotype probability calculation at marker#: 60
Forward founder genotype probability calculation at marker#: 70
Forward founder genotype probability calculation at marker#: 80
Forward founder genotype probability calculation at marker#: 90
Forward founder genotype probability calculation at marker#: 100
Forward founder genotype probability calculation at marker#: 110
Forward founder genotype probability calculation at marker#: 120
Forward founder genotype probability calculation at marker#: 130
Forward founder genotype probability calculation at marker#: 140
Forward founder genotype probability calculation at marker#: 150
Forward founder genotype probability calculation at marker#: 160
Forward founder genotype probability calculation at marker#: 170
Forward founder genotype probability calculation at marker#: 180
Forward founder genotype probability calculation at marker#: 190
Forward founder genotype probability calculation at marker#: 200
Forward founder genotype probability calculation at marker#: 210
Forward founder genotype probability calculation at marker#: 220
Forward founder genotype probability calculation at marker#: 230
Forward founder genotype probability calculation at marker#: 240
Forward founder genotype probability calculation: Done!
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!
Cycle 1: Estimating allele read bias and mismapping pattern...
Cycle 2: Forward path...
Forward founder genotype probability calculation at marker#: 10
Forward founder genotype probability calculation at marker#: 20
Forward founder genotype probability calculation at marker#: 30
Forward founder genotype probability calculation at marker#: 40
Forward founder genotype probability calculation at marker#: 50
Forward founder genotype probability calculation at marker#: 60
Forward founder genotype probability calculation at marker#: 70
Forward founder genotype probability calculation at marker#: 80
Forward founder genotype probability calculation at marker#: 90
Forward founder genotype probability calculation at marker#: 100
Forward founder genotype probability calculation at marker#: 110
Forward founder genotype probability calculation at marker#: 120
Forward founder genotype probability calculation at marker#: 130
Forward founder genotype probability calculation at marker#: 140
Forward founder genotype probability calculation at marker#: 150
Forward founder genotype probability calculation at marker#: 160
Forward founder genotype probability calculation at marker#: 170
Forward founder genotype probability calculation at marker#: 180
Forward founder genotype probability calculation at marker#: 190
Forward founder genotype probability calculation at marker#: 200
Forward founder genotype probability calculation at marker#: 210
Forward founder genotype probability calculation at marker#: 220
Forward founder genotype probability calculation at marker#: 230
Forward founder genotype probability calculation at marker#: 240
Forward founder genotype probability calculation: Done!
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!
Cycle 2: Backward path...
Forward founder genotype probability calculation at marker#: 10
Forward founder genotype probability calculation at marker#: 20
Forward founder genotype probability calculation at marker#: 30
Forward founder genotype probability calculation at marker#: 40
Forward founder genotype probability calculation at marker#: 50
Forward founder genotype probability calculation at marker#: 60
Forward founder genotype probability calculation at marker#: 70
Forward founder genotype probability calculation at marker#: 80
Forward founder genotype probability calculation at marker#: 90
Forward founder genotype probability calculation at marker#: 100
Forward founder genotype probability calculation at marker#: 110
Forward founder genotype probability calculation at marker#: 120
Forward founder genotype probability calculation at marker#: 130
Forward founder genotype probability calculation at marker#: 140
Forward founder genotype probability calculation at marker#: 150
Forward founder genotype probability calculation at marker#: 160
Forward founder genotype probability calculation at marker#: 170
Forward founder genotype probability calculation at marker#: 180
Forward founder genotype probability calculation at marker#: 190
Forward founder genotype probability calculation at marker#: 200
Forward founder genotype probability calculation at marker#: 210
Forward founder genotype probability calculation at marker#: 220
Forward founder genotype probability calculation at marker#: 230
Forward founder genotype probability calculation at marker#: 240
Forward founder genotype probability calculation: Done!
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!
Summarizing output...
Done!
The connection to the GDS file was closed.
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 271 ]
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 271 ]
>
> proc.time()
user system elapsed
23.639 6.617 30.308
GBScleanR.Rcheck/GBScleanR-Ex.timings
| name | user | system | elapsed | |
| GbsrGenotypeData-class | 0.023 | 0.002 | 0.027 | |
| GbsrScheme-class | 0.070 | 0.001 | 0.073 | |
| addScheme | 0.102 | 0.002 | 0.105 | |
| boxplotGBSR | 0.771 | 0.015 | 0.788 | |
| closeGDS | 0.005 | 0.001 | 0.007 | |
| countGenotype | 0.647 | 0.028 | 0.676 | |
| countRead | 0.652 | 0.024 | 0.677 | |
| estGeno | 2.752 | 4.450 | 7.212 | |
| gbsrGDS2CSV | 0.052 | 0.002 | 0.055 | |
| gbsrGDS2VCF | 1.272 | 0.023 | 1.309 | |
| gbsrVCF2GDS | 0.127 | 0.026 | 0.155 | |
| getAllele | 0.009 | 0.002 | 0.012 | |
| getChromosome | 0.008 | 0.002 | 0.010 | |
| getCountAlleleAlt | 0.018 | 0.002 | 0.020 | |
| getCountAlleleMissing | 0.018 | 0.002 | 0.020 | |
| getCountAlleleRef | 0.018 | 0.002 | 0.021 | |
| getCountGenoAlt | 0.018 | 0.003 | 0.021 | |
| getCountGenoHet | 0.018 | 0.002 | 0.020 | |
| getCountGenoMissing | 0.018 | 0.002 | 0.020 | |
| getCountGenoRef | 0.015 | 0.003 | 0.018 | |
| getCountRead | 0.054 | 0.003 | 0.057 | |
| getCountReadAlt | 0.046 | 0.003 | 0.055 | |
| getCountReadRef | 0.027 | 0.004 | 0.031 | |
| getGenotype | 0.089 | 0.002 | 0.091 | |
| getHaplotype | 2.697 | 4.527 | 7.234 | |
| getInfo | 0.008 | 0.001 | 0.009 | |
| getMAC | 0.016 | 0.002 | 0.019 | |
| getMAF | 0.016 | 0.002 | 0.017 | |
| getMarID | 0.008 | 0.002 | 0.010 | |
| getMeanReadAlt | 0.026 | 0.003 | 0.029 | |
| getMeanReadRef | 0.025 | 0.003 | 0.028 | |
| getMedianReadAlt | 0.022 | 0.003 | 0.025 | |
| getMedianReadRef | 0.027 | 0.004 | 0.030 | |
| getParents | 0.013 | 0.002 | 0.015 | |
| getPosition | 0.009 | 0.002 | 0.011 | |
| getRead | 0.010 | 0.001 | 0.016 | |
| getSDReadAlt | 0.026 | 0.003 | 0.040 | |
| getSDReadRef | 0.026 | 0.003 | 0.028 | |
| getSamID | 0.008 | 0.002 | 0.008 | |
| histGBSR | 0.603 | 0.015 | 0.622 | |
| initScheme | 0.013 | 0.002 | 0.016 | |
| isOpenGDS | 0.011 | 0.003 | 0.014 | |
| loadGDS | 0.123 | 0.026 | 0.150 | |
| nmar | 0.008 | 0.002 | 0.011 | |
| nsam | 0.009 | 0.002 | 0.010 | |
| pairsGBSR | 0.320 | 0.013 | 0.336 | |
| plotDosage | 0.333 | 0.003 | 0.338 | |
| plotGBSR | 0.368 | 0.003 | 0.372 | |
| plotReadRatio | 0.290 | 0.003 | 0.294 | |
| reopenGDS | 0.012 | 0.002 | 0.014 | |
| resetCallFilter | 0.543 | 0.173 | 0.722 | |
| resetFilter | 0.608 | 0.171 | 0.782 | |
| resetMarFilter | 0.040 | 0.003 | 0.042 | |
| resetSamFilter | 0.150 | 0.027 | 0.178 | |
| setCallFilter | 1.029 | 0.309 | 1.341 | |
| setInfoFilter | 0.008 | 0.001 | 0.009 | |
| setMarFilter | 0.035 | 0.002 | 0.037 | |
| setParents | 2.164 | 4.639 | 6.811 | |
| setSamFilter | 0.052 | 0.004 | 0.057 | |
| showScheme | 0.011 | 0.001 | 0.012 | |
| thinMarker | 0.020 | 0.003 | 0.022 | |
| validMar | 0.008 | 0.002 | 0.010 | |
| validSam | 0.007 | 0.001 | 0.009 | |