Tomoyuki Furuta
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 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) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:03 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| 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 770/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GBScleanR 2.0.2 (landing page) Tomoyuki Furuta
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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: 2.0.2 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:GBScleanR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings GBScleanR_2.0.2.tar.gz |
| StartedAt: 2024-12-19 23:58:55 -0500 (Thu, 19 Dec 2024) |
| EndedAt: 2024-12-20 00:05:41 -0500 (Fri, 20 Dec 2024) |
| EllapsedTime: 405.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GBScleanR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:GBScleanR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings GBScleanR_2.0.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/GBScleanR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
installed size is 6.1Mb
sub-directories of 1Mb or more:
libs 4.8Mb
* 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 loading without being on the library search path ... 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 ‘/home/biocbuild/bbs-3.20-bioc/R/site-library/GBScleanR/libs/GBScleanR.so’:
Found ‘_ZSt4cout’, 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
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/home/biocbuild/bbs-3.20-bioc/meat/GBScleanR.Rcheck/00check.log’
for details.
GBScleanR.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL GBScleanR
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘GBScleanR’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c gbsrCalcProb.cpp -o gbsrCalcProb.o
gbsrCalcProb.cpp: In function ‘std::vector<double> calcGenoprob(const double&, const double&, const double&, const double&, const double&, const bool&, const int&)’:
gbsrCalcProb.cpp:25:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
25 | for(int g = 0; g < prob.size(); ++g){
| ~~^~~~~~~~~~~~~
gbsrCalcProb.cpp:37:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
37 | for(int g = 0; g < prob.size(); ++g){
| ~~^~~~~~~~~~~~~
gbsrCalcProb.cpp: In function ‘void calcMissmap(std::vector<double>&, const double&, const double&, const bool&, const int&)’:
gbsrCalcProb.cpp:72:21: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
72 | } else if(g == ploidy){
| ~~^~~~~~~~~
gbsrCalcProb.cpp:74:22: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
74 | if(h == ploidy){
| ~~^~~~~~~~~
gbsrCalcProb.cpp:87:29: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
87 | } else if(h == ploidy){
| ~~^~~~~~~~~
gbsrCalcProb.cpp:127:29: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
127 | } else if(g == ploidy){
| ~~^~~~~~~~~
gbsrCalcProb.cpp: In function ‘void offsetProb(std::vector<double>&, const bool&, const int&)’:
gbsrCalcProb.cpp:170:28: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
170 | if(g == 0 && g == ploidy){
| ~~^~~~~~~~~
gbsrCalcProb.cpp:185:32: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
185 | if(g == 0 && g == ploidy){
| ~~^~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c gbsrFB.cpp -o gbsrFB.o
gbsrFB.cpp: In member function ‘virtual void ParFB::operator()(size_t, size_t)’:
gbsrFB.cpp:109:17: warning: ‘hap_offset_ij’ may be used uninitialized [-Wmaybe-uninitialized]
109 | int hap_offset_ij;
| ^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c gbsrIPO.cpp -o gbsrIPO.o
gbsrIPO.cpp: In member function ‘virtual void ParGenoProb::operator()(size_t, size_t)’:
gbsrIPO.cpp:57:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
57 | for(int g = 0; g < prob.size(); ++g){
| ~~^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c gbsrStats.cpp -o gbsrStats.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c gbsrViterbi.cpp -o gbsrViterbi.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c gbsrutil.cpp -o gbsrutil.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o GBScleanR.so RcppExports.o gbsrCalcProb.o gbsrFB.o gbsrIPO.o gbsrStats.o gbsrViterbi.o gbsrutil.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/site-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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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 '/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/sample203adb2336075e.gds' (95.5K)
# of fragments: 69
save to '/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/sample203adb2336075e.gds.tmp'
rename '/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/sample203adb2336075e.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 '/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/sample203adb6a627ae2.gds' (95.5K)
# of fragments: 69
save to '/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/sample203adb6a627ae2.gds.tmp'
rename '/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/sample203adb6a627ae2.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 '/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/sample203adb19aaa950.gds' (95.5K)
# of fragments: 69
save to '/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/sample203adb19aaa950.gds.tmp'
rename '/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/sample203adb19aaa950.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.
Fri Dec 20 00:04:50 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:
/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/sample203adbd568093.gds
[Progress Info: sample203adbd568093.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.
Fri Dec 20 00:04:50 2024
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file '/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/sample203adbd568093.gds' (53.4K)
# of fragments: 108
save to '/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/sample203adbd568093.gds.tmp'
rename '/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/sample203adbd568093.gds.tmp' (52.8K, reduced: 648B)
# of fragments: 54
Fri Dec 20 00:04:50 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 '/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/sample203adbd568093.gds' (95.5K)
# of fragments: 69
save to '/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/sample203adbd568093.gds.tmp'
rename '/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/sample203adbd568093.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 '/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/sample203adb436e1924.gds' (95.5K)
# of fragments: 69
save to '/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/sample203adb436e1924.gds.tmp'
rename '/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/sample203adb436e1924.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.
Fri Dec 20 00:04:59 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:
/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/sample203adb594923c6.gds
[Progress Info: sample203adb594923c6.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.
Fri Dec 20 00:04:59 2024
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file '/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/sample203adb594923c6.gds' (53.4K)
# of fragments: 108
save to '/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/sample203adb594923c6.gds.tmp'
rename '/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/sample203adb594923c6.gds.tmp' (52.8K, reduced: 648B)
# of fragments: 54
Fri Dec 20 00:04:59 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 '/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/sample203adb594923c6.gds' (95.5K)
# of fragments: 69
save to '/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/sample203adb594923c6.gds.tmp'
rename '/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/sample203adb594923c6.gds.tmp' (95.4K, reduced: 108B)
# of fragments: 60
No parents info.
Fri Dec 20 00:04:59 2024
Variant Call Format (VCF) Import:
file:
out203adb25bd104f.vcf (56.6K)
file format: VCFv4.2
genome reference: <unknown>
# of sets of chromosomes (ploidy): 2
# of samples: 50
genotype field: GT
genotype storage: bit2
compression method: customized
# of samples: 50
INFO:
FORMAT: AD
Output:
/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/newgds203adb5b33c535.gds
[Progress Info: newgds203adb5b33c535.gds.progress]
Parsing 'out203adb25bd104f.vcf':
+ genotype/data { Bit2 2x50x125 ZIP_ra, 16B }
Digests:
sample.id [md5: dbfa9e1f51af97362002af9ddd4a7ee3]
variant.id [md5: e224d154ade7b77f5c001fd9ae402636]
position [md5: 42547bba07ae58f577ab48776a948003]
chromosome [md5: 4b6f25096f2be9c0479e767d280aaa7a]
allele [md5: ff9096d595e2d9e45381071baad53dff]
genotype [md5: 3c7596ff425f01ebe9754186602f5b99]
phase [md5: 67c9c7bcfca2b666e6e418abdf87354f]
annotation/id [md5: 3bfb43e6bee0feae6e1a869fa28c84ff]
annotation/qual [md5: 8340755cf0c41a4e948c24d0689a2835]
annotation/filter [md5: 45b25adf91dec06a92aa44cb05c33cd6]
annotation/format/AD [md5: ccc83414688ae020f38019977161d634]
Done.
Fri Dec 20 00:04:59 2024
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file '/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/newgds203adb5b33c535.gds' (19.9K)
# of fragments: 107
save to '/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/newgds203adb5b33c535.gds.tmp'
rename '/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/newgds203adb5b33c535.gds.tmp' (19.3K, reduced: 636B)
# of fragments: 54
Fri Dec 20 00:04:59 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 '/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/newgds203adb5b33c535.gds' (30.9K)
# of fragments: 69
save to '/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/newgds203adb5b33c535.gds.tmp'
rename '/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/newgds203adb5b33c535.gds.tmp' (30.8K, reduced: 108B)
# of fragments: 60
No parents info.
Fri Dec 20 00:04:59 2024
Variant Call Format (VCF) Import:
file:
out203adb66784d24.vcf (107.0K)
file format: VCFv4.2
genome reference: <unknown>
# of sets of chromosomes (ploidy): 2
# of samples: 50
genotype field: GT
genotype storage: bit2
compression method: customized
# of samples: 50
INFO:
FORMAT: AD,FAD,FGT
Output:
/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/newgds203adb1f9c14e7.gds
[Progress Info: newgds203adb1f9c14e7.gds.progress]
Parsing 'out203adb66784d24.vcf':
+ genotype/data { Bit2 2x50x125 ZIP_ra, 16B }
Digests:
sample.id [md5: dbfa9e1f51af97362002af9ddd4a7ee3]
variant.id [md5: e224d154ade7b77f5c001fd9ae402636]
position [md5: 42547bba07ae58f577ab48776a948003]
chromosome [md5: 4b6f25096f2be9c0479e767d280aaa7a]
allele [md5: ff9096d595e2d9e45381071baad53dff]
genotype [md5: 3c7596ff425f01ebe9754186602f5b99]
phase [md5: 67c9c7bcfca2b666e6e418abdf87354f]
annotation/id [md5: 3bfb43e6bee0feae6e1a869fa28c84ff]
annotation/qual [md5: 8340755cf0c41a4e948c24d0689a2835]
annotation/filter [md5: 45b25adf91dec06a92aa44cb05c33cd6]
annotation/format/AD [md5: ccc83414688ae020f38019977161d634]
annotation/format/FAD [md5: 73e02dfbc54ae24710c14470b6ed5b00]
annotation/format/FGT [md5: f9afea470effac87dc0f096bb0a98dc1]
Done.
Fri Dec 20 00:04:59 2024
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file '/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/newgds203adb1f9c14e7.gds' (28.9K)
# of fragments: 129
save to '/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/newgds203adb1f9c14e7.gds.tmp'
rename '/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/newgds203adb1f9c14e7.gds.tmp' (28.1K, reduced: 780B)
# of fragments: 64
Fri Dec 20 00:04:59 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 '/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/newgds203adb1f9c14e7.gds' (49.7K)
# of fragments: 86
save to '/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/newgds203adb1f9c14e7.gds.tmp'
rename '/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/newgds203adb1f9c14e7.gds.tmp' (48.4K, reduced: 1.3K)
# 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 '/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/sample203adb4ab2d87b.gds' (95.5K)
# of fragments: 69
save to '/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/sample203adb4ab2d87b.gds.tmp'
rename '/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2d136i/sample203adb4ab2d87b.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
23.721 0.880 24.589
GBScleanR.Rcheck/GBScleanR-Ex.timings
| name | user | system | elapsed | |
| GbsrGenotypeData-class | 0.011 | 0.001 | 0.016 | |
| GbsrScheme-class | 0.009 | 0.001 | 0.010 | |
| addScheme | 0.005 | 0.003 | 0.008 | |
| assignScheme | 0.071 | 0.014 | 0.085 | |
| boxplotGBSR | 0.702 | 0.029 | 0.730 | |
| closeGDS | 0.003 | 0.002 | 0.004 | |
| countGenotype | 0.589 | 0.037 | 0.626 | |
| countRead | 0.612 | 0.047 | 0.659 | |
| estGeno | 1.730 | 0.031 | 1.762 | |
| gbsrGDS2CSV | 0.027 | 0.000 | 0.027 | |
| gbsrGDS2VCF | 0.004 | 0.000 | 0.004 | |
| gbsrVCF2GDS | 0.068 | 0.009 | 0.078 | |
| getAllele | 0.004 | 0.000 | 0.004 | |
| getChromosome | 0.004 | 0.001 | 0.004 | |
| getCountAlleleAlt | 0.365 | 0.060 | 0.425 | |
| getCountAlleleMissing | 0.360 | 0.001 | 0.361 | |
| getCountAlleleRef | 0.366 | 0.001 | 0.367 | |
| getCountGenoAlt | 0.358 | 0.000 | 0.358 | |
| getCountGenoHet | 0.367 | 0.039 | 0.406 | |
| getCountGenoMissing | 0.346 | 0.001 | 0.347 | |
| getCountGenoRef | 0.357 | 0.000 | 0.357 | |
| getCountRead | 0.363 | 0.003 | 0.367 | |
| getCountReadAlt | 0.359 | 0.000 | 0.358 | |
| getCountReadRef | 0.360 | 0.001 | 0.361 | |
| getFixedBias | 0.062 | 0.005 | 0.068 | |
| getGenotype | 0.029 | 0.000 | 0.030 | |
| getHaplotype | 2.058 | 0.071 | 2.128 | |
| getInfo | 0.003 | 0.001 | 0.004 | |
| getMAC | 0.353 | 0.000 | 0.354 | |
| getMAF | 0.365 | 0.001 | 0.366 | |
| getMarID | 0.003 | 0.001 | 0.005 | |
| getMeanReadAlt | 0.370 | 0.042 | 0.413 | |
| getMeanReadRef | 0.352 | 0.002 | 0.354 | |
| getMedianReadAlt | 0.353 | 0.001 | 0.355 | |
| getMedianReadRef | 0.369 | 0.001 | 0.370 | |
| getParents | 0.006 | 0.001 | 0.007 | |
| getPosition | 0.003 | 0.001 | 0.004 | |
| getRead | 0.006 | 0.000 | 0.006 | |
| getReplicates | 0.004 | 0.001 | 0.005 | |
| getSDReadAlt | 0.349 | 0.003 | 0.352 | |
| getSDReadRef | 0.358 | 0.000 | 0.358 | |
| getSamID | 0.003 | 0.002 | 0.004 | |
| histGBSR | 0.561 | 0.000 | 0.560 | |
| initScheme | 0.005 | 0.001 | 0.006 | |
| isOpenGDS | 0.004 | 0.001 | 0.005 | |
| loadGDS | 0.067 | 0.004 | 0.071 | |
| makeScheme | 0.007 | 0.000 | 0.007 | |
| nmar | 0.004 | 0.000 | 0.004 | |
| nsam | 0.003 | 0.001 | 0.004 | |
| pairsGBSR | 0.477 | 0.003 | 0.480 | |
| plotDosage | 0.202 | 0.004 | 0.207 | |
| plotGBSR | 0.534 | 0.057 | 0.590 | |
| plotReadRatio | 0.168 | 0.002 | 0.169 | |
| reopenGDS | 0.005 | 0.001 | 0.006 | |
| resetCallFilter | 0.450 | 0.015 | 0.464 | |
| resetFilter | 1.163 | 0.006 | 1.169 | |
| resetMarFilter | 0.718 | 0.044 | 0.762 | |
| resetSamFilter | 0.788 | 0.006 | 0.793 | |
| setCallFilter | 0.838 | 0.015 | 0.853 | |
| setFixedBias | 0.064 | 0.002 | 0.066 | |
| setInfoFilter | 0.004 | 0.000 | 0.005 | |
| setMarFilter | 0.708 | 0.001 | 0.709 | |
| setParents | 1.687 | 0.009 | 1.696 | |
| setReplicates | 0.004 | 0.001 | 0.005 | |
| setSamFilter | 0.716 | 0.000 | 0.716 | |
| showScheme | 0.005 | 0.001 | 0.006 | |
| thinMarker | 0.355 | 0.001 | 0.356 | |
| validMar | 0.003 | 0.001 | 0.004 | |
| validSam | 0.002 | 0.001 | 0.003 | |