Tomoyuki Furuta
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/GBScleanR |
| git_branch: RELEASE_3_16 |
| git_last_commit: 48ea0c3 |
| git_last_commit_date: 2023-04-06 03:59:09 -0400 (Thu, 06 Apr 2023) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:33 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 737/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GBScleanR 1.2.14 (landing page) Tomoyuki Furuta
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: GBScleanR |
| Version: 1.2.14 |
| Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GBScleanR.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings GBScleanR_1.2.14.tar.gz |
| StartedAt: 2023-04-11 01:41:08 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 01:44:10 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 182.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: GBScleanR.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GBScleanR.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings GBScleanR_1.2.14.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/GBScleanR.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (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 '1.2.14'
* 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 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 ... WARNING
Invalid citation information in 'inst/CITATION':
Error in parse(con): 12:3: unexpected symbol
11: doi = "10.1093/genetics/iyad055"
12: volume
^
* 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 ... NOTE
.getJnum: no visible binding for global variable 'head'
Undefined global functions or variables:
head
Consider adding
importFrom("utils", "head")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'assignScheme.Rd':
'asignScheme'
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'initScheme':
'crosstype'
Undocumented arguments in documentation object 'showScheme'
'pedigree'
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 for x64 is not available
File 'F:/biocbuild/bbs-3.16-bioc/R/library/GBScleanR/libs/x64/GBScleanR.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
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. 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'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_06_gds2vcf.R:28:5'): gbsrGDS2VCF ───────────────────────────────
Error in `openfn.gds(gds.fn, readonly = readonly, allow.fork = TRUE, allow.duplicate = allow.duplicate)`: Stream Read Error, need 12 byte(s) but receive 0
Backtrace:
▆
1. ├─GBScleanR::gbsrGDS2VCF(gds, out_fn) at test_06_gds2vcf.R:28:4
2. └─GBScleanR::gbsrGDS2VCF(gds, out_fn)
3. └─GBScleanR (local) .local(object, out_fn, parents, ...)
4. └─GBScleanR:::.modGDS(object, check)
5. └─SeqArray::seqOpen(tmp_gds, FALSE)
6. └─gdsfmt::openfn.gds(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 267 ]
Error: Test failures
Execution halted
* 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: 1 ERROR, 3 WARNINGs, 3 NOTEs
See
'F:/biocbuild/bbs-3.16-bioc/meat/GBScleanR.Rcheck/00check.log'
for details.
GBScleanR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL GBScleanR ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library' * installing *source* package 'GBScleanR' ... ** using staged installation ** libs g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppParallel/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppParallel/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c gbsrCalcProb.cpp -o gbsrCalcProb.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppParallel/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c gbsrFB.cpp -o gbsrFB.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppParallel/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c gbsrIPO.cpp -o gbsrIPO.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppParallel/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c gbsrStats.cpp -o gbsrStats.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppParallel/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c gbsrViterbi.cpp -o gbsrViterbi.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppParallel/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c gbsrutil.cpp -o gbsrutil.o g++ -shared -s -static-libgcc -o GBScleanR.dll tmp.def RcppExports.o gbsrCalcProb.o gbsrFB.o gbsrIPO.o gbsrStats.o gbsrViterbi.o gbsrutil.o -LF:/biocbuild/bbs-3.16-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.16-bioc/R/library/00LOCK-GBScleanR/00new/GBScleanR/libs/x64 ** 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 ** 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.fail
R version 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 'F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpQbPG18\sample41dc7dc54214.gds' (95.5K)
# of fragments: 69
save to 'F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpQbPG18\sample41dc7dc54214.gds.tmp'
rename 'F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpQbPG18\sample41dc7dc54214.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 'F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpQbPG18\sample41dc14ba2d13.gds' (95.5K)
# of fragments: 69
save to 'F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpQbPG18\sample41dc14ba2d13.gds.tmp'
rename 'F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpQbPG18\sample41dc14ba2d13.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 'F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpQbPG18\sample41dc56ab6701.gds' (95.5K)
# of fragments: 69
save to 'F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpQbPG18\sample41dc56ab6701.gds.tmp'
rename 'F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpQbPG18\sample41dc56ab6701.gds.tmp' (95.4K, reduced: 108B)
# of fragments: 60
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Tue Apr 11 01:43:50 2023
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:
F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpQbPG18\sample41dc6aa5d9d.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.
Tue Apr 11 01:43:50 2023
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpQbPG18\sample41dc6aa5d9d.gds' (53.4K)
# of fragments: 108
save to 'F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpQbPG18\sample41dc6aa5d9d.gds.tmp'
rename 'F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpQbPG18\sample41dc6aa5d9d.gds.tmp' (52.8K, reduced: 648B)
# of fragments: 54
Tue Apr 11 01:43:50 2023
Loading GDS file.
Working on 'genotype' ...
Working on 'phase' ...
Working on 'annotation/format/AD' ...
Clean up the fragments of GDS file:
open the file 'F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpQbPG18\sample41dc6aa5d9d.gds' (95.5K)
# of fragments: 69
save to 'F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpQbPG18\sample41dc6aa5d9d.gds.tmp'
rename 'F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpQbPG18\sample41dc6aa5d9d.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 'F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpQbPG18\sample41dc4d4152e7.gds' (95.5K)
# of fragments: 69
save to 'F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpQbPG18\sample41dc4d4152e7.gds.tmp'
rename 'F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpQbPG18\sample41dc4d4152e7.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.
Tue Apr 11 01:43:55 2023
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:
F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpQbPG18\sample41dc6c17143.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.
Tue Apr 11 01:43:55 2023
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpQbPG18\sample41dc6c17143.gds' (53.4K)
# of fragments: 108
save to 'F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpQbPG18\sample41dc6c17143.gds.tmp'
rename 'F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpQbPG18\sample41dc6c17143.gds.tmp' (52.8K, reduced: 648B)
# of fragments: 54
Tue Apr 11 01:43:55 2023
Loading GDS file.
Working on 'genotype' ...
Working on 'phase' ...
Working on 'annotation/format/AD' ...
Clean up the fragments of GDS file:
open the file 'F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpQbPG18\sample41dc6c17143.gds' (95.5K)
# of fragments: 69
save to 'F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpQbPG18\sample41dc6c17143.gds.tmp'
rename 'F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpQbPG18\sample41dc6c17143.gds.tmp' (95.4K, reduced: 108B)
# of fragments: 60
No parents info.
Tue Apr 11 01:43:55 2023
Variant Call Format (VCF) Import:
file(s):
out41dc64967cb2.vcf (64.0K)
file format: VCFv4.2
genome reference: <unknown>
the number of sets of chromosomes (ploidy): 2
the number of samples: 58
genotype storage: bit2
compression method: customized
# of samples: 58
Output:
F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpQbPG18\newgds41dcf897407.gds
Parsing 'out41dc64967cb2.vcf':
+ genotype/data { Bit2 2x58x124 ZIP_ra, 16B }
Digests:
sample.id [md5: e0f67186bb10274ad67f8433357a6aa5]
variant.id [md5: 43796264d31bd83842b0aa403fce0906]
position [md5: ad4acce439119981f454628c52a264eb]
chromosome [md5: 60b3fe36b6edd92bcd04f5335c4a669b]
allele [md5: 98550986e926885efb67f9e530491d9e]
genotype [md5: 74b30c4113cd4f4194e4cb191ad0bcfc]
phase [md5: 14a6d1b06bfc96e8b626b366289bbd8e]
annotation/id [md5: fd36da67f3d467c045dbb9816ccf1c9f]
annotation/qual [md5: 6cc8f26d6552e7eaab7c984d5ff4b83c]
annotation/filter [md5: aa5bfe55f7fbf2b12c60e9c055da37bf]
annotation/format/AD [md5: 04af664ea67e43951f13d1627b817e06]
Done.
Tue Apr 11 01:43:55 2023
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpQbPG18\newgds41dcf897407.gds' (21.8K)
# of fragments: 107
save to 'F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpQbPG18\newgds41dcf897407.gds.tmp'
rename 'F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpQbPG18\newgds41dcf897407.gds.tmp' (21.2K, reduced: 636B)
# of fragments: 54
Tue Apr 11 01:43:55 2023
Loading GDS file.
Working on 'genotype' ...
Working on 'phase' ...
Working on 'annotation/format/AD' ...
Clean up the fragments of GDS file:
open the file 'F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpQbPG18\newgds41dcf897407.gds' (34.5K)
# of fragments: 69
save to 'F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpQbPG18\newgds41dcf897407.gds.tmp'
rename 'F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpQbPG18\newgds41dcf897407.gds.tmp' (34.4K, reduced: 108B)
# of fragments: 60
No parents info.
Loading GDS file.
Working on 'genotype' ...
Working on 'phase' ...
Working on 'annotation/format/AD' ...
Clean up the fragments of GDS file:
open the file 'F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpQbPG18\sample41dc1aa930ec.gds' (95.5K)
# of fragments: 69
save to 'F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpQbPG18\sample41dc1aa930ec.gds.tmp'
rename 'F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpQbPG18\sample41dc1aa930ec.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...
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 1 | WARN 0 | SKIP 0 | PASS 267 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_06_gds2vcf.R:28:5'): gbsrGDS2VCF ───────────────────────────────
Error in `openfn.gds(gds.fn, readonly = readonly, allow.fork = TRUE, allow.duplicate = allow.duplicate)`: Stream Read Error, need 12 byte(s) but receive 0
Backtrace:
▆
1. ├─GBScleanR::gbsrGDS2VCF(gds, out_fn) at test_06_gds2vcf.R:28:4
2. └─GBScleanR::gbsrGDS2VCF(gds, out_fn)
3. └─GBScleanR (local) .local(object, out_fn, parents, ...)
4. └─GBScleanR:::.modGDS(object, check)
5. └─SeqArray::seqOpen(tmp_gds, FALSE)
6. └─gdsfmt::openfn.gds(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 267 ]
Error: Test failures
Execution halted
GBScleanR.Rcheck/GBScleanR-Ex.timings
| name | user | system | elapsed | |
| GbsrGenotypeData-class | 0.01 | 0.00 | 0.02 | |
| GbsrScheme-class | 0.05 | 0.00 | 0.04 | |
| addScheme | 0.04 | 0.00 | 0.08 | |
| assignScheme | 0.07 | 0.00 | 0.08 | |
| boxplotGBSR | 0.50 | 0.03 | 0.53 | |
| closeGDS | 0.00 | 0.00 | 0.02 | |
| countGenotype | 0.37 | 0.02 | 0.40 | |
| countRead | 0.27 | 0.00 | 0.27 | |
| estGeno | 1.87 | 0.06 | 1.98 | |
| gbsrGDS2CSV | 0.1 | 0.0 | 0.1 | |
| gbsrGDS2VCF | 0.01 | 0.00 | 0.01 | |
| gbsrVCF2GDS | 0.11 | 0.02 | 0.22 | |
| getAllele | 0.00 | 0.01 | 0.02 | |
| getChromosome | 0.02 | 0.00 | 0.01 | |
| getCountAlleleAlt | 0.01 | 0.00 | 0.02 | |
| getCountAlleleMissing | 0.00 | 0.00 | 0.01 | |
| getCountAlleleRef | 0.02 | 0.00 | 0.03 | |
| getCountGenoAlt | 0.01 | 0.00 | 0.02 | |
| getCountGenoHet | 0.04 | 0.00 | 0.03 | |
| getCountGenoMissing | 0.01 | 0.00 | 0.02 | |
| getCountGenoRef | 0.02 | 0.00 | 0.03 | |
| getCountRead | 0.04 | 0.00 | 0.04 | |
| getCountReadAlt | 0.02 | 0.00 | 0.02 | |
| getCountReadRef | 0.00 | 0.02 | 0.03 | |
| getGenotype | 0.05 | 0.00 | 0.05 | |
| getHaplotype | 1.42 | 0.00 | 1.45 | |
| getInfo | 0.01 | 0.00 | 0.02 | |
| getMAC | 0.03 | 0.01 | 0.04 | |
| getMAF | 0.02 | 0.00 | 0.02 | |
| getMarID | 0.02 | 0.00 | 0.01 | |
| getMeanReadAlt | 0.03 | 0.00 | 0.04 | |
| getMeanReadRef | 0.03 | 0.00 | 0.03 | |
| getMedianReadAlt | 0.01 | 0.00 | 0.03 | |
| getMedianReadRef | 0.02 | 0.00 | 0.03 | |
| getParents | 0.00 | 0.02 | 0.02 | |
| getPosition | 0.00 | 0.00 | 0.01 | |
| getRead | 0.02 | 0.00 | 0.02 | |
| getSDReadAlt | 0.03 | 0.00 | 0.03 | |
| getSDReadRef | 0.01 | 0.01 | 0.03 | |
| getSamID | 0 | 0 | 0 | |
| histGBSR | 0.25 | 0.00 | 0.25 | |
| initScheme | 0.02 | 0.00 | 0.02 | |
| isOpenGDS | 0 | 0 | 0 | |
| loadGDS | 0.08 | 0.01 | 0.20 | |
| nmar | 0.01 | 0.00 | 0.02 | |
| nsam | 0.02 | 0.00 | 0.01 | |
| pairsGBSR | 0.18 | 0.00 | 0.19 | |
| plotDosage | 0.21 | 0.00 | 0.21 | |
| plotGBSR | 0.22 | 0.00 | 0.51 | |
| plotReadRatio | 0.15 | 0.00 | 0.17 | |
| reopenGDS | 0.0 | 0.0 | 0.1 | |
| resetCallFilter | 0.38 | 0.19 | 0.67 | |
| resetFilter | 0.90 | 0.25 | 1.98 | |
| resetMarFilter | 0.03 | 0.00 | 0.03 | |
| resetSamFilter | 0.11 | 0.02 | 0.37 | |
| setCallFilter | 0.56 | 0.51 | 1.68 | |
| setInfoFilter | 0 | 0 | 0 | |
| setMarFilter | 0.02 | 0.01 | 0.05 | |
| setParents | 2.19 | 0.05 | 2.30 | |
| setSamFilter | 0.03 | 0.00 | 0.03 | |
| showScheme | 0.00 | 0.00 | 0.01 | |
| thinMarker | 0.01 | 0.00 | 0.03 | |
| validMar | 0.02 | 0.00 | 0.02 | |
| validSam | 0.01 | 0.00 | 0.02 | |