| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:33 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 704/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GBScleanR 0.99.35 (landing page) Tomoyuki Furuta
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
| Package: GBScleanR |
| Version: 0.99.35 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GBScleanR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings GBScleanR_0.99.35.tar.gz |
| StartedAt: 2022-03-17 19:08:43 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:11:58 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 195.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: GBScleanR.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GBScleanR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings GBScleanR_0.99.35.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/GBScleanR.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GBScleanR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GBScleanR' version '0.99.35'
* 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 ... 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 ... NOTE
gbsrGDS2CSV,GbsrGenotypeData: no visible global function definition for
'write.table'
gbsrGDS2CSV,GbsrGenotypeData: no visible binding for global variable
'gds'
Undefined global functions or variables:
gds write.table
Consider adding
importFrom("utils", "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'gbsrGDS2CSV':
gbsrGDS2CSV
Code: function(object, out_fn, node = "raw", incl_parents = TRUE,
bp2cm = NULL, format = "", read = FALSE, ...)
Docs: function(object, out_fn, node = "raw", incl_parents = TRUE,
bp2cm = NULL, format = "", ...)
Argument names in code not in docs:
read
Mismatches in argument names:
Position: 7 Code: read Docs: ...
* 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 for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/GBScleanR/libs/x64/GBScleanR.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (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. 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 ... ERROR
Running examples in 'GBScleanR-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gbsrGDS2VCF
> ### Title: Write a VCF file based on data in a GDS file
> ### Aliases: gbsrGDS2VCF gbsrGDS2VCF,GbsrGenotypeData-method
>
> ### ** Examples
>
> # Load data in the GDS file and instantiate a [GbsrGenotypeData] object.
> gds_fn <- system.file("extdata", "sample.gds", package = "GBScleanR")
> gds <- loadGDS(gds_fn)
Loading GDS file.
Error in openfn.gds(x, FALSE) :
The file 'D:\biocbuild\bbs-3.15-bioc\R\library\GBScleanR\extdata\sample.gds' has been created or opened.
Calls: loadGDS -> openfn.gds
Execution halted
* 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: 1 ERROR, 1 WARNING, 3 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/GBScleanR.Rcheck/00check.log'
for details.
GBScleanR.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL GBScleanR
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'GBScleanR' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c GBSR_HMM.cpp -o GBSR_HMM.o
GBSR_HMM.cpp: In function 'std::vector<double> calcGenoprob(const double&, const double&, const double&, const double&, const double&, const double&, const int&)':
GBSR_HMM.cpp:206:16: warning: 'sum_prob' may be used uninitialized in this function [-Wmaybe-uninitialized]
sum_prob += prob[g];
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c RcppExports.cpp -o RcppExports.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o GBScleanR.dll tmp.def GBSR_HMM.o RcppExports.o -LD:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-GBScleanR/00new/GBScleanR/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'GBScleanR'
finding HTML links ... done
GBScleanR html
GbsrGenotypeData-class html
finding level-2 HTML links ... done
GbsrScheme-class html
addScan html
addScheme html
boxplotGBSR html
calcReadStats html
closeGDS html
countGenotype html
countRead html
estGeno html
gbsrGDS2CSV html
gbsrGDS2VCF html
gbsrVCF2GDS html
getAlleleA html
getAlleleB html
getChromosome html
getCountAlleleAlt html
getCountAlleleMissing html
getCountAlleleRef html
getCountGenoAlt html
getCountGenoHet html
getCountGenoMissing html
getCountGenoRef html
getCountRead html
getCountReadAlt html
getCountReadRef html
getFlipped html
getGenotype html
getHaplotype html
getInfo html
getMAC html
getMAF html
getMeanReadAlt html
getMeanReadRef html
getParents html
getPloidy html
getPosition html
getQtileReadAlt html
getQtileReadRef html
getRead html
getSDReadAlt html
getSDReadRef html
getScanID html
getSnpID html
getValidScan html
getValidSnp html
hasFlipped html
histGBSR html
initScheme html
isOpenGDS html
loadGDS html
loadScanAnnot html
loadSnpAnnot html
nscan html
nsnp html
openGDS html
pairsGBSR html
plotDosage html
plotGBSR html
plotReadRatio html
resetFilters html
resetScanFilters html
resetSnpFilters html
saveScanAnnot html
saveSnpAnnot html
setCallFilter html
setFiltGenotype html
setInfoFilter html
setParents html
setRawGenotype html
setScanFilter html
setSnpFilter html
setValidScan html
setValidSnp html
showScheme html
subsetGDS html
thinMarker html
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'staRank' is missing or broken
done
GBScleanR.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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)
>
> test_check("GBScleanR")
Loading GDS file.
Loading GDS file.
Loading GDS file.
Loading GDS file.
Set the number of threads: 40
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!
Loading GDS file.
Loading GDS file.
No data of flipped genotype markers.
Loading GDS file.
Check flipped markers.
Check flipped markers.
Check flipped markers.
Check flipped markers.
Loading GDS file.
Loading GDS file.
Loading GDS file.
Thu Mar 17 19:11:43 2022
Variant Call Format (VCF) Import:
file(s):
out3c9c241a3c2b.vcf (266.1K)
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:
D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpsJOCv2\file3c9c15d61f0egds
Parsing 'out3c9c241a3c2b.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: 35757de0572d72a4ddd02236fe6ba25e]
Done.
Thu Mar 17 19:11:43 2022
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpsJOCv2\file3c9c15d61f0egds' (49.8K)
# of fragments: 107
save to 'D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpsJOCv2\file3c9c15d61f0egds.tmp'
rename 'D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpsJOCv2\file3c9c15d61f0egds.tmp' (49.2K, reduced: 636B)
# of fragments: 54
Thu Mar 17 19:11:43 2022
Reformatting genotype data.
Thu Mar 17 19:11:43 2022
SeqArray GDS to SNP GDS format:
# of samples: 102
# of variants: 242
genotype compression: LZMA_RA
annotation compression: LZMA_RA
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Done.
Thu Mar 17 19:11:43 2022
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpsJOCv2\newgds3c9c24456295.gds' (9.6K)
# of fragments: 31
save to 'D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpsJOCv2\newgds3c9c24456295.gds.tmp'
rename 'D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpsJOCv2\newgds3c9c24456295.gds.tmp' (9.4K, reduced: 192B)
# of fragments: 15
Thu Mar 17 19:11:43 2022
Loading GDS file.
Thu Mar 17 19:11:44 2022
Variant Call Format (VCF) Import:
file(s):
out3c9c214b4825.vcf (70.6K)
file format: VCFv4.2
genome reference: <unknown>
the number of sets of chromosomes (ploidy): 2
the number of samples: 51
genotype storage: bit2
compression method: customized
# of samples: 51
Output:
D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpsJOCv2\file3c9c24ed5e3fgds
Parsing 'out3c9c214b4825.vcf':
+ genotype/data { Bit2 2x51x123 ZIP_ra, 16B }
Digests:
sample.id [md5: ac1938f9641a66031291196d7ca4dc1d]
variant.id [md5: 5a4e8bfc1e37fcd1800d6ca6831cbd4e]
position [md5: c1fcac5c052726c7053819cbb2816a8d]
chromosome [md5: f6bfc37d611c76b81e9d7b504bb3162c]
allele [md5: 09532742b0f4c374e773d5b891853613]
genotype [md5: 2ee71c6b008a5543d639f3522f53e50e]
phase [md5: f6a7a580c720bf064f3ac4fd112039e6]
annotation/id [md5: a9e0a5e7748b6d9c9d71d136dd4e8948]
annotation/qual [md5: aba5ad5b4581d374c611cfab79690308]
annotation/filter [md5: eb14a330fb0decef5fabef1ce0f58772]
annotation/format/AD [md5: d55e5dc3f0c3e7d45b73fded6a376a96]
Done.
Thu Mar 17 19:11:44 2022
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpsJOCv2\file3c9c24ed5e3fgds' (18.9K)
# of fragments: 107
save to 'D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpsJOCv2\file3c9c24ed5e3fgds.tmp'
rename 'D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpsJOCv2\file3c9c24ed5e3fgds.tmp' (18.3K, reduced: 636B)
# of fragments: 54
Thu Mar 17 19:11:44 2022
Reformatting genotype data.
Thu Mar 17 19:11:44 2022
SeqArray GDS to SNP GDS format:
# of samples: 51
# of variants: 123
genotype compression: LZMA_RA
annotation compression: LZMA_RA
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Done.
Thu Mar 17 19:11:44 2022
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpsJOCv2\newgds3c9c421025af.gds' (5.0K)
# of fragments: 31
save to 'D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpsJOCv2\newgds3c9c421025af.gds.tmp'
rename 'D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpsJOCv2\newgds3c9c421025af.gds.tmp' (4.9K, reduced: 192B)
# of fragments: 15
Thu Mar 17 19:11:44 2022
Loading GDS file.
Thu Mar 17 19:11:46 2022
Variant Call Format (VCF) Import:
file(s):
out3c9c404c2de6.vcf (68.6K)
file format: VCFv4.2
genome reference: <unknown>
the number of sets of chromosomes (ploidy): 2
the number of samples: 51
genotype storage: bit2
compression method: customized
# of samples: 51
Output:
D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpsJOCv2\file3c9c6d754662gds
Parsing 'out3c9c404c2de6.vcf':
+ genotype/data { Bit2 2x51x123 ZIP_ra, 16B }
Digests:
sample.id [md5: ac1938f9641a66031291196d7ca4dc1d]
variant.id [md5: 5a4e8bfc1e37fcd1800d6ca6831cbd4e]
position [md5: c1fcac5c052726c7053819cbb2816a8d]
chromosome [md5: f6bfc37d611c76b81e9d7b504bb3162c]
allele [md5: 09532742b0f4c374e773d5b891853613]
genotype [md5: 77e269cda239c1827255d7f27f563649]
phase [md5: f6a7a580c720bf064f3ac4fd112039e6]
annotation/id [md5: a9e0a5e7748b6d9c9d71d136dd4e8948]
annotation/qual [md5: aba5ad5b4581d374c611cfab79690308]
annotation/filter [md5: eb14a330fb0decef5fabef1ce0f58772]
annotation/format/AD [md5: af13dad063f62a01298870c7aab37bad]
Done.
Thu Mar 17 19:11:46 2022
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpsJOCv2\file3c9c6d754662gds' (17.2K)
# of fragments: 107
save to 'D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpsJOCv2\file3c9c6d754662gds.tmp'
rename 'D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpsJOCv2\file3c9c6d754662gds.tmp' (16.6K, reduced: 636B)
# of fragments: 54
Thu Mar 17 19:11:46 2022
Reformatting genotype data.
Thu Mar 17 19:11:46 2022
SeqArray GDS to SNP GDS format:
# of samples: 51
# of variants: 123
genotype compression: LZMA_RA
annotation compression: LZMA_RA
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Done.
Thu Mar 17 19:11:46 2022
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpsJOCv2\newgds3c9c3289fd0.gds' (5.1K)
# of fragments: 31
save to 'D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpsJOCv2\newgds3c9c3289fd0.gds.tmp'
rename 'D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpsJOCv2\newgds3c9c3289fd0.gds.tmp' (4.9K, reduced: 192B)
# of fragments: 15
Thu Mar 17 19:11:46 2022
Loading GDS file.
[ FAIL 0 | WARN 39 | SKIP 0 | PASS 349 ]
[ FAIL 0 | WARN 39 | SKIP 0 | PASS 349 ]
>
> proc.time()
user system elapsed
53.62 6.98 36.90
GBScleanR.Rcheck/GBScleanR-Ex.timings
| name | user | system | elapsed | |
| GbsrGenotypeData-class | 0.11 | 0.09 | 0.21 | |
| GbsrScheme-class | 0.11 | 0.10 | 0.25 | |
| addScan | 0.28 | 0.15 | 0.44 | |
| addScheme | 0.16 | 0.10 | 0.25 | |
| boxplotGBSR | 1.66 | 0.23 | 1.94 | |
| calcReadStats | 1.69 | 0.27 | 2.22 | |
| closeGDS | 0.41 | 0.11 | 0.52 | |
| countGenotype | 0.65 | 0.19 | 0.84 | |
| countRead | 0.55 | 0.09 | 0.66 | |
| estGeno | 28.58 | 1.17 | 2.42 | |
| gbsrGDS2CSV | 0.26 | 0.16 | 0.48 | |