Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:05 -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: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GBScleanR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GBScleanR_2.0.2.tar.gz |
StartedAt: 2024-12-20 01:44:06 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 01:48:20 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 253.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GBScleanR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GBScleanR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GBScleanR_2.0.2.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/GBScleanR.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * 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 ... 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 * used C++ compiler: 'G__~1.EXE (GCC) 13.3.0' * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... 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 for x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/GBScleanR/libs/x64/GBScleanR.dll': Found '_exit', possibly from '_exit' (C) 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 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/GBScleanR.Rcheck/00check.log' for details.
GBScleanR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL GBScleanR ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'GBScleanR' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 13.3.0' using C++11 g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppParallel/include' -I"C:/rtools44/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-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppParallel/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 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 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 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 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 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 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 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 long unsigned int'} and 'const int' [-Wsign-compare] 185 | if(g == 0 && g == ploidy){ | ~~^~~~~~~~~ g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppParallel/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppParallel/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 long unsigned int'} [-Wsign-compare] 57 | for(int g = 0; g < prob.size(); ++g){ | ~~^~~~~~~~~~~~~ g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppParallel/include' -I"C:/rtools44/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-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppParallel/include' -I"C:/rtools44/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-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppParallel/include' -I"C:/rtools44/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-3.20-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-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
R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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-3.20-bioc\tmpdir\RtmpmABXA1\sample1b8fcf523f15.gds' (95.5K) # of fragments: 69 save to 'F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpmABXA1\sample1b8fcf523f15.gds.tmp' rename 'F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpmABXA1\sample1b8fcf523f15.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-3.20-bioc\tmpdir\RtmpmABXA1\sample1b8fc1bfc772b.gds' (95.5K) # of fragments: 69 save to 'F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpmABXA1\sample1b8fc1bfc772b.gds.tmp' rename 'F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpmABXA1\sample1b8fc1bfc772b.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 'F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpmABXA1\sample1b8fc215a2b33.gds' (95.5K) # of fragments: 69 save to 'F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpmABXA1\sample1b8fc215a2b33.gds.tmp' rename 'F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpmABXA1\sample1b8fc215a2b33.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 01:47:37 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: F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpmABXA1\sample1b8fc7ac9571b.gds [Progress Info: sample1b8fc7ac9571b.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 01:47:38 2024 Optimize the access efficiency ... Clean up the fragments of GDS file: open the file 'F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpmABXA1\sample1b8fc7ac9571b.gds' (53.4K) # of fragments: 108 save to 'F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpmABXA1\sample1b8fc7ac9571b.gds.tmp' rename 'F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpmABXA1\sample1b8fc7ac9571b.gds.tmp' (52.8K, reduced: 648B) # of fragments: 54 Fri Dec 20 01:47:38 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 'F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpmABXA1\sample1b8fc7ac9571b.gds' (95.5K) # of fragments: 69 save to 'F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpmABXA1\sample1b8fc7ac9571b.gds.tmp' rename 'F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpmABXA1\sample1b8fc7ac9571b.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-3.20-bioc\tmpdir\RtmpmABXA1\sample1b8fc2cdc545.gds' (95.5K) # of fragments: 69 save to 'F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpmABXA1\sample1b8fc2cdc545.gds.tmp' rename 'F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpmABXA1\sample1b8fc2cdc545.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. 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-3.20-bioc\tmpdir\RtmpmABXA1\sample1b8fc407c4857.gds' (95.5K) # of fragments: 69 save to 'F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpmABXA1\sample1b8fc407c4857.gds.tmp' rename 'F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpmABXA1\sample1b8fc407c4857.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 1 | PASS 263 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'test_06_gds2vcf.R:1:1' [ FAIL 0 | WARN 0 | SKIP 1 | PASS 263 ] > > proc.time() user system elapsed 31.85 1.20 35.75
GBScleanR.Rcheck/GBScleanR-Ex.timings
name | user | system | elapsed | |
GbsrGenotypeData-class | 0.00 | 0.00 | 0.01 | |
GbsrScheme-class | 0.01 | 0.00 | 0.02 | |
addScheme | 0.00 | 0.00 | 0.02 | |
assignScheme | 0.13 | 0.00 | 0.14 | |
boxplotGBSR | 0.97 | 0.03 | 1.00 | |
closeGDS | 0.03 | 0.00 | 0.03 | |
countGenotype | 0.86 | 0.00 | 0.86 | |
countRead | 0.81 | 0.00 | 0.84 | |
estGeno | 2.78 | 0.08 | 2.99 | |
gbsrGDS2CSV | 0.09 | 0.00 | 0.09 | |
gbsrGDS2VCF | 0.01 | 0.01 | 0.04 | |
gbsrVCF2GDS | 0.16 | 0.00 | 0.28 | |
getAllele | 0 | 0 | 0 | |
getChromosome | 0.01 | 0.00 | 0.02 | |
getCountAlleleAlt | 0.50 | 0.02 | 0.51 | |
getCountAlleleMissing | 0.52 | 0.00 | 0.54 | |
getCountAlleleRef | 0.48 | 0.00 | 0.50 | |
getCountGenoAlt | 0.47 | 0.00 | 0.48 | |
getCountGenoHet | 0.47 | 0.00 | 0.47 | |
getCountGenoMissing | 0.5 | 0.0 | 0.5 | |
getCountGenoRef | 0.48 | 0.00 | 0.50 | |
getCountRead | 0.50 | 0.00 | 0.51 | |
getCountReadAlt | 0.49 | 0.00 | 0.50 | |
getCountReadRef | 0.53 | 0.00 | 0.53 | |
getFixedBias | 0.11 | 0.04 | 0.25 | |
getGenotype | 0.03 | 0.00 | 0.03 | |
getHaplotype | 2.84 | 0.06 | 2.99 | |
getInfo | 0.02 | 0.00 | 0.02 | |
getMAC | 0.48 | 0.00 | 0.50 | |
getMAF | 0.52 | 0.01 | 0.53 | |
getMarID | 0.01 | 0.00 | 0.03 | |
getMeanReadAlt | 0.52 | 0.00 | 0.52 | |
getMeanReadRef | 0.5 | 0.0 | 0.5 | |
getMedianReadAlt | 0.51 | 0.02 | 0.53 | |
getMedianReadRef | 0.46 | 0.00 | 0.47 | |
getParents | 0.00 | 0.02 | 0.03 | |
getPosition | 0.01 | 0.00 | 0.01 | |
getRead | 0.00 | 0.00 | 0.02 | |
getReplicates | 0.02 | 0.00 | 0.03 | |
getSDReadAlt | 0.47 | 0.01 | 0.48 | |
getSDReadRef | 0.45 | 0.00 | 0.49 | |
getSamID | 0.00 | 0.00 | 0.01 | |
histGBSR | 0.86 | 0.00 | 0.89 | |
initScheme | 0.02 | 0.00 | 0.06 | |
isOpenGDS | 0.01 | 0.00 | 0.07 | |
loadGDS | 0.08 | 0.02 | 0.56 | |
makeScheme | 0 | 0 | 0 | |
nmar | 0.00 | 0.00 | 0.11 | |
nsam | 0.00 | 0.00 | 0.07 | |
pairsGBSR | 0.60 | 0.00 | 0.62 | |
plotDosage | 0.23 | 0.00 | 0.28 | |
plotGBSR | 0.61 | 0.00 | 0.64 | |
plotReadRatio | 0.27 | 0.00 | 0.30 | |
reopenGDS | 0.01 | 0.00 | 0.17 | |
resetCallFilter | 0.61 | 0.05 | 1.47 | |
resetFilter | 1.58 | 0.05 | 2.14 | |
resetMarFilter | 0.98 | 0.00 | 0.98 | |
resetSamFilter | 1.10 | 0.01 | 1.61 | |
setCallFilter | 1.17 | 0.06 | 1.69 | |
setFixedBias | 0.08 | 0.04 | 0.22 | |
setInfoFilter | 0 | 0 | 0 | |
setMarFilter | 1.07 | 0.00 | 1.07 | |
setParents | 2.89 | 0.06 | 3.03 | |
setReplicates | 0.00 | 0.00 | 0.02 | |
setSamFilter | 1.06 | 0.01 | 1.07 | |
showScheme | 0.00 | 0.00 | 0.02 | |
thinMarker | 0.52 | 0.00 | 0.53 | |
validMar | 0.02 | 0.00 | 0.03 | |
validSam | 0.00 | 0.00 | 0.01 | |