Xiuwen Zheng
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/SeqArray |
| Branch: RELEASE_3_8 |
| Last Commit: 585cb72 |
| Last Changed Date: 2019-03-10 01:42:10 -0400 (Sun, 10 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:22:44 -0400 (Sat, 13 Apr 2019).
| Package 1416/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SeqArray 1.22.6 Xiuwen Zheng
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | NA | |||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: SeqArray |
| Version: 1.22.6 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SeqArray.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings SeqArray_1.22.6.tar.gz |
| StartedAt: 2019-04-13 05:25:14 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 05:32:49 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 455.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SeqArray.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SeqArray.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings SeqArray_1.22.6.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/SeqArray.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SeqArray/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SeqArray' version '1.22.6'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'SeqArray' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/SeqArray/libs/i386/SeqArray.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
File 'SeqArray/libs/i386/SeqArray.dll':
Found non-API calls to R: 'R_GetConnection', 'R_ReadConnection',
'R_WriteConnection', 'R_new_custom_connection'
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.
Compiled code should not call non-API entry points in R.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
seqVCF2GDS 0.69 0.08 8.59
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
seqVCF2GDS 0.63 0.08 11.34
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'test.R'
OK
** running tests for arch 'x64' ...
Running 'test.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 NOTE
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/SeqArray.Rcheck/00check.log'
for details.
SeqArray.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/SeqArray_1.22.6.tar.gz && rm -rf SeqArray.buildbin-libdir && mkdir SeqArray.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SeqArray.buildbin-libdir SeqArray_1.22.6.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL SeqArray_1.22.6.zip && rm SeqArray_1.22.6.tar.gz SeqArray_1.22.6.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 1912k 100 1912k 0 0 28.3M 0 --:--:-- --:--:-- --:--:-- 30.1M
install for i386
* installing *source* package 'SeqArray' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c ConvToGDS.cpp -o ConvToGDS.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c FileMerge.cpp -o FileMerge.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c GetData.cpp -o GetData.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c Index.cpp -o Index.o
Index.cpp: In member function 'SeqArray::TSelection::TSampStruct* SeqArray::TSelection::GetStructSample()':
Index.cpp:658:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (num_samp*numPloidy != num)
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c LinkSNPRelate.cpp -o LinkSNPRelate.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c Methods.cpp -o Methods.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c R_SeqArray.c -o R_SeqArray.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c ReadBySample.cpp -o ReadBySample.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c ReadByVariant.cpp -o ReadByVariant.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c SeqArray.cpp -o SeqArray.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c pkg_test.cpp -o pkg_test.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c samtools_ext.c -o samtools_ext.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c vectorization.c -o vectorization.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o SeqArray.dll tmp.def ConvGDS2VCF.o ConvToGDS.o ConvVCF2GDS.o FileMerge.o GetData.o Index.o LinkSNPRelate.o Methods.o R_SeqArray.o ReadBySample.o ReadByVariant.o SeqArray.o pkg_test.o samtools_ext.o vectorization.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/SeqArray.buildbin-libdir/SeqArray/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'SeqArray'
finding HTML links ... done
KG_P1_SampData html
SeqArray-package html
SeqVarGDSClass-class html
finding level-2 HTML links ... done
seqAlleleFreq html
seqApply html
seqAsVCF html
seqBED2GDS html
seqBlockApply html
seqCheck html
seqClose html
seqDelete html
seqDigest html
seqExampleFileName html
seqExport html
seqGDS2SNP html
seqGDS2VCF html
seqGetData html
seqGetFilter html
seqMerge html
seqMissing html
seqNumAllele html
seqOpen html
seqOptimize html
seqParallel html
seqParallelSetup html
seqRecompress html
seqSNP2GDS html
seqSetFilter html
seqSetFilterCond html
seqStorageOption html
seqSummary html
seqSystem html
seqTranspose html
seqVCF2GDS html
seqVCF_Header html
seqVCF_SampID html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'SeqArray' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c ConvToGDS.cpp -o ConvToGDS.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c FileMerge.cpp -o FileMerge.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c GetData.cpp -o GetData.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c Index.cpp -o Index.o
Index.cpp: In member function 'SeqArray::TSelection::TSampStruct* SeqArray::TSelection::GetStructSample()':
Index.cpp:658:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (num_samp*numPloidy != num)
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c LinkSNPRelate.cpp -o LinkSNPRelate.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c Methods.cpp -o Methods.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c R_SeqArray.c -o R_SeqArray.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c ReadBySample.cpp -o ReadBySample.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c ReadByVariant.cpp -o ReadByVariant.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c SeqArray.cpp -o SeqArray.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c pkg_test.cpp -o pkg_test.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c samtools_ext.c -o samtools_ext.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -DUSING_R -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c vectorization.c -o vectorization.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o SeqArray.dll tmp.def ConvGDS2VCF.o ConvToGDS.o ConvVCF2GDS.o FileMerge.o GetData.o Index.o LinkSNPRelate.o Methods.o R_SeqArray.o ReadBySample.o ReadByVariant.o SeqArray.o pkg_test.o samtools_ext.o vectorization.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/SeqArray.buildbin-libdir/SeqArray/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SeqArray' as SeqArray_1.22.6.zip
* DONE (SeqArray)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'SeqArray' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
SeqArray.Rcheck/tests_i386/test.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.
> BiocGenerics:::testPackage("SeqArray")
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: GenomeInfoDb
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
The following object is masked from 'package:SeqArray':
rowRanges
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:SeqArray':
rowRanges
The following objects are masked from 'package:base':
aperm, apply
Attaching package: 'SummarizedExperiment'
The following object is masked from 'package:SeqArray':
colData
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:DelayedArray':
type
The following object is masked from 'package:base':
strsplit
Attaching package: 'VariantAnnotation'
The following objects are masked from 'package:SeqArray':
alt, filt, fixed, geno, header, info, qual, ref
The following object is masked from 'package:base':
tabulate
# of selected samples: 5
# of selected variants: 10
# of selected variants: 898
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 90
# of selected variants: 1,348
RUNIT TEST PROTOCOL -- Sat Apr 13 05:31:05 2019
***********************************************
Number of test functions: 27
Number of errors: 0
Number of failures: 0
1 Test Suite :
SeqArray RUnit Tests - 27 test functions, 0 errors, 0 failures
Number of test functions: 27
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
77.18 10.96 107.03
|
SeqArray.Rcheck/tests_x64/test.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.
> BiocGenerics:::testPackage("SeqArray")
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: GenomeInfoDb
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
The following object is masked from 'package:SeqArray':
rowRanges
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:SeqArray':
rowRanges
The following objects are masked from 'package:base':
aperm, apply
Attaching package: 'SummarizedExperiment'
The following object is masked from 'package:SeqArray':
colData
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:DelayedArray':
type
The following object is masked from 'package:base':
strsplit
Attaching package: 'VariantAnnotation'
The following objects are masked from 'package:SeqArray':
alt, filt, fixed, geno, header, info, qual, ref
The following object is masked from 'package:base':
tabulate
# of selected samples: 5
# of selected variants: 10
# of selected variants: 898
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 90
# of selected variants: 1,348
RUNIT TEST PROTOCOL -- Sat Apr 13 05:32:44 2019
***********************************************
Number of test functions: 27
Number of errors: 0
Number of failures: 0
1 Test Suite :
SeqArray RUnit Tests - 27 test functions, 0 errors, 0 failures
Number of test functions: 27
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
78.96 2.75 98.01
|
|
SeqArray.Rcheck/examples_i386/SeqArray-Ex.timings
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SeqArray.Rcheck/examples_x64/SeqArray-Ex.timings
|