* using log directory 'C:/msys64/home/tomas/utf/ucrt64/inst_all/SeqArray.Rcheck' * using R Under development (unstable) (2020-06-23 r78739) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * checking for file 'SeqArray/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'SeqArray' version '1.24.2' * checking package namespace information ... OK * checking package dependencies ... NOTE Packages suggested but not available for checking: 'Rsamtools', 'VariantAnnotation' * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'SeqArray' can be installed ... 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE ':::' call which should be '::': 'parallel:::mc.reset.stream' See the note in ?`:::` about the use of this operator. Missing objects imported by ':::' calls: 'parallel:::cleanup' 'parallel:::prepareCleanup' 'parallel:::processID' 'parallel:::readChild' 'parallel:::selectChildren' * 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 ... NOTE Packages unavailable to check Rd xrefs: 'VariantAnnotation', 'Rsamtools' * 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 use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE File 'SeqArray/libs/x64/SeqArray.dll': Found non-API calls to R: 'R_GetConnection', 'R_ReadConnection', 'R_WriteConnection', 'R_new_custom_connection' Compiled code should not call non-API entry points in R. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... ERROR Running examples in 'SeqArray-Ex.R' failed The error most likely occurred in: > ### Name: seqExport > ### Title: Export to a GDS File > ### Aliases: seqExport > ### Keywords: gds VCF sequencing genetics > > ### ** Examples > > # open the GDS file > (gds.fn <- seqExampleFileName("gds")) [1] "C:/msys64/home/tomas/utf/ucrt64/inst_all/SeqArray.Rcheck/SeqArray/extdata/CEU_Exon.gds" > (f <- seqOpen(gds.fn)) Object of class "SeqVarGDSClass" File: C:\msys64\home\tomas\utf\ucrt64\inst_all\SeqArray.Rcheck\SeqArray\extdata\CEU_Exon.gds (299.1K) + [ ] * |--+ description [ ] * |--+ sample.id { Str8 90 LZMA_ra(35.8%), 258B } * |--+ variant.id { Int32 1348 LZMA_ra(16.8%), 906B } * |--+ position { Int32 1348 LZMA_ra(64.6%), 3.4K } * |--+ chromosome { Str8 1348 LZMA_ra(4.63%), 158B } * |--+ allele { Str8 1348 LZMA_ra(16.7%), 902B } * |--+ genotype [ ] * | |--+ data { Bit2 2x90x1348 LZMA_ra(26.3%), 15.6K } * | |--+ ~data { Bit2 2x1348x90 LZMA_ra(29.3%), 17.3K } | |--+ extra.index { Int32 3x0 LZMA_ra, 19B } * | \--+ extra { Int16 0 LZMA_ra, 19B } |--+ phase [ ] | |--+ data { Bit1 90x1348 LZMA_ra(0.91%), 138B } * | |--+ ~data { Bit1 1348x90 LZMA_ra(0.91%), 138B } | |--+ extra.index { Int32 3x0 LZMA_ra, 19B } * | \--+ extra { Bit1 0 LZMA_ra, 19B } |--+ annotation [ ] | |--+ id { Str8 1348 LZMA_ra(38.4%), 5.5K } * | |--+ qual { Float32 1348 LZMA_ra(2.26%), 122B } * | |--+ filter { Int32,factor 1348 LZMA_ra(2.26%), 122B } * | |--+ info [ ] | | |--+ AA { Str8 1348 LZMA_ra(25.6%), 690B } * | | |--+ AC { Int32 1348 LZMA_ra(24.2%), 1.3K } * | | |--+ AN { Int32 1348 LZMA_ra(19.8%), 1.0K } * | | |--+ DP { Int32 1348 LZMA_ra(47.9%), 2.5K } * | | |--+ HM2 { Bit1 1348 LZMA_ra(150.3%), 254B } * | | |--+ HM3 { Bit1 1348 LZMA_ra(150.3%), 254B } * | | |--+ OR { Str8 1348 LZMA_ra(20.1%), 342B } * | | |--+ GP { Str8 1348 LZMA_ra(24.4%), 3.8K } * | | \--+ BN { Int32 1348 LZMA_ra(20.9%), 1.1K } * | \--+ format [ ] | \--+ DP [ ] * | |--+ data { Int32 90x1348 LZMA_ra(25.1%), 118.8K } * | \--+ ~data { Int32 1348x90 LZMA_ra(24.1%), 114.2K } \--+ sample.annotation [ ] \--+ family { Str8 90 LZMA_ra(57.1%), 222B } > > # get 'sample.id' > head(samp.id <- seqGetData(f, "sample.id")) [1] "NA06984" "NA06985" "NA06986" "NA06989" "NA06994" "NA07000" > > # get 'variant.id' > head(variant.id <- seqGetData(f, "variant.id")) [1] 1 2 3 4 5 6 > > set.seed(100) > # set sample and variant filters > seqSetFilter(f, sample.id=samp.id[c(2,4,6,8,10,12,14,16)]) # of selected samples: 8 > seqSetFilter(f, variant.id=sample(variant.id, 100)) # of selected variants: 100 > > > # export > seqExport(f, "tmp.gds") Export to 'tmp.gds' sample.id (8) [md5: 7269c374a455e3c2d046ce1e3b2854a8] variant.id (100) [md5: 5260e8825b753db5240e1adc3208fae4] position [md5: c7ef4e9e68da9f32fa43f52f900b48c5] chromosome [md5: 31101f0b9c3a15be71aa9904b49776e0] allele [md5: 7b70b62ea10c297f4b44411c0247a346] genotype [md5: 418d339cc0bad5eed558e6555970240b] [md5: 9af8a70f41fa6c1822aff9ec427e78bf] phase [md5: fbfc323ca650cabd3df3affdc857c9da] [md5: fbfc323ca650cabd3df3affdc857c9da] annotation/id [md5: 43e4c471f036cf267d9ad898c9a4d552] annotation/qual [md5: 3ed8eb4b551fd4ee34f546f1170b1ed7] annotation/filterError in apply.gdsn(src, margin = length(dm), FUN = c, selection = seldim, : the returned value from the user-defined function should be numeric, character or NULL. Calls: seqExport -> cp -> assign.gdsn -> apply.gdsn Execution halted * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'test.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... 'OverviewSlides.Rmd'... OK 'R_Integration.Rmd' using 'UTF-8'... OK 'SeqArrayTutorial.Rmd' using 'UTF-8'... OK NONE * checking re-building of vignette outputs ... WARNING Error(s) in re-building vignettes: --- re-building 'OverviewSlides.Rmd' using rmarkdown Warning in engine$weave(file, quiet = quiet, encoding = enc) : Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1. --- finished re-building 'OverviewSlides.Rmd' --- re-building 'R_Integration.Rmd' using rmarkdown Warning in engine$weave(file, quiet = quiet, encoding = enc) : Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1. starting worker pid=34204 on localhost:11633 at 01:32:33.737 starting worker pid=30616 on localhost:11633 at 01:32:33.753 Loading required package: gdsfmt Loading required package: gdsfmt Quitting from lines 291-292 (R_Integration.Rmd) Error: processing vignette 'R_Integration.Rmd' failed with diagnostics: there is no package called 'VariantAnnotation' --- failed re-building 'R_Integration.Rmd' --- re-building 'SeqArrayTutorial.Rmd' using rmarkdown Warning in engine$weave(file, quiet = quiet, encoding = enc) : Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1. starting worker pid=83728 on localhost:11175 at 01:33:45.904 starting worker pid=85132 on localhost:11175 at 01:33:46.138 Loading required package: gdsfmt Loading required package: gdsfmt starting worker pid=21860 on localhost:11175 at 01:34:07.938 starting worker pid=122840 on localhost:11175 at 01:34:08.048 Loading required package: gdsfmt Loading required package: gdsfmt starting worker pid=166392 on localhost:11175 at 01:34:28.097 starting worker pid=99432 on localhost:11175 at 01:34:28.176 Loading required package: gdsfmt Loading required package: gdsfmt starting worker pid=26640 on localhost:11175 at 01:34:35.005 starting worker pid=102484 on localhost:11175 at 01:34:35.005 Loading required package: gdsfmt Loading required package: gdsfmt starting worker pid=73088 on localhost:11175 at 01:34:41.302 starting worker pid=82736 on localhost:11175 at 01:34:41.302 Loading required package: gdsfmt Loading required package: gdsfmt --- finished re-building 'SeqArrayTutorial.Rmd' SUMMARY: processing the following file failed: 'R_Integration.Rmd' Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 WARNING, 4 NOTEs See 'C:/msys64/home/tomas/utf/ucrt64/inst_all/SeqArray.Rcheck/00check.log' for details.