CRAN Package Check Results for Package poplite

Last updated on 2020-11-09 07:52:16 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.99.23 10.11 105.13 115.24 ERROR
r-devel-linux-x86_64-debian-gcc 0.99.23 7.52 77.55 85.07 ERROR
r-devel-linux-x86_64-fedora-clang 0.99.23 148.20 ERROR
r-devel-linux-x86_64-fedora-gcc 0.99.23 130.41 ERROR
r-devel-windows-ix86+x86_64 0.99.23 23.00 139.00 162.00 OK
r-patched-linux-x86_64 0.99.23 ERROR
r-patched-solaris-x86 0.99.23 200.80 ERROR
r-release-linux-x86_64 0.99.23 9.44 95.79 105.23 ERROR
r-release-macos-x86_64 0.99.23 OK
r-release-windows-ix86+x86_64 0.99.23 35.00 154.00 189.00 OK
r-oldrel-macos-x86_64 0.99.23 NOTE
r-oldrel-windows-ix86+x86_64 0.99.23 11.00 84.00 95.00 ERROR

Check Details

Version: 0.99.23
Check: examples
Result: ERROR
    Running examples in 'poplite-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: External methods
    > ### Title: Specific methods for generics defined in external packages.
    > ### Aliases: filter select
    > ### Keywords: utilities
    >
    > ### ** Examples
    >
    > if (require(Lahman))
    + {
    + baseball.teams <- makeSchemaFromData(TeamsFranchises, name="team_franch")
    + baseball.teams <- append(baseball.teams, makeSchemaFromData(Teams, name="teams"))
    +
    + relationship(baseball.teams, from="team_franch", to="teams") <- franchID ~ franchID
    +
    + baseball.db <- Database(baseball.teams, tempfile())
    +
    + populate(baseball.db, teams=Teams, team_franch=TeamsFranchises)
    +
    + select(baseball.db, .tables="teams")
    +
    + select(baseball.db, .tables=c("teams", "team_franch"))
    +
    + select(baseball.db, yearID:WCWin, franchName)
    +
    + filter(baseball.db, active == "Y")
    +
    + select(filter(baseball.db, active == "Y" & W > 50 & teamID == "CAL"), active, W, teamID)
    + }
    Loading required package: Lahman
    Starting team_franch
    Starting teams
    Warning: `select_()` is deprecated as of dplyr 0.7.0.
    Please use `select()` instead.
    This warning is displayed once every 8 hours.
    Call `lifecycle::last_warnings()` to see where this warning was generated.
    Warning: call dbDisconnect() when finished working with a connection
    Error in UseMethod("select_") :
     no applicable method for 'select_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"
    Calls: select ... join -> join -> .local -> .get.select.cols -> select_
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.99.23
Check: tests
Result: ERROR
     Running 'testthat.R' [30s/35s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(Lahman)
     > library(DBI)
     > library(RSQLite)
     > library(poplite)
     Loading required package: dplyr
    
     Attaching package: 'dplyr'
    
     The following object is masked from 'package:testthat':
    
     matches
    
     The following objects are masked from 'package:stats':
    
     filter, lag
    
     The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    
     Attaching package: 'poplite'
    
     The following object is masked from 'package:dplyr':
    
     select
    
     The following object is masked from 'package:stats':
    
     filter
    
     >
     > test.db.1 <- function()
     + {
     + samples <- data.frame(sample_id=as.integer(sapply(1:100, function(x) rep(x,2))), wave=as.integer(sapply(1:100, function(x) 1:2)), did_collect=sample(c("Y", "N"), size=100, replace=T))
     +
     + dna <- samples[samples$did_collect == "Y",c("sample_id", "wave")]
     + dna$lab_id <- paste("dna", paste(dna$sample_id, dna$wave, sep="_"), sep="_")
     + dna$lab_id[sample.int(nrow(dna), size=10)] <- NA
     + dna$ng.ul <- abs(rnorm(n=nrow(dna), mean=146, sd=98))
     + dna$ng.ul[is.na(dna$lab_id)] <- NA
     +
     + clinical <- data.frame(sample_id=1:100, sex=sample(c("M", "F"), size=100, replace=T), age=sample(1:20, 100, replace=T), status=sample(c(0L,1L), size=100, replace=T), var_wave_1=rnorm(n=100), var_wave_2=rnorm(n=100))
     + clinical <- clinical[-sample.int(nrow(clinical), 12),]
     +
     + return(list(samples=samples, dna=dna, clinical=clinical))
     + }
     >
     > test.db.2 <- eval(structure(list(allele = structure(list(allele_id = 1:10, alleles = c(".",
     + "G", "A", ".", "A", "T", ".", "C", "A", "."), allele_num = c(-1L,
     + 0L, 1L, -1L, 0L, 1L, -1L, 0L, 1L, -1L), ref_id = c(1L, 1L, 1L,
     + 2L, 2L, 2L, 3L, 3L, 3L, 4L)), .Names = c("allele_id", "alleles",
     + "allele_num", "ref_id"), row.names = c(NA, -10L), class = "data.frame"),
     + genotype = structure(list(geno_id = c(1L, 2L, 3L, 4L, 5L,
     + 6L, 7L, 8L, 9L, 11L), geno_chr = c(1L, 1L, 1L, 1L, 1L, 1L,
     + 1L, 1L, 1L, 1L), allele_num = c(1L, 1L, 1L, 1L, 1L, 1L, 1L,
     + 1L, 1L, 1L), strain = c("NODShiLtJ", "NODShiLtJ", "NODShiLtJ",
     + "NODShiLtJ", "NODShiLtJ", "NODShiLtJ", "NODShiLtJ", "NODShiLtJ",
     + "NODShiLtJ", "NODShiLtJ"), ref_id = c(1L, 2L, 3L, 4L, 5L,
     + 6L, 7L, 8L, 9L, 11L)), .Names = c("geno_id", "geno_chr",
     + "allele_num", "strain", "ref_id"), row.names = c(NA, -10L
     + ), class = "data.frame"), probe_align = structure(list(probe_align_id = 1:10,
     + probe_chr = c("1", "1", "1", "1", "1", "1", "1", "1",
     + "1", "1"), probe_start = c(3214633L, 3214895L, 3215576L,
     + 3216284L, 3216483L, 3216537L, 3216591L, 3421710L, 3421740L,
     + 3421808L), probe_end = c(3214657L, 3214919L, 3215600L,
     + 3216308L, 3216507L, 3216561L, 3216615L, 3421734L, 3421764L,
     + 3421832L), probe_ind = 23944:23953), .Names = c("probe_align_id",
     + "probe_chr", "probe_start", "probe_end", "probe_ind"), row.names = c(NA,
     + -10L), class = "data.frame"), probe_info = structure(list(
     + probe_ind = 1:10, fasta_name = c("chr1:3044331-3044355;+;GGGCTCAAATTCACCTGTGTTAACT",
     + "chr1:3044334-3044358;+;AGGGGGCTCAAATTCACCTGTGTTA", "chr1:3044335-3044359;+;GAGGGGGCTCAAATTCACCTGTGTT",
     + "chr1:3044336-3044360;+;GGAGGGGGCTCAAATTCACCTGTGT", "chr1:3044337-3044361;+;GGGAGGGGGCTCAAATTCACCTGTG",
     + "chr1:3044504-3044528;+;AAGGCTTGGGCTATGCGCTCTCCAG", "chr1:3044557-3044581;+;AAGGTCCTCGCTCCTCTTTCATATA",
     + "chr1:3044558-3044582;+;GAAGGTCCTCGCTCCTCTTTCATAT", "chr1:3044559-3044583;+;GGAAGGTCCTCGCTCCTCTTTCATA",
     + "chr1:3044560-3044584;+;AGGAAGGTCCTCGCTCCTCTTTCAT"),
     + probe_id = c(271822L, 866088L, 240008L, 34772L, 396933L,
     + 613322L, 984143L, 826914L, 1075207L, 160847L), align_status = c("MultiMapped",
     + "MultiMapped", "MultiMapped", "MultiMapped", "MultiMapped",
     + "MultiMapped", "MultiMapped", "MultiMapped", "MultiMapped",
     + "MultiMapped")), .Names = c("probe_ind", "fasta_name",
     + "probe_id", "align_status"), row.names = c(NA, -10L), class = "data.frame"),
     + probe_to_snp = structure(list(probe_snp_id = 1:10, ref_id = c(1L,
     + 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 9L), probe_align_id = c(137L,
     + 137L, 252L, 263L, 561L, 601L, 606L, 622L, 635L, 636L)), .Names = c("probe_snp_id",
     + "ref_id", "probe_align_id"), row.names = c(NA, -10L), class = "data.frame"),
     + reference = structure(list(ref_id = c(1L, 2L, 3L, 4L, 5L,
     + 6L, 7L, 8L, 9L, 11L), seqnames = c("1", "1", "1", "1", "1",
     + "1", "1", "1", "1", "1"), start = c(4785683L, 4785703L, 8595537L,
     + 8682000L, 10719780L, 12990759L, 13114284L, 13122474L, 13125617L,
     + 13150850L), end = c(4785683L, 4785703L, 8595537L, 8682000L,
     + 10719780L, 12990759L, 13114284L, 13122474L, 13125617L, 13150850L
     + ), filter = c("TRUE", "TRUE", "TRUE", "TRUE", "TRUE", "TRUE",
     + "TRUE", "TRUE", "TRUE", "TRUE"), vcf_annot_id = c(1L, 1L,
     + 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L)), .Names = c("ref_id", "seqnames",
     + "start", "end", "filter", "vcf_annot_id"), row.names = c(NA,
     + -10L), class = "data.frame"), vcf_annot = structure(list(
     + vcf_annot_id = 1L, vcf_name = "/Users/bottomly/Desktop/resources/vcfs/mgp.v3.snps.rsIDdbSNPv137.vcf.gz",
     + type = "SNV"), .Names = c("vcf_annot_id", "vcf_name",
     + "type"), row.names = c(NA, -1L), class = "data.frame")), .Names = c("allele",
     + "genotype", "probe_align", "probe_info", "probe_to_snp", "reference",
     + "vcf_annot")))
     >
     > test.schema.2 <- list(probe_info=list(db.cols=c("probe_ind", "fasta_name", "probe_id", "align_status"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "TEXT", "INTEGER", "TEXT"),
     + db.constr="CONSTRAINT probe_idx UNIQUE (fasta_name)",
     + dta.func=function(x) x, should.ignore=FALSE, foreign.keys=NULL),
     + probe_align=list(db.cols=c("probe_align_id", "probe_chr", "probe_start", "probe_end", "probe_ind"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "TEXT", "INTEGER", "INTEGER", "INTEGER"),
     + db.constr="CONSTRAINT geno_idx UNIQUE (probe_chr, probe_start, probe_end, probe_ind)",
     + dta.func=function(x) x, should.ignore=FALSE, foreign.keys=list(probe_info=list(local.keys="probe_ind", ext.keys="fasta_name"))),
     + vcf_annot=list(db.cols=c("vcf_annot_id", "vcf_name", "type"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "TEXT", "TEXT"),
     + db.constr="CONSTRAINT probe_idx UNIQUE (vcf_name, type)",
     + dta.func=function(x) x,
     + should.ignore=TRUE, foreign.keys=NULL),
     + reference=list(db.cols=c("ref_id", "seqnames", "start", "end", "filter", "vcf_annot_id"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "TEXT", "INTEGER", "INTEGER", "TEXT", "INTEGER"),
     + db.constr="CONSTRAINT ref_idx UNIQUE (seqnames, start, end, vcf_annot_id)",
     + dta.func=function(x) x, should.ignore=TRUE, foreign.keys=list(vcf_annot=list(local.keys="vcf_annot_id", ext.keys=c("vcf_name", "type")))),
     + allele=list(db.cols=c("allele_id", "alleles", "allele_num", "ref_id"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "TEXT", "INTEGER", "INTEGER"),
     + db.constr="CONSTRAINT alelle_idx UNIQUE (alleles, allele_num, ref_id)",
     + dta.func=function(x) x, should.ignore=TRUE, foreign.keys=list(vcf_annot=list(local.keys="vcf_annot_id", ext.keys=c("vcf_name", "type")),
     + reference=list(local.keys="ref_id", ext.keys=c("seqnames", "start", "end", "vcf_annot_id")))),
     + genotype=list(db.cols=c("geno_id", "geno_chr", "allele_num","strain", "ref_id"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "INTEGER", "INTEGER", "TEXT", "INTEGER"),
     + db.constr="CONSTRAINT geno_idx UNIQUE (ref_id, strain, geno_chr, allele_num)",
     + dta.func=function(x) x, should.ignore=TRUE, foreign.keys=list(vcf_annot=list(local.keys="vcf_annot_id", ext.keys=c("vcf_name", "type")),
     + reference=list(local.keys="ref_id", ext.keys=c("seqnames", "start", "end", "vcf_annot_id")))),
     + probe_to_snp=list(db.cols=c("probe_snp_id", "ref_id", "probe_align_id"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "INTEGER", "INTEGER"),
     + db.constr="CONSTRAINT p_s_idx UNIQUE (ref_id, probe_align_id)",
     + dta.func=function(x) x, should.ignore=TRUE, foreign.keys=list(vcf_annot=list(local.keys="vcf_annot_id", ext.keys=c("vcf_name", "type")),
     + reference=list(local.keys="ref_id", ext.keys=c("seqnames", "start", "end", "vcf_annot_id")),
     + probe_align=list(local.keys="probe_align_id", ext.keys=c("probe_chr", "probe_start", "probe_end")))))
     >
     >
     >
     >
     >
     > test_check("poplite")
     -- Warning (test-poplite.R:598:5): Querying with Database objects --------------
     `select_()` is deprecated as of dplyr 0.7.0.
     Please use `select()` instead.
     This warning is displayed once every 8 hours.
     Call `lifecycle::last_warnings()` to see where this warning was generated.
    
     -- ERROR (test-poplite.R:655:5): Querying with Database objects ----------------
     Error: no applicable method for 'select_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"
     Backtrace:
     x
     1. \-poplite::select(sample.tracking.db, sample_id:dna_ind, .tables = "samples") test-poplite.R:655:4
     2. +-dplyr::select_(.data, .dots = use.dots)
     3. \-poplite:::select_.Database(.data, .dots = use.dots)
     4. +-poplite:::join(.data, use.tables)
     5. \-poplite:::join(.data, use.tables)
     6. \-poplite:::.local(obj, ...)
     7. \-dplyr::select_(...)
    
     -- ERROR (test-poplite.R:883:5): oligoMask queries that break poplite ----------
     Error: no applicable method for 'select_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"
     Backtrace:
     x
     1. +-base::as.data.frame(...) test-poplite.R:883:4
     2. \-poplite::select(test.database.1, probe_id, fasta_name, align_status)
     3. +-dplyr::select_(.data, .dots = use.dots)
     4. \-poplite:::select_.Database(.data, .dots = use.dots)
     5. +-dplyr::select_(join(.data, use.tables), .dots = as.list(clean.cols))
     6. +-poplite:::join(.data, use.tables)
     7. \-poplite:::join(.data, use.tables)
     8. \-poplite:::.local(obj, ...)
     9. \-dplyr::select_(...)
    
     == testthat results ===========================================================
     Warning (test-poplite.R:598:5): Querying with Database objects
     ERROR (test-poplite.R:655:5): Querying with Database objects
     ERROR (test-poplite.R:883:5): oligoMask queries that break poplite
    
     [ FAIL 2 | WARN 1 | SKIP 0 | PASS 129 ]
     Error: Test failures
     In addition: Warning message:
     call dbDisconnect() when finished working with a connection
     Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.99.23
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building 'poplite.Rnw' using Sweave
    Loading required package: dplyr
    
    Attaching package: 'dplyr'
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    Loading required package: DBI
    
    Attaching package: 'poplite'
    
    The following object is masked from 'package:dplyr':
    
     select
    
    The following object is masked from 'package:stats':
    
     filter
    
    Error in makeSchemaFromData(dna, "dna") :
     ERROR: The names of the supplied data.frame need to be modified for the database see correct.df.names
    Starting clinical
    Starting samples
    Starting dna
    Warning: `select_()` is deprecated as of dplyr 0.7.0.
    Please use `select()` instead.
    This warning is displayed once every 8 hours.
    Call `lifecycle::last_warnings()` to see where this warning was generated.
    
    Error: processing vignette 'poplite.Rnw' failed with diagnostics:
     chunk 9
    Error in UseMethod("select_") :
     no applicable method for 'select_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"
    
    --- failed re-building 'poplite.Rnw'
    
    SUMMARY: processing the following file failed:
     'poplite.Rnw'
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64

Version: 0.99.23
Check: tests
Result: ERROR
     Running ‘testthat.R’ [23s/37s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(Lahman)
     > library(DBI)
     > library(RSQLite)
     > library(poplite)
     Loading required package: dplyr
    
     Attaching package: 'dplyr'
    
     The following object is masked from 'package:testthat':
    
     matches
    
     The following objects are masked from 'package:stats':
    
     filter, lag
    
     The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    
     Attaching package: 'poplite'
    
     The following object is masked from 'package:dplyr':
    
     select
    
     The following object is masked from 'package:stats':
    
     filter
    
     >
     > test.db.1 <- function()
     + {
     + samples <- data.frame(sample_id=as.integer(sapply(1:100, function(x) rep(x,2))), wave=as.integer(sapply(1:100, function(x) 1:2)), did_collect=sample(c("Y", "N"), size=100, replace=T))
     +
     + dna <- samples[samples$did_collect == "Y",c("sample_id", "wave")]
     + dna$lab_id <- paste("dna", paste(dna$sample_id, dna$wave, sep="_"), sep="_")
     + dna$lab_id[sample.int(nrow(dna), size=10)] <- NA
     + dna$ng.ul <- abs(rnorm(n=nrow(dna), mean=146, sd=98))
     + dna$ng.ul[is.na(dna$lab_id)] <- NA
     +
     + clinical <- data.frame(sample_id=1:100, sex=sample(c("M", "F"), size=100, replace=T), age=sample(1:20, 100, replace=T), status=sample(c(0L,1L), size=100, replace=T), var_wave_1=rnorm(n=100), var_wave_2=rnorm(n=100))
     + clinical <- clinical[-sample.int(nrow(clinical), 12),]
     +
     + return(list(samples=samples, dna=dna, clinical=clinical))
     + }
     >
     > test.db.2 <- eval(structure(list(allele = structure(list(allele_id = 1:10, alleles = c(".",
     + "G", "A", ".", "A", "T", ".", "C", "A", "."), allele_num = c(-1L,
     + 0L, 1L, -1L, 0L, 1L, -1L, 0L, 1L, -1L), ref_id = c(1L, 1L, 1L,
     + 2L, 2L, 2L, 3L, 3L, 3L, 4L)), .Names = c("allele_id", "alleles",
     + "allele_num", "ref_id"), row.names = c(NA, -10L), class = "data.frame"),
     + genotype = structure(list(geno_id = c(1L, 2L, 3L, 4L, 5L,
     + 6L, 7L, 8L, 9L, 11L), geno_chr = c(1L, 1L, 1L, 1L, 1L, 1L,
     + 1L, 1L, 1L, 1L), allele_num = c(1L, 1L, 1L, 1L, 1L, 1L, 1L,
     + 1L, 1L, 1L), strain = c("NODShiLtJ", "NODShiLtJ", "NODShiLtJ",
     + "NODShiLtJ", "NODShiLtJ", "NODShiLtJ", "NODShiLtJ", "NODShiLtJ",
     + "NODShiLtJ", "NODShiLtJ"), ref_id = c(1L, 2L, 3L, 4L, 5L,
     + 6L, 7L, 8L, 9L, 11L)), .Names = c("geno_id", "geno_chr",
     + "allele_num", "strain", "ref_id"), row.names = c(NA, -10L
     + ), class = "data.frame"), probe_align = structure(list(probe_align_id = 1:10,
     + probe_chr = c("1", "1", "1", "1", "1", "1", "1", "1",
     + "1", "1"), probe_start = c(3214633L, 3214895L, 3215576L,
     + 3216284L, 3216483L, 3216537L, 3216591L, 3421710L, 3421740L,
     + 3421808L), probe_end = c(3214657L, 3214919L, 3215600L,
     + 3216308L, 3216507L, 3216561L, 3216615L, 3421734L, 3421764L,
     + 3421832L), probe_ind = 23944:23953), .Names = c("probe_align_id",
     + "probe_chr", "probe_start", "probe_end", "probe_ind"), row.names = c(NA,
     + -10L), class = "data.frame"), probe_info = structure(list(
     + probe_ind = 1:10, fasta_name = c("chr1:3044331-3044355;+;GGGCTCAAATTCACCTGTGTTAACT",
     + "chr1:3044334-3044358;+;AGGGGGCTCAAATTCACCTGTGTTA", "chr1:3044335-3044359;+;GAGGGGGCTCAAATTCACCTGTGTT",
     + "chr1:3044336-3044360;+;GGAGGGGGCTCAAATTCACCTGTGT", "chr1:3044337-3044361;+;GGGAGGGGGCTCAAATTCACCTGTG",
     + "chr1:3044504-3044528;+;AAGGCTTGGGCTATGCGCTCTCCAG", "chr1:3044557-3044581;+;AAGGTCCTCGCTCCTCTTTCATATA",
     + "chr1:3044558-3044582;+;GAAGGTCCTCGCTCCTCTTTCATAT", "chr1:3044559-3044583;+;GGAAGGTCCTCGCTCCTCTTTCATA",
     + "chr1:3044560-3044584;+;AGGAAGGTCCTCGCTCCTCTTTCAT"),
     + probe_id = c(271822L, 866088L, 240008L, 34772L, 396933L,
     + 613322L, 984143L, 826914L, 1075207L, 160847L), align_status = c("MultiMapped",
     + "MultiMapped", "MultiMapped", "MultiMapped", "MultiMapped",
     + "MultiMapped", "MultiMapped", "MultiMapped", "MultiMapped",
     + "MultiMapped")), .Names = c("probe_ind", "fasta_name",
     + "probe_id", "align_status"), row.names = c(NA, -10L), class = "data.frame"),
     + probe_to_snp = structure(list(probe_snp_id = 1:10, ref_id = c(1L,
     + 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 9L), probe_align_id = c(137L,
     + 137L, 252L, 263L, 561L, 601L, 606L, 622L, 635L, 636L)), .Names = c("probe_snp_id",
     + "ref_id", "probe_align_id"), row.names = c(NA, -10L), class = "data.frame"),
     + reference = structure(list(ref_id = c(1L, 2L, 3L, 4L, 5L,
     + 6L, 7L, 8L, 9L, 11L), seqnames = c("1", "1", "1", "1", "1",
     + "1", "1", "1", "1", "1"), start = c(4785683L, 4785703L, 8595537L,
     + 8682000L, 10719780L, 12990759L, 13114284L, 13122474L, 13125617L,
     + 13150850L), end = c(4785683L, 4785703L, 8595537L, 8682000L,
     + 10719780L, 12990759L, 13114284L, 13122474L, 13125617L, 13150850L
     + ), filter = c("TRUE", "TRUE", "TRUE", "TRUE", "TRUE", "TRUE",
     + "TRUE", "TRUE", "TRUE", "TRUE"), vcf_annot_id = c(1L, 1L,
     + 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L)), .Names = c("ref_id", "seqnames",
     + "start", "end", "filter", "vcf_annot_id"), row.names = c(NA,
     + -10L), class = "data.frame"), vcf_annot = structure(list(
     + vcf_annot_id = 1L, vcf_name = "/Users/bottomly/Desktop/resources/vcfs/mgp.v3.snps.rsIDdbSNPv137.vcf.gz",
     + type = "SNV"), .Names = c("vcf_annot_id", "vcf_name",
     + "type"), row.names = c(NA, -1L), class = "data.frame")), .Names = c("allele",
     + "genotype", "probe_align", "probe_info", "probe_to_snp", "reference",
     + "vcf_annot")))
     >
     > test.schema.2 <- list(probe_info=list(db.cols=c("probe_ind", "fasta_name", "probe_id", "align_status"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "TEXT", "INTEGER", "TEXT"),
     + db.constr="CONSTRAINT probe_idx UNIQUE (fasta_name)",
     + dta.func=function(x) x, should.ignore=FALSE, foreign.keys=NULL),
     + probe_align=list(db.cols=c("probe_align_id", "probe_chr", "probe_start", "probe_end", "probe_ind"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "TEXT", "INTEGER", "INTEGER", "INTEGER"),
     + db.constr="CONSTRAINT geno_idx UNIQUE (probe_chr, probe_start, probe_end, probe_ind)",
     + dta.func=function(x) x, should.ignore=FALSE, foreign.keys=list(probe_info=list(local.keys="probe_ind", ext.keys="fasta_name"))),
     + vcf_annot=list(db.cols=c("vcf_annot_id", "vcf_name", "type"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "TEXT", "TEXT"),
     + db.constr="CONSTRAINT probe_idx UNIQUE (vcf_name, type)",
     + dta.func=function(x) x,
     + should.ignore=TRUE, foreign.keys=NULL),
     + reference=list(db.cols=c("ref_id", "seqnames", "start", "end", "filter", "vcf_annot_id"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "TEXT", "INTEGER", "INTEGER", "TEXT", "INTEGER"),
     + db.constr="CONSTRAINT ref_idx UNIQUE (seqnames, start, end, vcf_annot_id)",
     + dta.func=function(x) x, should.ignore=TRUE, foreign.keys=list(vcf_annot=list(local.keys="vcf_annot_id", ext.keys=c("vcf_name", "type")))),
     + allele=list(db.cols=c("allele_id", "alleles", "allele_num", "ref_id"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "TEXT", "INTEGER", "INTEGER"),
     + db.constr="CONSTRAINT alelle_idx UNIQUE (alleles, allele_num, ref_id)",
     + dta.func=function(x) x, should.ignore=TRUE, foreign.keys=list(vcf_annot=list(local.keys="vcf_annot_id", ext.keys=c("vcf_name", "type")),
     + reference=list(local.keys="ref_id", ext.keys=c("seqnames", "start", "end", "vcf_annot_id")))),
     + genotype=list(db.cols=c("geno_id", "geno_chr", "allele_num","strain", "ref_id"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "INTEGER", "INTEGER", "TEXT", "INTEGER"),
     + db.constr="CONSTRAINT geno_idx UNIQUE (ref_id, strain, geno_chr, allele_num)",
     + dta.func=function(x) x, should.ignore=TRUE, foreign.keys=list(vcf_annot=list(local.keys="vcf_annot_id", ext.keys=c("vcf_name", "type")),
     + reference=list(local.keys="ref_id", ext.keys=c("seqnames", "start", "end", "vcf_annot_id")))),
     + probe_to_snp=list(db.cols=c("probe_snp_id", "ref_id", "probe_align_id"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "INTEGER", "INTEGER"),
     + db.constr="CONSTRAINT p_s_idx UNIQUE (ref_id, probe_align_id)",
     + dta.func=function(x) x, should.ignore=TRUE, foreign.keys=list(vcf_annot=list(local.keys="vcf_annot_id", ext.keys=c("vcf_name", "type")),
     + reference=list(local.keys="ref_id", ext.keys=c("seqnames", "start", "end", "vcf_annot_id")),
     + probe_align=list(local.keys="probe_align_id", ext.keys=c("probe_chr", "probe_start", "probe_end")))))
     >
     >
     >
     >
     >
     > test_check("poplite")
     ── Warning (test-poplite.R:598:5): Querying with Database objects ──────────────
     `select_()` is deprecated as of dplyr 0.7.0.
     Please use `select()` instead.
     This warning is displayed once every 8 hours.
     Call `lifecycle::last_warnings()` to see where this warning was generated.
    
     ── ERROR (test-poplite.R:655:5): Querying with Database objects ────────────────
     Error: no applicable method for 'select_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"
     Backtrace:
     █
     1. └─poplite::select(sample.tracking.db, sample_id:dna_ind, .tables = "samples") test-poplite.R:655:4
     2. ├─dplyr::select_(.data, .dots = use.dots)
     3. └─poplite:::select_.Database(.data, .dots = use.dots)
     4. ├─poplite:::join(.data, use.tables)
     5. └─poplite:::join(.data, use.tables)
     6. └─poplite:::.local(obj, ...)
     7. └─dplyr::select_(...)
    
     ── ERROR (test-poplite.R:883:5): oligoMask queries that break poplite ──────────
     Error: no applicable method for 'select_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"
     Backtrace:
     █
     1. ├─base::as.data.frame(...) test-poplite.R:883:4
     2. └─poplite::select(test.database.1, probe_id, fasta_name, align_status)
     3. ├─dplyr::select_(.data, .dots = use.dots)
     4. └─poplite:::select_.Database(.data, .dots = use.dots)
     5. ├─dplyr::select_(join(.data, use.tables), .dots = as.list(clean.cols))
     6. ├─poplite:::join(.data, use.tables)
     7. └─poplite:::join(.data, use.tables)
     8. └─poplite:::.local(obj, ...)
     9. └─dplyr::select_(...)
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     Warning (test-poplite.R:598:5): Querying with Database objects
     ERROR (test-poplite.R:655:5): Querying with Database objects
     ERROR (test-poplite.R:883:5): oligoMask queries that break poplite
    
     [ FAIL 2 | WARN 1 | SKIP 0 | PASS 129 ]
     Error: Test failures
     In addition: Warning message:
     call dbDisconnect() when finished working with a connection
     Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.99.23
Check: examples
Result: ERROR
    Running examples in ‘poplite-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: External methods
    > ### Title: Specific methods for generics defined in external packages.
    > ### Aliases: filter select
    > ### Keywords: utilities
    >
    > ### ** Examples
    >
    > if (require(Lahman))
    + {
    + baseball.teams <- makeSchemaFromData(TeamsFranchises, name="team_franch")
    + baseball.teams <- append(baseball.teams, makeSchemaFromData(Teams, name="teams"))
    +
    + relationship(baseball.teams, from="team_franch", to="teams") <- franchID ~ franchID
    +
    + baseball.db <- Database(baseball.teams, tempfile())
    +
    + populate(baseball.db, teams=Teams, team_franch=TeamsFranchises)
    +
    + select(baseball.db, .tables="teams")
    +
    + select(baseball.db, .tables=c("teams", "team_franch"))
    +
    + select(baseball.db, yearID:WCWin, franchName)
    +
    + filter(baseball.db, active == "Y")
    +
    + select(filter(baseball.db, active == "Y" & W > 50 & teamID == "CAL"), active, W, teamID)
    + }
    Loading required package: Lahman
    Starting team_franch
    Starting teams
    Warning: `select_()` is deprecated as of dplyr 0.7.0.
    Please use `select()` instead.
    This warning is displayed once every 8 hours.
    Call `lifecycle::last_warnings()` to see where this warning was generated.
    Warning: call dbDisconnect() when finished working with a connection
    Error in UseMethod("select_") :
     no applicable method for 'select_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"
    Calls: select ... join -> join -> .local -> .get.select.cols -> select_
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86, r-oldrel-windows-ix86+x86_64

Version: 0.99.23
Check: tests
Result: ERROR
     Running ‘testthat.R’ [38s/92s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(Lahman)
     > library(DBI)
     > library(RSQLite)
     > library(poplite)
     Loading required package: dplyr
    
     Attaching package: 'dplyr'
    
     The following object is masked from 'package:testthat':
    
     matches
    
     The following objects are masked from 'package:stats':
    
     filter, lag
    
     The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    
     Attaching package: 'poplite'
    
     The following object is masked from 'package:dplyr':
    
     select
    
     The following object is masked from 'package:stats':
    
     filter
    
     >
     > test.db.1 <- function()
     + {
     + samples <- data.frame(sample_id=as.integer(sapply(1:100, function(x) rep(x,2))), wave=as.integer(sapply(1:100, function(x) 1:2)), did_collect=sample(c("Y", "N"), size=100, replace=T))
     +
     + dna <- samples[samples$did_collect == "Y",c("sample_id", "wave")]
     + dna$lab_id <- paste("dna", paste(dna$sample_id, dna$wave, sep="_"), sep="_")
     + dna$lab_id[sample.int(nrow(dna), size=10)] <- NA
     + dna$ng.ul <- abs(rnorm(n=nrow(dna), mean=146, sd=98))
     + dna$ng.ul[is.na(dna$lab_id)] <- NA
     +
     + clinical <- data.frame(sample_id=1:100, sex=sample(c("M", "F"), size=100, replace=T), age=sample(1:20, 100, replace=T), status=sample(c(0L,1L), size=100, replace=T), var_wave_1=rnorm(n=100), var_wave_2=rnorm(n=100))
     + clinical <- clinical[-sample.int(nrow(clinical), 12),]
     +
     + return(list(samples=samples, dna=dna, clinical=clinical))
     + }
     >
     > test.db.2 <- eval(structure(list(allele = structure(list(allele_id = 1:10, alleles = c(".",
     + "G", "A", ".", "A", "T", ".", "C", "A", "."), allele_num = c(-1L,
     + 0L, 1L, -1L, 0L, 1L, -1L, 0L, 1L, -1L), ref_id = c(1L, 1L, 1L,
     + 2L, 2L, 2L, 3L, 3L, 3L, 4L)), .Names = c("allele_id", "alleles",
     + "allele_num", "ref_id"), row.names = c(NA, -10L), class = "data.frame"),
     + genotype = structure(list(geno_id = c(1L, 2L, 3L, 4L, 5L,
     + 6L, 7L, 8L, 9L, 11L), geno_chr = c(1L, 1L, 1L, 1L, 1L, 1L,
     + 1L, 1L, 1L, 1L), allele_num = c(1L, 1L, 1L, 1L, 1L, 1L, 1L,
     + 1L, 1L, 1L), strain = c("NODShiLtJ", "NODShiLtJ", "NODShiLtJ",
     + "NODShiLtJ", "NODShiLtJ", "NODShiLtJ", "NODShiLtJ", "NODShiLtJ",
     + "NODShiLtJ", "NODShiLtJ"), ref_id = c(1L, 2L, 3L, 4L, 5L,
     + 6L, 7L, 8L, 9L, 11L)), .Names = c("geno_id", "geno_chr",
     + "allele_num", "strain", "ref_id"), row.names = c(NA, -10L
     + ), class = "data.frame"), probe_align = structure(list(probe_align_id = 1:10,
     + probe_chr = c("1", "1", "1", "1", "1", "1", "1", "1",
     + "1", "1"), probe_start = c(3214633L, 3214895L, 3215576L,
     + 3216284L, 3216483L, 3216537L, 3216591L, 3421710L, 3421740L,
     + 3421808L), probe_end = c(3214657L, 3214919L, 3215600L,
     + 3216308L, 3216507L, 3216561L, 3216615L, 3421734L, 3421764L,
     + 3421832L), probe_ind = 23944:23953), .Names = c("probe_align_id",
     + "probe_chr", "probe_start", "probe_end", "probe_ind"), row.names = c(NA,
     + -10L), class = "data.frame"), probe_info = structure(list(
     + probe_ind = 1:10, fasta_name = c("chr1:3044331-3044355;+;GGGCTCAAATTCACCTGTGTTAACT",
     + "chr1:3044334-3044358;+;AGGGGGCTCAAATTCACCTGTGTTA", "chr1:3044335-3044359;+;GAGGGGGCTCAAATTCACCTGTGTT",
     + "chr1:3044336-3044360;+;GGAGGGGGCTCAAATTCACCTGTGT", "chr1:3044337-3044361;+;GGGAGGGGGCTCAAATTCACCTGTG",
     + "chr1:3044504-3044528;+;AAGGCTTGGGCTATGCGCTCTCCAG", "chr1:3044557-3044581;+;AAGGTCCTCGCTCCTCTTTCATATA",
     + "chr1:3044558-3044582;+;GAAGGTCCTCGCTCCTCTTTCATAT", "chr1:3044559-3044583;+;GGAAGGTCCTCGCTCCTCTTTCATA",
     + "chr1:3044560-3044584;+;AGGAAGGTCCTCGCTCCTCTTTCAT"),
     + probe_id = c(271822L, 866088L, 240008L, 34772L, 396933L,
     + 613322L, 984143L, 826914L, 1075207L, 160847L), align_status = c("MultiMapped",
     + "MultiMapped", "MultiMapped", "MultiMapped", "MultiMapped",
     + "MultiMapped", "MultiMapped", "MultiMapped", "MultiMapped",
     + "MultiMapped")), .Names = c("probe_ind", "fasta_name",
     + "probe_id", "align_status"), row.names = c(NA, -10L), class = "data.frame"),
     + probe_to_snp = structure(list(probe_snp_id = 1:10, ref_id = c(1L,
     + 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 9L), probe_align_id = c(137L,
     + 137L, 252L, 263L, 561L, 601L, 606L, 622L, 635L, 636L)), .Names = c("probe_snp_id",
     + "ref_id", "probe_align_id"), row.names = c(NA, -10L), class = "data.frame"),
     + reference = structure(list(ref_id = c(1L, 2L, 3L, 4L, 5L,
     + 6L, 7L, 8L, 9L, 11L), seqnames = c("1", "1", "1", "1", "1",
     + "1", "1", "1", "1", "1"), start = c(4785683L, 4785703L, 8595537L,
     + 8682000L, 10719780L, 12990759L, 13114284L, 13122474L, 13125617L,
     + 13150850L), end = c(4785683L, 4785703L, 8595537L, 8682000L,
     + 10719780L, 12990759L, 13114284L, 13122474L, 13125617L, 13150850L
     + ), filter = c("TRUE", "TRUE", "TRUE", "TRUE", "TRUE", "TRUE",
     + "TRUE", "TRUE", "TRUE", "TRUE"), vcf_annot_id = c(1L, 1L,
     + 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L)), .Names = c("ref_id", "seqnames",
     + "start", "end", "filter", "vcf_annot_id"), row.names = c(NA,
     + -10L), class = "data.frame"), vcf_annot = structure(list(
     + vcf_annot_id = 1L, vcf_name = "/Users/bottomly/Desktop/resources/vcfs/mgp.v3.snps.rsIDdbSNPv137.vcf.gz",
     + type = "SNV"), .Names = c("vcf_annot_id", "vcf_name",
     + "type"), row.names = c(NA, -1L), class = "data.frame")), .Names = c("allele",
     + "genotype", "probe_align", "probe_info", "probe_to_snp", "reference",
     + "vcf_annot")))
     >
     > test.schema.2 <- list(probe_info=list(db.cols=c("probe_ind", "fasta_name", "probe_id", "align_status"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "TEXT", "INTEGER", "TEXT"),
     + db.constr="CONSTRAINT probe_idx UNIQUE (fasta_name)",
     + dta.func=function(x) x, should.ignore=FALSE, foreign.keys=NULL),
     + probe_align=list(db.cols=c("probe_align_id", "probe_chr", "probe_start", "probe_end", "probe_ind"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "TEXT", "INTEGER", "INTEGER", "INTEGER"),
     + db.constr="CONSTRAINT geno_idx UNIQUE (probe_chr, probe_start, probe_end, probe_ind)",
     + dta.func=function(x) x, should.ignore=FALSE, foreign.keys=list(probe_info=list(local.keys="probe_ind", ext.keys="fasta_name"))),
     + vcf_annot=list(db.cols=c("vcf_annot_id", "vcf_name", "type"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "TEXT", "TEXT"),
     + db.constr="CONSTRAINT probe_idx UNIQUE (vcf_name, type)",
     + dta.func=function(x) x,
     + should.ignore=TRUE, foreign.keys=NULL),
     + reference=list(db.cols=c("ref_id", "seqnames", "start", "end", "filter", "vcf_annot_id"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "TEXT", "INTEGER", "INTEGER", "TEXT", "INTEGER"),
     + db.constr="CONSTRAINT ref_idx UNIQUE (seqnames, start, end, vcf_annot_id)",
     + dta.func=function(x) x, should.ignore=TRUE, foreign.keys=list(vcf_annot=list(local.keys="vcf_annot_id", ext.keys=c("vcf_name", "type")))),
     + allele=list(db.cols=c("allele_id", "alleles", "allele_num", "ref_id"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "TEXT", "INTEGER", "INTEGER"),
     + db.constr="CONSTRAINT alelle_idx UNIQUE (alleles, allele_num, ref_id)",
     + dta.func=function(x) x, should.ignore=TRUE, foreign.keys=list(vcf_annot=list(local.keys="vcf_annot_id", ext.keys=c("vcf_name", "type")),
     + reference=list(local.keys="ref_id", ext.keys=c("seqnames", "start", "end", "vcf_annot_id")))),
     + genotype=list(db.cols=c("geno_id", "geno_chr", "allele_num","strain", "ref_id"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "INTEGER", "INTEGER", "TEXT", "INTEGER"),
     + db.constr="CONSTRAINT geno_idx UNIQUE (ref_id, strain, geno_chr, allele_num)",
     + dta.func=function(x) x, should.ignore=TRUE, foreign.keys=list(vcf_annot=list(local.keys="vcf_annot_id", ext.keys=c("vcf_name", "type")),
     + reference=list(local.keys="ref_id", ext.keys=c("seqnames", "start", "end", "vcf_annot_id")))),
     + probe_to_snp=list(db.cols=c("probe_snp_id", "ref_id", "probe_align_id"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "INTEGER", "INTEGER"),
     + db.constr="CONSTRAINT p_s_idx UNIQUE (ref_id, probe_align_id)",
     + dta.func=function(x) x, should.ignore=TRUE, foreign.keys=list(vcf_annot=list(local.keys="vcf_annot_id", ext.keys=c("vcf_name", "type")),
     + reference=list(local.keys="ref_id", ext.keys=c("seqnames", "start", "end", "vcf_annot_id")),
     + probe_align=list(local.keys="probe_align_id", ext.keys=c("probe_chr", "probe_start", "probe_end")))))
     >
     >
     >
     >
     >
     > test_check("poplite")
     ── Warning (test-poplite.R:598:5): Querying with Database objects ──────────────
     `select_()` is deprecated as of dplyr 0.7.0.
     Please use `select()` instead.
     This warning is displayed once every 8 hours.
     Call `lifecycle::last_warnings()` to see where this warning was generated.
    
     ── ERROR (test-poplite.R:655:5): Querying with Database objects ────────────────
     Error: no applicable method for 'select_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"
     Backtrace:
     █
     1. └─poplite::select(sample.tracking.db, sample_id:dna_ind, .tables = "samples") test-poplite.R:655:4
     2. ├─dplyr::select_(.data, .dots = use.dots)
     3. └─poplite:::select_.Database(.data, .dots = use.dots)
     4. ├─poplite:::join(.data, use.tables)
     5. └─poplite:::join(.data, use.tables)
     6. └─poplite:::.local(obj, ...)
     7. └─dplyr::select_(...)
    
     ── ERROR (test-poplite.R:883:5): oligoMask queries that break poplite ──────────
     Error: no applicable method for 'select_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"
     Backtrace:
     █
     1. ├─base::as.data.frame(...) test-poplite.R:883:4
     2. └─poplite::select(test.database.1, probe_id, fasta_name, align_status)
     3. ├─dplyr::select_(.data, .dots = use.dots)
     4. └─poplite:::select_.Database(.data, .dots = use.dots)
     5. ├─dplyr::select_(join(.data, use.tables), .dots = as.list(clean.cols))
     6. ├─poplite:::join(.data, use.tables)
     7. └─poplite:::join(.data, use.tables)
     8. └─poplite:::.local(obj, ...)
     9. └─dplyr::select_(...)
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     Warning (test-poplite.R:598:5): Querying with Database objects
     ERROR (test-poplite.R:655:5): Querying with Database objects
     ERROR (test-poplite.R:883:5): oligoMask queries that break poplite
    
     [ FAIL 2 | WARN 1 | SKIP 0 | PASS 129 ]
     Error: Test failures
     In addition: Warning message:
     call dbDisconnect() when finished working with a connection
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.99.23
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘poplite.Rnw’ using Sweave
    Loading required package: dplyr
    
    Attaching package: ‘dplyr’
    
    The following objects are masked from ‘package:stats’:
    
     filter, lag
    
    The following objects are masked from ‘package:base’:
    
     intersect, setdiff, setequal, union
    
    Loading required package: DBI
    
    Attaching package: ‘poplite’
    
    The following object is masked from ‘package:dplyr’:
    
     select
    
    The following object is masked from ‘package:stats’:
    
     filter
    
    Error in makeSchemaFromData(dna, "dna") :
     ERROR: The names of the supplied data.frame need to be modified for the database see correct.df.names
    Starting clinical
    Starting samples
    Starting dna
    Warning: `select_()` is deprecated as of dplyr 0.7.0.
    Please use `select()` instead.
    This warning is displayed once every 8 hours.
    Call `lifecycle::last_warnings()` to see where this warning was generated.
    
    Error: processing vignette 'poplite.Rnw' failed with diagnostics:
     chunk 9
    Error in UseMethod("select_") :
     no applicable method for 'select_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"
    
    --- failed re-building ‘poplite.Rnw’
    
    SUMMARY: processing the following file failed:
     ‘poplite.Rnw’
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-oldrel-windows-ix86+x86_64

Version: 0.99.23
Check: tests
Result: ERROR
     Running ‘testthat.R’ [36s/44s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(Lahman)
     > library(DBI)
     > library(RSQLite)
     > library(poplite)
     Loading required package: dplyr
    
     Attaching package: 'dplyr'
    
     The following object is masked from 'package:testthat':
    
     matches
    
     The following objects are masked from 'package:stats':
    
     filter, lag
    
     The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    
     Attaching package: 'poplite'
    
     The following object is masked from 'package:dplyr':
    
     select
    
     The following object is masked from 'package:stats':
    
     filter
    
     >
     > test.db.1 <- function()
     + {
     + samples <- data.frame(sample_id=as.integer(sapply(1:100, function(x) rep(x,2))), wave=as.integer(sapply(1:100, function(x) 1:2)), did_collect=sample(c("Y", "N"), size=100, replace=T))
     +
     + dna <- samples[samples$did_collect == "Y",c("sample_id", "wave")]
     + dna$lab_id <- paste("dna", paste(dna$sample_id, dna$wave, sep="_"), sep="_")
     + dna$lab_id[sample.int(nrow(dna), size=10)] <- NA
     + dna$ng.ul <- abs(rnorm(n=nrow(dna), mean=146, sd=98))
     + dna$ng.ul[is.na(dna$lab_id)] <- NA
     +
     + clinical <- data.frame(sample_id=1:100, sex=sample(c("M", "F"), size=100, replace=T), age=sample(1:20, 100, replace=T), status=sample(c(0L,1L), size=100, replace=T), var_wave_1=rnorm(n=100), var_wave_2=rnorm(n=100))
     + clinical <- clinical[-sample.int(nrow(clinical), 12),]
     +
     + return(list(samples=samples, dna=dna, clinical=clinical))
     + }
     >
     > test.db.2 <- eval(structure(list(allele = structure(list(allele_id = 1:10, alleles = c(".",
     + "G", "A", ".", "A", "T", ".", "C", "A", "."), allele_num = c(-1L,
     + 0L, 1L, -1L, 0L, 1L, -1L, 0L, 1L, -1L), ref_id = c(1L, 1L, 1L,
     + 2L, 2L, 2L, 3L, 3L, 3L, 4L)), .Names = c("allele_id", "alleles",
     + "allele_num", "ref_id"), row.names = c(NA, -10L), class = "data.frame"),
     + genotype = structure(list(geno_id = c(1L, 2L, 3L, 4L, 5L,
     + 6L, 7L, 8L, 9L, 11L), geno_chr = c(1L, 1L, 1L, 1L, 1L, 1L,
     + 1L, 1L, 1L, 1L), allele_num = c(1L, 1L, 1L, 1L, 1L, 1L, 1L,
     + 1L, 1L, 1L), strain = c("NODShiLtJ", "NODShiLtJ", "NODShiLtJ",
     + "NODShiLtJ", "NODShiLtJ", "NODShiLtJ", "NODShiLtJ", "NODShiLtJ",
     + "NODShiLtJ", "NODShiLtJ"), ref_id = c(1L, 2L, 3L, 4L, 5L,
     + 6L, 7L, 8L, 9L, 11L)), .Names = c("geno_id", "geno_chr",
     + "allele_num", "strain", "ref_id"), row.names = c(NA, -10L
     + ), class = "data.frame"), probe_align = structure(list(probe_align_id = 1:10,
     + probe_chr = c("1", "1", "1", "1", "1", "1", "1", "1",
     + "1", "1"), probe_start = c(3214633L, 3214895L, 3215576L,
     + 3216284L, 3216483L, 3216537L, 3216591L, 3421710L, 3421740L,
     + 3421808L), probe_end = c(3214657L, 3214919L, 3215600L,
     + 3216308L, 3216507L, 3216561L, 3216615L, 3421734L, 3421764L,
     + 3421832L), probe_ind = 23944:23953), .Names = c("probe_align_id",
     + "probe_chr", "probe_start", "probe_end", "probe_ind"), row.names = c(NA,
     + -10L), class = "data.frame"), probe_info = structure(list(
     + probe_ind = 1:10, fasta_name = c("chr1:3044331-3044355;+;GGGCTCAAATTCACCTGTGTTAACT",
     + "chr1:3044334-3044358;+;AGGGGGCTCAAATTCACCTGTGTTA", "chr1:3044335-3044359;+;GAGGGGGCTCAAATTCACCTGTGTT",
     + "chr1:3044336-3044360;+;GGAGGGGGCTCAAATTCACCTGTGT", "chr1:3044337-3044361;+;GGGAGGGGGCTCAAATTCACCTGTG",
     + "chr1:3044504-3044528;+;AAGGCTTGGGCTATGCGCTCTCCAG", "chr1:3044557-3044581;+;AAGGTCCTCGCTCCTCTTTCATATA",
     + "chr1:3044558-3044582;+;GAAGGTCCTCGCTCCTCTTTCATAT", "chr1:3044559-3044583;+;GGAAGGTCCTCGCTCCTCTTTCATA",
     + "chr1:3044560-3044584;+;AGGAAGGTCCTCGCTCCTCTTTCAT"),
     + probe_id = c(271822L, 866088L, 240008L, 34772L, 396933L,
     + 613322L, 984143L, 826914L, 1075207L, 160847L), align_status = c("MultiMapped",
     + "MultiMapped", "MultiMapped", "MultiMapped", "MultiMapped",
     + "MultiMapped", "MultiMapped", "MultiMapped", "MultiMapped",
     + "MultiMapped")), .Names = c("probe_ind", "fasta_name",
     + "probe_id", "align_status"), row.names = c(NA, -10L), class = "data.frame"),
     + probe_to_snp = structure(list(probe_snp_id = 1:10, ref_id = c(1L,
     + 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 9L), probe_align_id = c(137L,
     + 137L, 252L, 263L, 561L, 601L, 606L, 622L, 635L, 636L)), .Names = c("probe_snp_id",
     + "ref_id", "probe_align_id"), row.names = c(NA, -10L), class = "data.frame"),
     + reference = structure(list(ref_id = c(1L, 2L, 3L, 4L, 5L,
     + 6L, 7L, 8L, 9L, 11L), seqnames = c("1", "1", "1", "1", "1",
     + "1", "1", "1", "1", "1"), start = c(4785683L, 4785703L, 8595537L,
     + 8682000L, 10719780L, 12990759L, 13114284L, 13122474L, 13125617L,
     + 13150850L), end = c(4785683L, 4785703L, 8595537L, 8682000L,
     + 10719780L, 12990759L, 13114284L, 13122474L, 13125617L, 13150850L
     + ), filter = c("TRUE", "TRUE", "TRUE", "TRUE", "TRUE", "TRUE",
     + "TRUE", "TRUE", "TRUE", "TRUE"), vcf_annot_id = c(1L, 1L,
     + 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L)), .Names = c("ref_id", "seqnames",
     + "start", "end", "filter", "vcf_annot_id"), row.names = c(NA,
     + -10L), class = "data.frame"), vcf_annot = structure(list(
     + vcf_annot_id = 1L, vcf_name = "/Users/bottomly/Desktop/resources/vcfs/mgp.v3.snps.rsIDdbSNPv137.vcf.gz",
     + type = "SNV"), .Names = c("vcf_annot_id", "vcf_name",
     + "type"), row.names = c(NA, -1L), class = "data.frame")), .Names = c("allele",
     + "genotype", "probe_align", "probe_info", "probe_to_snp", "reference",
     + "vcf_annot")))
     >
     > test.schema.2 <- list(probe_info=list(db.cols=c("probe_ind", "fasta_name", "probe_id", "align_status"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "TEXT", "INTEGER", "TEXT"),
     + db.constr="CONSTRAINT probe_idx UNIQUE (fasta_name)",
     + dta.func=function(x) x, should.ignore=FALSE, foreign.keys=NULL),
     + probe_align=list(db.cols=c("probe_align_id", "probe_chr", "probe_start", "probe_end", "probe_ind"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "TEXT", "INTEGER", "INTEGER", "INTEGER"),
     + db.constr="CONSTRAINT geno_idx UNIQUE (probe_chr, probe_start, probe_end, probe_ind)",
     + dta.func=function(x) x, should.ignore=FALSE, foreign.keys=list(probe_info=list(local.keys="probe_ind", ext.keys="fasta_name"))),
     + vcf_annot=list(db.cols=c("vcf_annot_id", "vcf_name", "type"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "TEXT", "TEXT"),
     + db.constr="CONSTRAINT probe_idx UNIQUE (vcf_name, type)",
     + dta.func=function(x) x,
     + should.ignore=TRUE, foreign.keys=NULL),
     + reference=list(db.cols=c("ref_id", "seqnames", "start", "end", "filter", "vcf_annot_id"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "TEXT", "INTEGER", "INTEGER", "TEXT", "INTEGER"),
     + db.constr="CONSTRAINT ref_idx UNIQUE (seqnames, start, end, vcf_annot_id)",
     + dta.func=function(x) x, should.ignore=TRUE, foreign.keys=list(vcf_annot=list(local.keys="vcf_annot_id", ext.keys=c("vcf_name", "type")))),
     + allele=list(db.cols=c("allele_id", "alleles", "allele_num", "ref_id"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "TEXT", "INTEGER", "INTEGER"),
     + db.constr="CONSTRAINT alelle_idx UNIQUE (alleles, allele_num, ref_id)",
     + dta.func=function(x) x, should.ignore=TRUE, foreign.keys=list(vcf_annot=list(local.keys="vcf_annot_id", ext.keys=c("vcf_name", "type")),
     + reference=list(local.keys="ref_id", ext.keys=c("seqnames", "start", "end", "vcf_annot_id")))),
     + genotype=list(db.cols=c("geno_id", "geno_chr", "allele_num","strain", "ref_id"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "INTEGER", "INTEGER", "TEXT", "INTEGER"),
     + db.constr="CONSTRAINT geno_idx UNIQUE (ref_id, strain, geno_chr, allele_num)",
     + dta.func=function(x) x, should.ignore=TRUE, foreign.keys=list(vcf_annot=list(local.keys="vcf_annot_id", ext.keys=c("vcf_name", "type")),
     + reference=list(local.keys="ref_id", ext.keys=c("seqnames", "start", "end", "vcf_annot_id")))),
     + probe_to_snp=list(db.cols=c("probe_snp_id", "ref_id", "probe_align_id"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "INTEGER", "INTEGER"),
     + db.constr="CONSTRAINT p_s_idx UNIQUE (ref_id, probe_align_id)",
     + dta.func=function(x) x, should.ignore=TRUE, foreign.keys=list(vcf_annot=list(local.keys="vcf_annot_id", ext.keys=c("vcf_name", "type")),
     + reference=list(local.keys="ref_id", ext.keys=c("seqnames", "start", "end", "vcf_annot_id")),
     + probe_align=list(local.keys="probe_align_id", ext.keys=c("probe_chr", "probe_start", "probe_end")))))
     >
     >
     >
     >
     >
     > test_check("poplite")
     ── Warning (test-poplite.R:598:5): Querying with Database objects ──────────────
     `select_()` is deprecated as of dplyr 0.7.0.
     Please use `select()` instead.
     This warning is displayed once every 8 hours.
     Call `lifecycle::last_warnings()` to see where this warning was generated.
    
     ── ERROR (test-poplite.R:655:5): Querying with Database objects ────────────────
     Error: no applicable method for 'select_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"
     Backtrace:
     █
     1. └─poplite::select(sample.tracking.db, sample_id:dna_ind, .tables = "samples") test-poplite.R:655:4
     2. ├─dplyr::select_(.data, .dots = use.dots)
     3. └─poplite:::select_.Database(.data, .dots = use.dots)
     4. ├─poplite:::join(.data, use.tables)
     5. └─poplite:::join(.data, use.tables)
     6. └─poplite:::.local(obj, ...)
     7. └─dplyr::select_(...)
    
     ── ERROR (test-poplite.R:883:5): oligoMask queries that break poplite ──────────
     Error: no applicable method for 'select_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"
     Backtrace:
     █
     1. ├─base::as.data.frame(...) test-poplite.R:883:4
     2. └─poplite::select(test.database.1, probe_id, fasta_name, align_status)
     3. ├─dplyr::select_(.data, .dots = use.dots)
     4. └─poplite:::select_.Database(.data, .dots = use.dots)
     5. ├─dplyr::select_(join(.data, use.tables), .dots = as.list(clean.cols))
     6. ├─poplite:::join(.data, use.tables)
     7. └─poplite:::join(.data, use.tables)
     8. └─poplite:::.local(obj, ...)
     9. └─dplyr::select_(...)
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     Warning (test-poplite.R:598:5): Querying with Database objects
     ERROR (test-poplite.R:655:5): Querying with Database objects
     ERROR (test-poplite.R:883:5): oligoMask queries that break poplite
    
     [ FAIL 2 | WARN 1 | SKIP 0 | PASS 129 ]
     Error: Test failures
     In addition: Warning message:
     call dbDisconnect() when finished working with a connection
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 0.99.23
Check: tests
Result: ERROR
     Running ‘testthat.R’ [30s/34s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(Lahman)
     > library(DBI)
     > library(RSQLite)
     > library(poplite)
     Loading required package: dplyr
    
     Attaching package: 'dplyr'
    
     The following object is masked from 'package:testthat':
    
     matches
    
     The following objects are masked from 'package:stats':
    
     filter, lag
    
     The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    
     Attaching package: 'poplite'
    
     The following object is masked from 'package:dplyr':
    
     select
    
     The following object is masked from 'package:stats':
    
     filter
    
     >
     > test.db.1 <- function()
     + {
     + samples <- data.frame(sample_id=as.integer(sapply(1:100, function(x) rep(x,2))), wave=as.integer(sapply(1:100, function(x) 1:2)), did_collect=sample(c("Y", "N"), size=100, replace=T))
     +
     + dna <- samples[samples$did_collect == "Y",c("sample_id", "wave")]
     + dna$lab_id <- paste("dna", paste(dna$sample_id, dna$wave, sep="_"), sep="_")
     + dna$lab_id[sample.int(nrow(dna), size=10)] <- NA
     + dna$ng.ul <- abs(rnorm(n=nrow(dna), mean=146, sd=98))
     + dna$ng.ul[is.na(dna$lab_id)] <- NA
     +
     + clinical <- data.frame(sample_id=1:100, sex=sample(c("M", "F"), size=100, replace=T), age=sample(1:20, 100, replace=T), status=sample(c(0L,1L), size=100, replace=T), var_wave_1=rnorm(n=100), var_wave_2=rnorm(n=100))
     + clinical <- clinical[-sample.int(nrow(clinical), 12),]
     +
     + return(list(samples=samples, dna=dna, clinical=clinical))
     + }
     >
     > test.db.2 <- eval(structure(list(allele = structure(list(allele_id = 1:10, alleles = c(".",
     + "G", "A", ".", "A", "T", ".", "C", "A", "."), allele_num = c(-1L,
     + 0L, 1L, -1L, 0L, 1L, -1L, 0L, 1L, -1L), ref_id = c(1L, 1L, 1L,
     + 2L, 2L, 2L, 3L, 3L, 3L, 4L)), .Names = c("allele_id", "alleles",
     + "allele_num", "ref_id"), row.names = c(NA, -10L), class = "data.frame"),
     + genotype = structure(list(geno_id = c(1L, 2L, 3L, 4L, 5L,
     + 6L, 7L, 8L, 9L, 11L), geno_chr = c(1L, 1L, 1L, 1L, 1L, 1L,
     + 1L, 1L, 1L, 1L), allele_num = c(1L, 1L, 1L, 1L, 1L, 1L, 1L,
     + 1L, 1L, 1L), strain = c("NODShiLtJ", "NODShiLtJ", "NODShiLtJ",
     + "NODShiLtJ", "NODShiLtJ", "NODShiLtJ", "NODShiLtJ", "NODShiLtJ",
     + "NODShiLtJ", "NODShiLtJ"), ref_id = c(1L, 2L, 3L, 4L, 5L,
     + 6L, 7L, 8L, 9L, 11L)), .Names = c("geno_id", "geno_chr",
     + "allele_num", "strain", "ref_id"), row.names = c(NA, -10L
     + ), class = "data.frame"), probe_align = structure(list(probe_align_id = 1:10,
     + probe_chr = c("1", "1", "1", "1", "1", "1", "1", "1",
     + "1", "1"), probe_start = c(3214633L, 3214895L, 3215576L,
     + 3216284L, 3216483L, 3216537L, 3216591L, 3421710L, 3421740L,
     + 3421808L), probe_end = c(3214657L, 3214919L, 3215600L,
     + 3216308L, 3216507L, 3216561L, 3216615L, 3421734L, 3421764L,
     + 3421832L), probe_ind = 23944:23953), .Names = c("probe_align_id",
     + "probe_chr", "probe_start", "probe_end", "probe_ind"), row.names = c(NA,
     + -10L), class = "data.frame"), probe_info = structure(list(
     + probe_ind = 1:10, fasta_name = c("chr1:3044331-3044355;+;GGGCTCAAATTCACCTGTGTTAACT",
     + "chr1:3044334-3044358;+;AGGGGGCTCAAATTCACCTGTGTTA", "chr1:3044335-3044359;+;GAGGGGGCTCAAATTCACCTGTGTT",
     + "chr1:3044336-3044360;+;GGAGGGGGCTCAAATTCACCTGTGT", "chr1:3044337-3044361;+;GGGAGGGGGCTCAAATTCACCTGTG",
     + "chr1:3044504-3044528;+;AAGGCTTGGGCTATGCGCTCTCCAG", "chr1:3044557-3044581;+;AAGGTCCTCGCTCCTCTTTCATATA",
     + "chr1:3044558-3044582;+;GAAGGTCCTCGCTCCTCTTTCATAT", "chr1:3044559-3044583;+;GGAAGGTCCTCGCTCCTCTTTCATA",
     + "chr1:3044560-3044584;+;AGGAAGGTCCTCGCTCCTCTTTCAT"),
     + probe_id = c(271822L, 866088L, 240008L, 34772L, 396933L,
     + 613322L, 984143L, 826914L, 1075207L, 160847L), align_status = c("MultiMapped",
     + "MultiMapped", "MultiMapped", "MultiMapped", "MultiMapped",
     + "MultiMapped", "MultiMapped", "MultiMapped", "MultiMapped",
     + "MultiMapped")), .Names = c("probe_ind", "fasta_name",
     + "probe_id", "align_status"), row.names = c(NA, -10L), class = "data.frame"),
     + probe_to_snp = structure(list(probe_snp_id = 1:10, ref_id = c(1L,
     + 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 9L), probe_align_id = c(137L,
     + 137L, 252L, 263L, 561L, 601L, 606L, 622L, 635L, 636L)), .Names = c("probe_snp_id",
     + "ref_id", "probe_align_id"), row.names = c(NA, -10L), class = "data.frame"),
     + reference = structure(list(ref_id = c(1L, 2L, 3L, 4L, 5L,
     + 6L, 7L, 8L, 9L, 11L), seqnames = c("1", "1", "1", "1", "1",
     + "1", "1", "1", "1", "1"), start = c(4785683L, 4785703L, 8595537L,
     + 8682000L, 10719780L, 12990759L, 13114284L, 13122474L, 13125617L,
     + 13150850L), end = c(4785683L, 4785703L, 8595537L, 8682000L,
     + 10719780L, 12990759L, 13114284L, 13122474L, 13125617L, 13150850L
     + ), filter = c("TRUE", "TRUE", "TRUE", "TRUE", "TRUE", "TRUE",
     + "TRUE", "TRUE", "TRUE", "TRUE"), vcf_annot_id = c(1L, 1L,
     + 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L)), .Names = c("ref_id", "seqnames",
     + "start", "end", "filter", "vcf_annot_id"), row.names = c(NA,
     + -10L), class = "data.frame"), vcf_annot = structure(list(
     + vcf_annot_id = 1L, vcf_name = "/Users/bottomly/Desktop/resources/vcfs/mgp.v3.snps.rsIDdbSNPv137.vcf.gz",
     + type = "SNV"), .Names = c("vcf_annot_id", "vcf_name",
     + "type"), row.names = c(NA, -1L), class = "data.frame")), .Names = c("allele",
     + "genotype", "probe_align", "probe_info", "probe_to_snp", "reference",
     + "vcf_annot")))
     >
     > test.schema.2 <- list(probe_info=list(db.cols=c("probe_ind", "fasta_name", "probe_id", "align_status"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "TEXT", "INTEGER", "TEXT"),
     + db.constr="CONSTRAINT probe_idx UNIQUE (fasta_name)",
     + dta.func=function(x) x, should.ignore=FALSE, foreign.keys=NULL),
     + probe_align=list(db.cols=c("probe_align_id", "probe_chr", "probe_start", "probe_end", "probe_ind"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "TEXT", "INTEGER", "INTEGER", "INTEGER"),
     + db.constr="CONSTRAINT geno_idx UNIQUE (probe_chr, probe_start, probe_end, probe_ind)",
     + dta.func=function(x) x, should.ignore=FALSE, foreign.keys=list(probe_info=list(local.keys="probe_ind", ext.keys="fasta_name"))),
     + vcf_annot=list(db.cols=c("vcf_annot_id", "vcf_name", "type"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "TEXT", "TEXT"),
     + db.constr="CONSTRAINT probe_idx UNIQUE (vcf_name, type)",
     + dta.func=function(x) x,
     + should.ignore=TRUE, foreign.keys=NULL),
     + reference=list(db.cols=c("ref_id", "seqnames", "start", "end", "filter", "vcf_annot_id"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "TEXT", "INTEGER", "INTEGER", "TEXT", "INTEGER"),
     + db.constr="CONSTRAINT ref_idx UNIQUE (seqnames, start, end, vcf_annot_id)",
     + dta.func=function(x) x, should.ignore=TRUE, foreign.keys=list(vcf_annot=list(local.keys="vcf_annot_id", ext.keys=c("vcf_name", "type")))),
     + allele=list(db.cols=c("allele_id", "alleles", "allele_num", "ref_id"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "TEXT", "INTEGER", "INTEGER"),
     + db.constr="CONSTRAINT alelle_idx UNIQUE (alleles, allele_num, ref_id)",
     + dta.func=function(x) x, should.ignore=TRUE, foreign.keys=list(vcf_annot=list(local.keys="vcf_annot_id", ext.keys=c("vcf_name", "type")),
     + reference=list(local.keys="ref_id", ext.keys=c("seqnames", "start", "end", "vcf_annot_id")))),
     + genotype=list(db.cols=c("geno_id", "geno_chr", "allele_num","strain", "ref_id"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "INTEGER", "INTEGER", "TEXT", "INTEGER"),
     + db.constr="CONSTRAINT geno_idx UNIQUE (ref_id, strain, geno_chr, allele_num)",
     + dta.func=function(x) x, should.ignore=TRUE, foreign.keys=list(vcf_annot=list(local.keys="vcf_annot_id", ext.keys=c("vcf_name", "type")),
     + reference=list(local.keys="ref_id", ext.keys=c("seqnames", "start", "end", "vcf_annot_id")))),
     + probe_to_snp=list(db.cols=c("probe_snp_id", "ref_id", "probe_align_id"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "INTEGER", "INTEGER"),
     + db.constr="CONSTRAINT p_s_idx UNIQUE (ref_id, probe_align_id)",
     + dta.func=function(x) x, should.ignore=TRUE, foreign.keys=list(vcf_annot=list(local.keys="vcf_annot_id", ext.keys=c("vcf_name", "type")),
     + reference=list(local.keys="ref_id", ext.keys=c("seqnames", "start", "end", "vcf_annot_id")),
     + probe_align=list(local.keys="probe_align_id", ext.keys=c("probe_chr", "probe_start", "probe_end")))))
     >
     >
     >
     >
     >
     > test_check("poplite")
     ── Warning (test-poplite.R:598:5): Querying with Database objects ──────────────
     `select_()` is deprecated as of dplyr 0.7.0.
     Please use `select()` instead.
     This warning is displayed once every 8 hours.
     Call `lifecycle::last_warnings()` to see where this warning was generated.
    
     ── ERROR (test-poplite.R:655:5): Querying with Database objects ────────────────
     Error: no applicable method for 'select_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"
     Backtrace:
     █
     1. └─poplite::select(sample.tracking.db, sample_id:dna_ind, .tables = "samples") test-poplite.R:655:4
     2. ├─dplyr::select_(.data, .dots = use.dots)
     3. └─poplite:::select_.Database(.data, .dots = use.dots)
     4. ├─poplite:::join(.data, use.tables)
     5. └─poplite:::join(.data, use.tables)
     6. └─poplite:::.local(obj, ...)
     7. └─dplyr::select_(...)
    
     ── ERROR (test-poplite.R:883:5): oligoMask queries that break poplite ──────────
     Error: no applicable method for 'select_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"
     Backtrace:
     █
     1. ├─base::as.data.frame(...) test-poplite.R:883:4
     2. └─poplite::select(test.database.1, probe_id, fasta_name, align_status)
     3. ├─dplyr::select_(.data, .dots = use.dots)
     4. └─poplite:::select_.Database(.data, .dots = use.dots)
     5. ├─dplyr::select_(join(.data, use.tables), .dots = as.list(clean.cols))
     6. ├─poplite:::join(.data, use.tables)
     7. └─poplite:::join(.data, use.tables)
     8. └─poplite:::.local(obj, ...)
     9. └─dplyr::select_(...)
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     Warning (test-poplite.R:598:5): Querying with Database objects
     ERROR (test-poplite.R:655:5): Querying with Database objects
     ERROR (test-poplite.R:883:5): oligoMask queries that break poplite
    
     [ FAIL 2 | WARN 1 | SKIP 0 | PASS 129 ]
     Error: Test failures
     In addition: Warning message:
     call dbDisconnect() when finished working with a connection
     Execution halted
Flavor: r-patched-linux-x86_64

Version: 0.99.23
Check: tests
Result: ERROR
     Running ‘testthat.R’ [51s/57s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(Lahman)
     > library(DBI)
     > library(RSQLite)
     > library(poplite)
     Loading required package: dplyr
    
     Attaching package: 'dplyr'
    
     The following object is masked from 'package:testthat':
    
     matches
    
     The following objects are masked from 'package:stats':
    
     filter, lag
    
     The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    
     Attaching package: 'poplite'
    
     The following object is masked from 'package:dplyr':
    
     select
    
     The following object is masked from 'package:stats':
    
     filter
    
     >
     > test.db.1 <- function()
     + {
     + samples <- data.frame(sample_id=as.integer(sapply(1:100, function(x) rep(x,2))), wave=as.integer(sapply(1:100, function(x) 1:2)), did_collect=sample(c("Y", "N"), size=100, replace=T))
     +
     + dna <- samples[samples$did_collect == "Y",c("sample_id", "wave")]
     + dna$lab_id <- paste("dna", paste(dna$sample_id, dna$wave, sep="_"), sep="_")
     + dna$lab_id[sample.int(nrow(dna), size=10)] <- NA
     + dna$ng.ul <- abs(rnorm(n=nrow(dna), mean=146, sd=98))
     + dna$ng.ul[is.na(dna$lab_id)] <- NA
     +
     + clinical <- data.frame(sample_id=1:100, sex=sample(c("M", "F"), size=100, replace=T), age=sample(1:20, 100, replace=T), status=sample(c(0L,1L), size=100, replace=T), var_wave_1=rnorm(n=100), var_wave_2=rnorm(n=100))
     + clinical <- clinical[-sample.int(nrow(clinical), 12),]
     +
     + return(list(samples=samples, dna=dna, clinical=clinical))
     + }
     >
     > test.db.2 <- eval(structure(list(allele = structure(list(allele_id = 1:10, alleles = c(".",
     + "G", "A", ".", "A", "T", ".", "C", "A", "."), allele_num = c(-1L,
     + 0L, 1L, -1L, 0L, 1L, -1L, 0L, 1L, -1L), ref_id = c(1L, 1L, 1L,
     + 2L, 2L, 2L, 3L, 3L, 3L, 4L)), .Names = c("allele_id", "alleles",
     + "allele_num", "ref_id"), row.names = c(NA, -10L), class = "data.frame"),
     + genotype = structure(list(geno_id = c(1L, 2L, 3L, 4L, 5L,
     + 6L, 7L, 8L, 9L, 11L), geno_chr = c(1L, 1L, 1L, 1L, 1L, 1L,
     + 1L, 1L, 1L, 1L), allele_num = c(1L, 1L, 1L, 1L, 1L, 1L, 1L,
     + 1L, 1L, 1L), strain = c("NODShiLtJ", "NODShiLtJ", "NODShiLtJ",
     + "NODShiLtJ", "NODShiLtJ", "NODShiLtJ", "NODShiLtJ", "NODShiLtJ",
     + "NODShiLtJ", "NODShiLtJ"), ref_id = c(1L, 2L, 3L, 4L, 5L,
     + 6L, 7L, 8L, 9L, 11L)), .Names = c("geno_id", "geno_chr",
     + "allele_num", "strain", "ref_id"), row.names = c(NA, -10L
     + ), class = "data.frame"), probe_align = structure(list(probe_align_id = 1:10,
     + probe_chr = c("1", "1", "1", "1", "1", "1", "1", "1",
     + "1", "1"), probe_start = c(3214633L, 3214895L, 3215576L,
     + 3216284L, 3216483L, 3216537L, 3216591L, 3421710L, 3421740L,
     + 3421808L), probe_end = c(3214657L, 3214919L, 3215600L,
     + 3216308L, 3216507L, 3216561L, 3216615L, 3421734L, 3421764L,
     + 3421832L), probe_ind = 23944:23953), .Names = c("probe_align_id",
     + "probe_chr", "probe_start", "probe_end", "probe_ind"), row.names = c(NA,
     + -10L), class = "data.frame"), probe_info = structure(list(
     + probe_ind = 1:10, fasta_name = c("chr1:3044331-3044355;+;GGGCTCAAATTCACCTGTGTTAACT",
     + "chr1:3044334-3044358;+;AGGGGGCTCAAATTCACCTGTGTTA", "chr1:3044335-3044359;+;GAGGGGGCTCAAATTCACCTGTGTT",
     + "chr1:3044336-3044360;+;GGAGGGGGCTCAAATTCACCTGTGT", "chr1:3044337-3044361;+;GGGAGGGGGCTCAAATTCACCTGTG",
     + "chr1:3044504-3044528;+;AAGGCTTGGGCTATGCGCTCTCCAG", "chr1:3044557-3044581;+;AAGGTCCTCGCTCCTCTTTCATATA",
     + "chr1:3044558-3044582;+;GAAGGTCCTCGCTCCTCTTTCATAT", "chr1:3044559-3044583;+;GGAAGGTCCTCGCTCCTCTTTCATA",
     + "chr1:3044560-3044584;+;AGGAAGGTCCTCGCTCCTCTTTCAT"),
     + probe_id = c(271822L, 866088L, 240008L, 34772L, 396933L,
     + 613322L, 984143L, 826914L, 1075207L, 160847L), align_status = c("MultiMapped",
     + "MultiMapped", "MultiMapped", "MultiMapped", "MultiMapped",
     + "MultiMapped", "MultiMapped", "MultiMapped", "MultiMapped",
     + "MultiMapped")), .Names = c("probe_ind", "fasta_name",
     + "probe_id", "align_status"), row.names = c(NA, -10L), class = "data.frame"),
     + probe_to_snp = structure(list(probe_snp_id = 1:10, ref_id = c(1L,
     + 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 9L), probe_align_id = c(137L,
     + 137L, 252L, 263L, 561L, 601L, 606L, 622L, 635L, 636L)), .Names = c("probe_snp_id",
     + "ref_id", "probe_align_id"), row.names = c(NA, -10L), class = "data.frame"),
     + reference = structure(list(ref_id = c(1L, 2L, 3L, 4L, 5L,
     + 6L, 7L, 8L, 9L, 11L), seqnames = c("1", "1", "1", "1", "1",
     + "1", "1", "1", "1", "1"), start = c(4785683L, 4785703L, 8595537L,
     + 8682000L, 10719780L, 12990759L, 13114284L, 13122474L, 13125617L,
     + 13150850L), end = c(4785683L, 4785703L, 8595537L, 8682000L,
     + 10719780L, 12990759L, 13114284L, 13122474L, 13125617L, 13150850L
     + ), filter = c("TRUE", "TRUE", "TRUE", "TRUE", "TRUE", "TRUE",
     + "TRUE", "TRUE", "TRUE", "TRUE"), vcf_annot_id = c(1L, 1L,
     + 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L)), .Names = c("ref_id", "seqnames",
     + "start", "end", "filter", "vcf_annot_id"), row.names = c(NA,
     + -10L), class = "data.frame"), vcf_annot = structure(list(
     + vcf_annot_id = 1L, vcf_name = "/Users/bottomly/Desktop/resources/vcfs/mgp.v3.snps.rsIDdbSNPv137.vcf.gz",
     + type = "SNV"), .Names = c("vcf_annot_id", "vcf_name",
     + "type"), row.names = c(NA, -1L), class = "data.frame")), .Names = c("allele",
     + "genotype", "probe_align", "probe_info", "probe_to_snp", "reference",
     + "vcf_annot")))
     >
     > test.schema.2 <- list(probe_info=list(db.cols=c("probe_ind", "fasta_name", "probe_id", "align_status"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "TEXT", "INTEGER", "TEXT"),
     + db.constr="CONSTRAINT probe_idx UNIQUE (fasta_name)",
     + dta.func=function(x) x, should.ignore=FALSE, foreign.keys=NULL),
     + probe_align=list(db.cols=c("probe_align_id", "probe_chr", "probe_start", "probe_end", "probe_ind"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "TEXT", "INTEGER", "INTEGER", "INTEGER"),
     + db.constr="CONSTRAINT geno_idx UNIQUE (probe_chr, probe_start, probe_end, probe_ind)",
     + dta.func=function(x) x, should.ignore=FALSE, foreign.keys=list(probe_info=list(local.keys="probe_ind", ext.keys="fasta_name"))),
     + vcf_annot=list(db.cols=c("vcf_annot_id", "vcf_name", "type"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "TEXT", "TEXT"),
     + db.constr="CONSTRAINT probe_idx UNIQUE (vcf_name, type)",
     + dta.func=function(x) x,
     + should.ignore=TRUE, foreign.keys=NULL),
     + reference=list(db.cols=c("ref_id", "seqnames", "start", "end", "filter", "vcf_annot_id"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "TEXT", "INTEGER", "INTEGER", "TEXT", "INTEGER"),
     + db.constr="CONSTRAINT ref_idx UNIQUE (seqnames, start, end, vcf_annot_id)",
     + dta.func=function(x) x, should.ignore=TRUE, foreign.keys=list(vcf_annot=list(local.keys="vcf_annot_id", ext.keys=c("vcf_name", "type")))),
     + allele=list(db.cols=c("allele_id", "alleles", "allele_num", "ref_id"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "TEXT", "INTEGER", "INTEGER"),
     + db.constr="CONSTRAINT alelle_idx UNIQUE (alleles, allele_num, ref_id)",
     + dta.func=function(x) x, should.ignore=TRUE, foreign.keys=list(vcf_annot=list(local.keys="vcf_annot_id", ext.keys=c("vcf_name", "type")),
     + reference=list(local.keys="ref_id", ext.keys=c("seqnames", "start", "end", "vcf_annot_id")))),
     + genotype=list(db.cols=c("geno_id", "geno_chr", "allele_num","strain", "ref_id"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "INTEGER", "INTEGER", "TEXT", "INTEGER"),
     + db.constr="CONSTRAINT geno_idx UNIQUE (ref_id, strain, geno_chr, allele_num)",
     + dta.func=function(x) x, should.ignore=TRUE, foreign.keys=list(vcf_annot=list(local.keys="vcf_annot_id", ext.keys=c("vcf_name", "type")),
     + reference=list(local.keys="ref_id", ext.keys=c("seqnames", "start", "end", "vcf_annot_id")))),
     + probe_to_snp=list(db.cols=c("probe_snp_id", "ref_id", "probe_align_id"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "INTEGER", "INTEGER"),
     + db.constr="CONSTRAINT p_s_idx UNIQUE (ref_id, probe_align_id)",
     + dta.func=function(x) x, should.ignore=TRUE, foreign.keys=list(vcf_annot=list(local.keys="vcf_annot_id", ext.keys=c("vcf_name", "type")),
     + reference=list(local.keys="ref_id", ext.keys=c("seqnames", "start", "end", "vcf_annot_id")),
     + probe_align=list(local.keys="probe_align_id", ext.keys=c("probe_chr", "probe_start", "probe_end")))))
     >
     >
     >
     >
     >
     > test_check("poplite")
     ── Warning (test-poplite.R:598:5): Querying with Database objects ──────────────
     `select_()` is deprecated as of dplyr 0.7.0.
     Please use `select()` instead.
     This warning is displayed once every 8 hours.
     Call `lifecycle::last_warnings()` to see where this warning was generated.
    
     ── ERROR (test-poplite.R:655:5): Querying with Database objects ────────────────
     Error: no applicable method for 'select_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"
     Backtrace:
     █
     1. └─poplite::select(sample.tracking.db, sample_id:dna_ind, .tables = "samples") test-poplite.R:655:4
     2. ├─dplyr::select_(.data, .dots = use.dots)
     3. └─poplite:::select_.Database(.data, .dots = use.dots)
     4. ├─poplite:::join(.data, use.tables)
     5. └─poplite:::join(.data, use.tables)
     6. └─poplite:::.local(obj, ...)
     7. └─dplyr::select_(...)
    
     ── ERROR (test-poplite.R:883:5): oligoMask queries that break poplite ──────────
     Error: no applicable method for 'select_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"
     Backtrace:
     █
     1. ├─base::as.data.frame(...) test-poplite.R:883:4
     2. └─poplite::select(test.database.1, probe_id, fasta_name, align_status)
     3. ├─dplyr::select_(.data, .dots = use.dots)
     4. └─poplite:::select_.Database(.data, .dots = use.dots)
     5. ├─dplyr::select_(join(.data, use.tables), .dots = as.list(clean.cols))
     6. ├─poplite:::join(.data, use.tables)
     7. └─poplite:::join(.data, use.tables)
     8. └─poplite:::.local(obj, ...)
     9. └─dplyr::select_(...)
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     Warning (test-poplite.R:598:5): Querying with Database objects
     ERROR (test-poplite.R:655:5): Querying with Database objects
     ERROR (test-poplite.R:883:5): oligoMask queries that break poplite
    
     [ FAIL 2 | WARN 1 | SKIP 0 | PASS 129 ]
     Error: Test failures
     In addition: Warning message:
     call dbDisconnect() when finished working with a connection
     Execution halted
Flavor: r-patched-solaris-x86

Version: 0.99.23
Check: tests
Result: ERROR
     Running ‘testthat.R’ [28s/31s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(Lahman)
     > library(DBI)
     > library(RSQLite)
     > library(poplite)
     Loading required package: dplyr
    
     Attaching package: 'dplyr'
    
     The following object is masked from 'package:testthat':
    
     matches
    
     The following objects are masked from 'package:stats':
    
     filter, lag
    
     The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    
     Attaching package: 'poplite'
    
     The following object is masked from 'package:dplyr':
    
     select
    
     The following object is masked from 'package:stats':
    
     filter
    
     >
     > test.db.1 <- function()
     + {
     + samples <- data.frame(sample_id=as.integer(sapply(1:100, function(x) rep(x,2))), wave=as.integer(sapply(1:100, function(x) 1:2)), did_collect=sample(c("Y", "N"), size=100, replace=T))
     +
     + dna <- samples[samples$did_collect == "Y",c("sample_id", "wave")]
     + dna$lab_id <- paste("dna", paste(dna$sample_id, dna$wave, sep="_"), sep="_")
     + dna$lab_id[sample.int(nrow(dna), size=10)] <- NA
     + dna$ng.ul <- abs(rnorm(n=nrow(dna), mean=146, sd=98))
     + dna$ng.ul[is.na(dna$lab_id)] <- NA
     +
     + clinical <- data.frame(sample_id=1:100, sex=sample(c("M", "F"), size=100, replace=T), age=sample(1:20, 100, replace=T), status=sample(c(0L,1L), size=100, replace=T), var_wave_1=rnorm(n=100), var_wave_2=rnorm(n=100))
     + clinical <- clinical[-sample.int(nrow(clinical), 12),]
     +
     + return(list(samples=samples, dna=dna, clinical=clinical))
     + }
     >
     > test.db.2 <- eval(structure(list(allele = structure(list(allele_id = 1:10, alleles = c(".",
     + "G", "A", ".", "A", "T", ".", "C", "A", "."), allele_num = c(-1L,
     + 0L, 1L, -1L, 0L, 1L, -1L, 0L, 1L, -1L), ref_id = c(1L, 1L, 1L,
     + 2L, 2L, 2L, 3L, 3L, 3L, 4L)), .Names = c("allele_id", "alleles",
     + "allele_num", "ref_id"), row.names = c(NA, -10L), class = "data.frame"),
     + genotype = structure(list(geno_id = c(1L, 2L, 3L, 4L, 5L,
     + 6L, 7L, 8L, 9L, 11L), geno_chr = c(1L, 1L, 1L, 1L, 1L, 1L,
     + 1L, 1L, 1L, 1L), allele_num = c(1L, 1L, 1L, 1L, 1L, 1L, 1L,
     + 1L, 1L, 1L), strain = c("NODShiLtJ", "NODShiLtJ", "NODShiLtJ",
     + "NODShiLtJ", "NODShiLtJ", "NODShiLtJ", "NODShiLtJ", "NODShiLtJ",
     + "NODShiLtJ", "NODShiLtJ"), ref_id = c(1L, 2L, 3L, 4L, 5L,
     + 6L, 7L, 8L, 9L, 11L)), .Names = c("geno_id", "geno_chr",
     + "allele_num", "strain", "ref_id"), row.names = c(NA, -10L
     + ), class = "data.frame"), probe_align = structure(list(probe_align_id = 1:10,
     + probe_chr = c("1", "1", "1", "1", "1", "1", "1", "1",
     + "1", "1"), probe_start = c(3214633L, 3214895L, 3215576L,
     + 3216284L, 3216483L, 3216537L, 3216591L, 3421710L, 3421740L,
     + 3421808L), probe_end = c(3214657L, 3214919L, 3215600L,
     + 3216308L, 3216507L, 3216561L, 3216615L, 3421734L, 3421764L,
     + 3421832L), probe_ind = 23944:23953), .Names = c("probe_align_id",
     + "probe_chr", "probe_start", "probe_end", "probe_ind"), row.names = c(NA,
     + -10L), class = "data.frame"), probe_info = structure(list(
     + probe_ind = 1:10, fasta_name = c("chr1:3044331-3044355;+;GGGCTCAAATTCACCTGTGTTAACT",
     + "chr1:3044334-3044358;+;AGGGGGCTCAAATTCACCTGTGTTA", "chr1:3044335-3044359;+;GAGGGGGCTCAAATTCACCTGTGTT",
     + "chr1:3044336-3044360;+;GGAGGGGGCTCAAATTCACCTGTGT", "chr1:3044337-3044361;+;GGGAGGGGGCTCAAATTCACCTGTG",
     + "chr1:3044504-3044528;+;AAGGCTTGGGCTATGCGCTCTCCAG", "chr1:3044557-3044581;+;AAGGTCCTCGCTCCTCTTTCATATA",
     + "chr1:3044558-3044582;+;GAAGGTCCTCGCTCCTCTTTCATAT", "chr1:3044559-3044583;+;GGAAGGTCCTCGCTCCTCTTTCATA",
     + "chr1:3044560-3044584;+;AGGAAGGTCCTCGCTCCTCTTTCAT"),
     + probe_id = c(271822L, 866088L, 240008L, 34772L, 396933L,
     + 613322L, 984143L, 826914L, 1075207L, 160847L), align_status = c("MultiMapped",
     + "MultiMapped", "MultiMapped", "MultiMapped", "MultiMapped",
     + "MultiMapped", "MultiMapped", "MultiMapped", "MultiMapped",
     + "MultiMapped")), .Names = c("probe_ind", "fasta_name",
     + "probe_id", "align_status"), row.names = c(NA, -10L), class = "data.frame"),
     + probe_to_snp = structure(list(probe_snp_id = 1:10, ref_id = c(1L,
     + 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 9L), probe_align_id = c(137L,
     + 137L, 252L, 263L, 561L, 601L, 606L, 622L, 635L, 636L)), .Names = c("probe_snp_id",
     + "ref_id", "probe_align_id"), row.names = c(NA, -10L), class = "data.frame"),
     + reference = structure(list(ref_id = c(1L, 2L, 3L, 4L, 5L,
     + 6L, 7L, 8L, 9L, 11L), seqnames = c("1", "1", "1", "1", "1",
     + "1", "1", "1", "1", "1"), start = c(4785683L, 4785703L, 8595537L,
     + 8682000L, 10719780L, 12990759L, 13114284L, 13122474L, 13125617L,
     + 13150850L), end = c(4785683L, 4785703L, 8595537L, 8682000L,
     + 10719780L, 12990759L, 13114284L, 13122474L, 13125617L, 13150850L
     + ), filter = c("TRUE", "TRUE", "TRUE", "TRUE", "TRUE", "TRUE",
     + "TRUE", "TRUE", "TRUE", "TRUE"), vcf_annot_id = c(1L, 1L,
     + 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L)), .Names = c("ref_id", "seqnames",
     + "start", "end", "filter", "vcf_annot_id"), row.names = c(NA,
     + -10L), class = "data.frame"), vcf_annot = structure(list(
     + vcf_annot_id = 1L, vcf_name = "/Users/bottomly/Desktop/resources/vcfs/mgp.v3.snps.rsIDdbSNPv137.vcf.gz",
     + type = "SNV"), .Names = c("vcf_annot_id", "vcf_name",
     + "type"), row.names = c(NA, -1L), class = "data.frame")), .Names = c("allele",
     + "genotype", "probe_align", "probe_info", "probe_to_snp", "reference",
     + "vcf_annot")))
     >
     > test.schema.2 <- list(probe_info=list(db.cols=c("probe_ind", "fasta_name", "probe_id", "align_status"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "TEXT", "INTEGER", "TEXT"),
     + db.constr="CONSTRAINT probe_idx UNIQUE (fasta_name)",
     + dta.func=function(x) x, should.ignore=FALSE, foreign.keys=NULL),
     + probe_align=list(db.cols=c("probe_align_id", "probe_chr", "probe_start", "probe_end", "probe_ind"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "TEXT", "INTEGER", "INTEGER", "INTEGER"),
     + db.constr="CONSTRAINT geno_idx UNIQUE (probe_chr, probe_start, probe_end, probe_ind)",
     + dta.func=function(x) x, should.ignore=FALSE, foreign.keys=list(probe_info=list(local.keys="probe_ind", ext.keys="fasta_name"))),
     + vcf_annot=list(db.cols=c("vcf_annot_id", "vcf_name", "type"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "TEXT", "TEXT"),
     + db.constr="CONSTRAINT probe_idx UNIQUE (vcf_name, type)",
     + dta.func=function(x) x,
     + should.ignore=TRUE, foreign.keys=NULL),
     + reference=list(db.cols=c("ref_id", "seqnames", "start", "end", "filter", "vcf_annot_id"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "TEXT", "INTEGER", "INTEGER", "TEXT", "INTEGER"),
     + db.constr="CONSTRAINT ref_idx UNIQUE (seqnames, start, end, vcf_annot_id)",
     + dta.func=function(x) x, should.ignore=TRUE, foreign.keys=list(vcf_annot=list(local.keys="vcf_annot_id", ext.keys=c("vcf_name", "type")))),
     + allele=list(db.cols=c("allele_id", "alleles", "allele_num", "ref_id"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "TEXT", "INTEGER", "INTEGER"),
     + db.constr="CONSTRAINT alelle_idx UNIQUE (alleles, allele_num, ref_id)",
     + dta.func=function(x) x, should.ignore=TRUE, foreign.keys=list(vcf_annot=list(local.keys="vcf_annot_id", ext.keys=c("vcf_name", "type")),
     + reference=list(local.keys="ref_id", ext.keys=c("seqnames", "start", "end", "vcf_annot_id")))),
     + genotype=list(db.cols=c("geno_id", "geno_chr", "allele_num","strain", "ref_id"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "INTEGER", "INTEGER", "TEXT", "INTEGER"),
     + db.constr="CONSTRAINT geno_idx UNIQUE (ref_id, strain, geno_chr, allele_num)",
     + dta.func=function(x) x, should.ignore=TRUE, foreign.keys=list(vcf_annot=list(local.keys="vcf_annot_id", ext.keys=c("vcf_name", "type")),
     + reference=list(local.keys="ref_id", ext.keys=c("seqnames", "start", "end", "vcf_annot_id")))),
     + probe_to_snp=list(db.cols=c("probe_snp_id", "ref_id", "probe_align_id"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "INTEGER", "INTEGER"),
     + db.constr="CONSTRAINT p_s_idx UNIQUE (ref_id, probe_align_id)",
     + dta.func=function(x) x, should.ignore=TRUE, foreign.keys=list(vcf_annot=list(local.keys="vcf_annot_id", ext.keys=c("vcf_name", "type")),
     + reference=list(local.keys="ref_id", ext.keys=c("seqnames", "start", "end", "vcf_annot_id")),
     + probe_align=list(local.keys="probe_align_id", ext.keys=c("probe_chr", "probe_start", "probe_end")))))
     >
     >
     >
     >
     >
     > test_check("poplite")
     ── Warning (test-poplite.R:598:5): Querying with Database objects ──────────────
     `select_()` is deprecated as of dplyr 0.7.0.
     Please use `select()` instead.
     This warning is displayed once every 8 hours.
     Call `lifecycle::last_warnings()` to see where this warning was generated.
    
     ── ERROR (test-poplite.R:655:5): Querying with Database objects ────────────────
     Error: no applicable method for 'select_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"
     Backtrace:
     █
     1. └─poplite::select(sample.tracking.db, sample_id:dna_ind, .tables = "samples") test-poplite.R:655:4
     2. ├─dplyr::select_(.data, .dots = use.dots)
     3. └─poplite:::select_.Database(.data, .dots = use.dots)
     4. ├─poplite:::join(.data, use.tables)
     5. └─poplite:::join(.data, use.tables)
     6. └─poplite:::.local(obj, ...)
     7. └─dplyr::select_(...)
    
     ── ERROR (test-poplite.R:883:5): oligoMask queries that break poplite ──────────
     Error: no applicable method for 'select_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"
     Backtrace:
     █
     1. ├─base::as.data.frame(...) test-poplite.R:883:4
     2. └─poplite::select(test.database.1, probe_id, fasta_name, align_status)
     3. ├─dplyr::select_(.data, .dots = use.dots)
     4. └─poplite:::select_.Database(.data, .dots = use.dots)
     5. ├─dplyr::select_(join(.data, use.tables), .dots = as.list(clean.cols))
     6. ├─poplite:::join(.data, use.tables)
     7. └─poplite:::join(.data, use.tables)
     8. └─poplite:::.local(obj, ...)
     9. └─dplyr::select_(...)
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     Warning (test-poplite.R:598:5): Querying with Database objects
     ERROR (test-poplite.R:655:5): Querying with Database objects
     ERROR (test-poplite.R:883:5): oligoMask queries that break poplite
    
     [ FAIL 2 | WARN 1 | SKIP 0 | PASS 129 ]
     Error: Test failures
     In addition: Warning message:
     call dbDisconnect() when finished working with a connection
     Execution halted
Flavor: r-release-linux-x86_64

Version: 0.99.23
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘VariantAnnotation’
Flavor: r-oldrel-macos-x86_64

Version: 0.99.23
Check: tests
Result: ERROR
     Running 'testthat.R' [23s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(Lahman)
     > library(DBI)
     > library(RSQLite)
     > library(poplite)
     Loading required package: dplyr
    
     Attaching package: 'dplyr'
    
     The following object is masked from 'package:testthat':
    
     matches
    
     The following objects are masked from 'package:stats':
    
     filter, lag
    
     The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    
     Attaching package: 'poplite'
    
     The following object is masked from 'package:dplyr':
    
     select
    
     The following object is masked from 'package:stats':
    
     filter
    
     >
     > test.db.1 <- function()
     + {
     + samples <- data.frame(sample_id=as.integer(sapply(1:100, function(x) rep(x,2))), wave=as.integer(sapply(1:100, function(x) 1:2)), did_collect=sample(c("Y", "N"), size=100, replace=T))
     +
     + dna <- samples[samples$did_collect == "Y",c("sample_id", "wave")]
     + dna$lab_id <- paste("dna", paste(dna$sample_id, dna$wave, sep="_"), sep="_")
     + dna$lab_id[sample.int(nrow(dna), size=10)] <- NA
     + dna$ng.ul <- abs(rnorm(n=nrow(dna), mean=146, sd=98))
     + dna$ng.ul[is.na(dna$lab_id)] <- NA
     +
     + clinical <- data.frame(sample_id=1:100, sex=sample(c("M", "F"), size=100, replace=T), age=sample(1:20, 100, replace=T), status=sample(c(0L,1L), size=100, replace=T), var_wave_1=rnorm(n=100), var_wave_2=rnorm(n=100))
     + clinical <- clinical[-sample.int(nrow(clinical), 12),]
     +
     + return(list(samples=samples, dna=dna, clinical=clinical))
     + }
     >
     > test.db.2 <- eval(structure(list(allele = structure(list(allele_id = 1:10, alleles = c(".",
     + "G", "A", ".", "A", "T", ".", "C", "A", "."), allele_num = c(-1L,
     + 0L, 1L, -1L, 0L, 1L, -1L, 0L, 1L, -1L), ref_id = c(1L, 1L, 1L,
     + 2L, 2L, 2L, 3L, 3L, 3L, 4L)), .Names = c("allele_id", "alleles",
     + "allele_num", "ref_id"), row.names = c(NA, -10L), class = "data.frame"),
     + genotype = structure(list(geno_id = c(1L, 2L, 3L, 4L, 5L,
     + 6L, 7L, 8L, 9L, 11L), geno_chr = c(1L, 1L, 1L, 1L, 1L, 1L,
     + 1L, 1L, 1L, 1L), allele_num = c(1L, 1L, 1L, 1L, 1L, 1L, 1L,
     + 1L, 1L, 1L), strain = c("NODShiLtJ", "NODShiLtJ", "NODShiLtJ",
     + "NODShiLtJ", "NODShiLtJ", "NODShiLtJ", "NODShiLtJ", "NODShiLtJ",
     + "NODShiLtJ", "NODShiLtJ"), ref_id = c(1L, 2L, 3L, 4L, 5L,
     + 6L, 7L, 8L, 9L, 11L)), .Names = c("geno_id", "geno_chr",
     + "allele_num", "strain", "ref_id"), row.names = c(NA, -10L
     + ), class = "data.frame"), probe_align = structure(list(probe_align_id = 1:10,
     + probe_chr = c("1", "1", "1", "1", "1", "1", "1", "1",
     + "1", "1"), probe_start = c(3214633L, 3214895L, 3215576L,
     + 3216284L, 3216483L, 3216537L, 3216591L, 3421710L, 3421740L,
     + 3421808L), probe_end = c(3214657L, 3214919L, 3215600L,
     + 3216308L, 3216507L, 3216561L, 3216615L, 3421734L, 3421764L,
     + 3421832L), probe_ind = 23944:23953), .Names = c("probe_align_id",
     + "probe_chr", "probe_start", "probe_end", "probe_ind"), row.names = c(NA,
     + -10L), class = "data.frame"), probe_info = structure(list(
     + probe_ind = 1:10, fasta_name = c("chr1:3044331-3044355;+;GGGCTCAAATTCACCTGTGTTAACT",
     + "chr1:3044334-3044358;+;AGGGGGCTCAAATTCACCTGTGTTA", "chr1:3044335-3044359;+;GAGGGGGCTCAAATTCACCTGTGTT",
     + "chr1:3044336-3044360;+;GGAGGGGGCTCAAATTCACCTGTGT", "chr1:3044337-3044361;+;GGGAGGGGGCTCAAATTCACCTGTG",
     + "chr1:3044504-3044528;+;AAGGCTTGGGCTATGCGCTCTCCAG", "chr1:3044557-3044581;+;AAGGTCCTCGCTCCTCTTTCATATA",
     + "chr1:3044558-3044582;+;GAAGGTCCTCGCTCCTCTTTCATAT", "chr1:3044559-3044583;+;GGAAGGTCCTCGCTCCTCTTTCATA",
     + "chr1:3044560-3044584;+;AGGAAGGTCCTCGCTCCTCTTTCAT"),
     + probe_id = c(271822L, 866088L, 240008L, 34772L, 396933L,
     + 613322L, 984143L, 826914L, 1075207L, 160847L), align_status = c("MultiMapped",
     + "MultiMapped", "MultiMapped", "MultiMapped", "MultiMapped",
     + "MultiMapped", "MultiMapped", "MultiMapped", "MultiMapped",
     + "MultiMapped")), .Names = c("probe_ind", "fasta_name",
     + "probe_id", "align_status"), row.names = c(NA, -10L), class = "data.frame"),
     + probe_to_snp = structure(list(probe_snp_id = 1:10, ref_id = c(1L,
     + 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 9L), probe_align_id = c(137L,
     + 137L, 252L, 263L, 561L, 601L, 606L, 622L, 635L, 636L)), .Names = c("probe_snp_id",
     + "ref_id", "probe_align_id"), row.names = c(NA, -10L), class = "data.frame"),
     + reference = structure(list(ref_id = c(1L, 2L, 3L, 4L, 5L,
     + 6L, 7L, 8L, 9L, 11L), seqnames = c("1", "1", "1", "1", "1",
     + "1", "1", "1", "1", "1"), start = c(4785683L, 4785703L, 8595537L,
     + 8682000L, 10719780L, 12990759L, 13114284L, 13122474L, 13125617L,
     + 13150850L), end = c(4785683L, 4785703L, 8595537L, 8682000L,
     + 10719780L, 12990759L, 13114284L, 13122474L, 13125617L, 13150850L
     + ), filter = c("TRUE", "TRUE", "TRUE", "TRUE", "TRUE", "TRUE",
     + "TRUE", "TRUE", "TRUE", "TRUE"), vcf_annot_id = c(1L, 1L,
     + 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L)), .Names = c("ref_id", "seqnames",
     + "start", "end", "filter", "vcf_annot_id"), row.names = c(NA,
     + -10L), class = "data.frame"), vcf_annot = structure(list(
     + vcf_annot_id = 1L, vcf_name = "/Users/bottomly/Desktop/resources/vcfs/mgp.v3.snps.rsIDdbSNPv137.vcf.gz",
     + type = "SNV"), .Names = c("vcf_annot_id", "vcf_name",
     + "type"), row.names = c(NA, -1L), class = "data.frame")), .Names = c("allele",
     + "genotype", "probe_align", "probe_info", "probe_to_snp", "reference",
     + "vcf_annot")))
     >
     > test.schema.2 <- list(probe_info=list(db.cols=c("probe_ind", "fasta_name", "probe_id", "align_status"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "TEXT", "INTEGER", "TEXT"),
     + db.constr="CONSTRAINT probe_idx UNIQUE (fasta_name)",
     + dta.func=function(x) x, should.ignore=FALSE, foreign.keys=NULL),
     + probe_align=list(db.cols=c("probe_align_id", "probe_chr", "probe_start", "probe_end", "probe_ind"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "TEXT", "INTEGER", "INTEGER", "INTEGER"),
     + db.constr="CONSTRAINT geno_idx UNIQUE (probe_chr, probe_start, probe_end, probe_ind)",
     + dta.func=function(x) x, should.ignore=FALSE, foreign.keys=list(probe_info=list(local.keys="probe_ind", ext.keys="fasta_name"))),
     + vcf_annot=list(db.cols=c("vcf_annot_id", "vcf_name", "type"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "TEXT", "TEXT"),
     + db.constr="CONSTRAINT probe_idx UNIQUE (vcf_name, type)",
     + dta.func=function(x) x,
     + should.ignore=TRUE, foreign.keys=NULL),
     + reference=list(db.cols=c("ref_id", "seqnames", "start", "end", "filter", "vcf_annot_id"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "TEXT", "INTEGER", "INTEGER", "TEXT", "INTEGER"),
     + db.constr="CONSTRAINT ref_idx UNIQUE (seqnames, start, end, vcf_annot_id)",
     + dta.func=function(x) x, should.ignore=TRUE, foreign.keys=list(vcf_annot=list(local.keys="vcf_annot_id", ext.keys=c("vcf_name", "type")))),
     + allele=list(db.cols=c("allele_id", "alleles", "allele_num", "ref_id"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "TEXT", "INTEGER", "INTEGER"),
     + db.constr="CONSTRAINT alelle_idx UNIQUE (alleles, allele_num, ref_id)",
     + dta.func=function(x) x, should.ignore=TRUE, foreign.keys=list(vcf_annot=list(local.keys="vcf_annot_id", ext.keys=c("vcf_name", "type")),
     + reference=list(local.keys="ref_id", ext.keys=c("seqnames", "start", "end", "vcf_annot_id")))),
     + genotype=list(db.cols=c("geno_id", "geno_chr", "allele_num","strain", "ref_id"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "INTEGER", "INTEGER", "TEXT", "INTEGER"),
     + db.constr="CONSTRAINT geno_idx UNIQUE (ref_id, strain, geno_chr, allele_num)",
     + dta.func=function(x) x, should.ignore=TRUE, foreign.keys=list(vcf_annot=list(local.keys="vcf_annot_id", ext.keys=c("vcf_name", "type")),
     + reference=list(local.keys="ref_id", ext.keys=c("seqnames", "start", "end", "vcf_annot_id")))),
     + probe_to_snp=list(db.cols=c("probe_snp_id", "ref_id", "probe_align_id"),
     + db.schema=c("INTEGER PRIMARY KEY AUTOINCREMENT", "INTEGER", "INTEGER"),
     + db.constr="CONSTRAINT p_s_idx UNIQUE (ref_id, probe_align_id)",
     + dta.func=function(x) x, should.ignore=TRUE, foreign.keys=list(vcf_annot=list(local.keys="vcf_annot_id", ext.keys=c("vcf_name", "type")),
     + reference=list(local.keys="ref_id", ext.keys=c("seqnames", "start", "end", "vcf_annot_id")),
     + probe_align=list(local.keys="probe_align_id", ext.keys=c("probe_chr", "probe_start", "probe_end")))))
     >
     >
     >
     >
     >
     > test_check("poplite")
     -- Warning (test-poplite.R:598:5): Querying with Database objects --------------
     `select_()` is deprecated as of dplyr 0.7.0.
     Please use `select()` instead.
     This warning is displayed once every 8 hours.
     Call `lifecycle::last_warnings()` to see where this warning was generated.
    
     -- ERROR (test-poplite.R:655:5): Querying with Database objects ----------------
     Error: no applicable method for 'select_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"
     Backtrace:
     x
     1. \-poplite::select(sample.tracking.db, sample_id:dna_ind, .tables = "samples") test-poplite.R:655:4
     2. +-dplyr::select_(.data, .dots = use.dots)
     3. \-poplite:::select_.Database(.data, .dots = use.dots)
     4. +-poplite:::join(.data, use.tables)
     5. \-poplite:::join(.data, use.tables)
     6. \-poplite:::.local(obj, ...)
     7. \-dplyr::select_(...)
    
     -- ERROR (test-poplite.R:883:5): oligoMask queries that break poplite ----------
     Error: no applicable method for 'select_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"
     Backtrace:
     x
     1. +-base::as.data.frame(...) test-poplite.R:883:4
     2. \-poplite::select(test.database.1, probe_id, fasta_name, align_status)
     3. +-dplyr::select_(.data, .dots = use.dots)
     4. \-poplite:::select_.Database(.data, .dots = use.dots)
     5. +-dplyr::select_(join(.data, use.tables), .dots = as.list(clean.cols))
     6. +-poplite:::join(.data, use.tables)
     7. \-poplite:::join(.data, use.tables)
     8. \-poplite:::.local(obj, ...)
     9. \-dplyr::select_(...)
    
     == testthat results ===========================================================
     Warning (test-poplite.R:598:5): Querying with Database objects
     ERROR (test-poplite.R:655:5): Querying with Database objects
     ERROR (test-poplite.R:883:5): oligoMask queries that break poplite
    
     [ FAIL 2 | WARN 1 | SKIP 0 | PASS 129 ]
     Error: Test failures
     In addition: Warning message:
     call dbDisconnect() when finished working with a connection
     Execution halted
Flavor: r-oldrel-windows-ix86+x86_64