CRAN Package Check Results for Package refGenome

Last updated on 2018-10-19 01:46:38 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.7.3 17.43 108.97 126.40 OK
r-devel-linux-x86_64-debian-gcc 1.7.3 15.28 84.74 100.02 OK
r-devel-linux-x86_64-fedora-clang 1.7.3 150.27 OK
r-devel-linux-x86_64-fedora-gcc 1.7.3 143.93 OK
r-devel-windows-ix86+x86_64 1.7.3 36.00 154.00 190.00 ERROR
r-patched-linux-x86_64 1.7.3 12.75 88.46 101.21 OK
r-patched-solaris-x86 1.7.3 178.10 OK
r-release-linux-x86_64 1.7.3 15.56 88.22 103.78 OK
r-release-windows-ix86+x86_64 1.7.3 37.00 208.00 245.00 ERROR
r-release-osx-x86_64 1.7.3 OK
r-oldrel-windows-ix86+x86_64 1.7.3 21.00 201.00 222.00 OK
r-oldrel-osx-x86_64 1.7.3 OK

Additional issues

valgrind

Check Details

Version: 1.7.3
Check: running tests for arch ‘i386’
Result: ERROR
     Running 'test-all.R' [3s]
    Running the tests in 'tests/test-all.R' failed.
    Complete output:
     >
     >
     > ##============================================================================##
     > ## A Load prerequisites
     > ##============================================================================##
     >
     > require(refGenome)
     Loading required package: refGenome
     Loading required package: doBy
     Loading required package: RSQLite
     >
     >
     > ##============================================================================##
     > ## B Initialize example data
     > ##============================================================================##
     >
     > ensfile <- system.file("extdata",
     + "hs.ensembl.62.small.RData",
     + package = "refGenome", mustWork=TRUE)
     >
     > ##----------------------------------------------------------------------------##
     > ## B.1 Load Ensembl genome
     > ##----------------------------------------------------------------------------##
     > ens <- loadGenome(ensfile)
     > enex<-refExons(ens)
     [refExons.refGenome] Extracting tables.
     [refExons.refGenome] Adding 'CDS'.
     [refExons.refGenome] Adding 'start_codon'.
     [refExons.refGenome] Adding 'stop_codon'.
     [refExons.refGenome] Finished.
     > gp <- getGenePositions(ens)
     > junc<-getSpliceTable(ens)
     >
     >
     >
     > ##============================================================================##
     > ## C Run tests
     > ##============================================================================##
     >
     > ##----------------------------------------------------------------------------##
     > ## C.1 Test overlap juncs
     > ##----------------------------------------------------------------------------##
     >
     > ## ##
     > ## Requires: Initialized objects (as done by test-all.R header)
     > ## ##
     >
     > ## ##
     > ## C.1.1 Overlap juncs
     > ## ##
     >
     > ## 1 2 3 4 5 6 7 ##
     > qry<-data.frame(id = 1:7, seqid = "1",
     + lstart = c(10100L, 11800L, 12220L, 12220L, 12220L, 32000L, 40000L),
     + lend = c(10100L, 12000L, 12225L, 12227L, 12227L, 32100L, 40100L),
     + rstart = c(10200L, 12200L, 12057L, 12613L, 12650L, 32200L, 40200L),
     + rend = c(10300L, 12250L, 12179L, 12620L, 12700L, 32300L, 40300L))
     > ## 1 2 3 4 5 6 7 ##
     >
     > ## ##
     > ## C.1.2
     > ## ##
     > res<-overlapJuncs(qry,junc)
     [overlapJuncs] Input preparation.
     [overlapJuncs] Query size : 7 Ref size : 92
     [overlapJuncs] - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     [overlapJuncs] i: 1 seqid: 1 query set: 7 ref set: 82
     [overlapJuncs] Result assemly.
     [overlapJuncs] Finished.
     >
     > if(! all(is.na(res$sod)==c(TRUE, FALSE, FALSE, FALSE, FALSE, TRUE, TRUE)) )
     + stop("[test_overlap_juncs] Wrong res$sod NA's.")
     Error: [test_overlap_juncs] Wrong res$sod NA's.
     Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 1.7.3
Check: running tests for arch ‘i386’
Result: ERROR
     Running 'test-all.R' [4s]
    Running the tests in 'tests/test-all.R' failed.
    Complete output:
     >
     >
     > ##============================================================================##
     > ## A Load prerequisites
     > ##============================================================================##
     >
     > require(refGenome)
     Loading required package: refGenome
     Loading required package: doBy
     Loading required package: RSQLite
     >
     >
     > ##============================================================================##
     > ## B Initialize example data
     > ##============================================================================##
     >
     > ensfile <- system.file("extdata",
     + "hs.ensembl.62.small.RData",
     + package = "refGenome", mustWork=TRUE)
     >
     > ##----------------------------------------------------------------------------##
     > ## B.1 Load Ensembl genome
     > ##----------------------------------------------------------------------------##
     > ens <- loadGenome(ensfile)
     > enex<-refExons(ens)
     [refExons.refGenome] Extracting tables.
     [refExons.refGenome] Adding 'CDS'.
     [refExons.refGenome] Adding 'start_codon'.
     [refExons.refGenome] Adding 'stop_codon'.
     [refExons.refGenome] Finished.
     > gp <- getGenePositions(ens)
     > junc<-getSpliceTable(ens)
     >
     >
     >
     > ##============================================================================##
     > ## C Run tests
     > ##============================================================================##
     >
     > ##----------------------------------------------------------------------------##
     > ## C.1 Test overlap juncs
     > ##----------------------------------------------------------------------------##
     >
     > ## ##
     > ## Requires: Initialized objects (as done by test-all.R header)
     > ## ##
     >
     > ## ##
     > ## C.1.1 Overlap juncs
     > ## ##
     >
     > ## 1 2 3 4 5 6 7 ##
     > qry<-data.frame(id = 1:7, seqid = "1",
     + lstart = c(10100L, 11800L, 12220L, 12220L, 12220L, 32000L, 40000L),
     + lend = c(10100L, 12000L, 12225L, 12227L, 12227L, 32100L, 40100L),
     + rstart = c(10200L, 12200L, 12057L, 12613L, 12650L, 32200L, 40200L),
     + rend = c(10300L, 12250L, 12179L, 12620L, 12700L, 32300L, 40300L))
     > ## 1 2 3 4 5 6 7 ##
     >
     > ## ##
     > ## C.1.2
     > ## ##
     > res<-overlapJuncs(qry,junc)
     [overlapJuncs] Input preparation.
     [overlapJuncs] Query size : 7 Ref size : 92
     [overlapJuncs] - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     [overlapJuncs] i: 1 seqid: 1 query set: 7 ref set: 82
     [overlapJuncs] Result assemly.
     [overlapJuncs] Finished.
     >
     > if(! all(is.na(res$sod)==c(TRUE, FALSE, FALSE, FALSE, FALSE, TRUE, TRUE)) )
     + stop("[test_overlap_juncs] Wrong res$sod NA's.")
     >
     > if(sum(res$nref) != 27)
     + stop("[test_overlap_juncs] Wrong sum of res$nref.")
     Error: [test_overlap_juncs] Wrong sum of res$nref.
     Execution halted
Flavor: r-release-windows-ix86+x86_64