CRAN Package Check Results for Package refGenome

Last updated on 2017-02-19 18:47:58.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.7.0 5.92 50.92 56.84 ERROR
r-devel-linux-x86_64-debian-gcc 1.7.0 6.40 49.05 55.45 ERROR
r-devel-linux-x86_64-fedora-clang 1.7.0 124.27 ERROR --no-stop-on-test-error
r-devel-linux-x86_64-fedora-gcc 1.7.0 125.60 ERROR --no-stop-on-test-error
r-devel-macos-x86_64-clang 1.7.0 97.21 ERROR --no-stop-on-test-error
r-devel-windows-ix86+x86_64 1.7.0 35.00 172.00 207.00 ERROR
r-patched-linux-x86_64 1.7.0 5.90 47.96 53.86 OK
r-patched-solaris-sparc 1.7.0 618.90 OK
r-patched-solaris-x86 1.7.0 138.20 OK
r-release-linux-x86_64 1.7.0 5.95 45.82 51.77 OK
r-release-osx-x86_64-mavericks 1.7.0 OK
r-release-windows-ix86+x86_64 1.7.0 19.00 120.00 139.00 OK
r-oldrel-windows-ix86+x86_64 1.7.0 25.00 169.00 194.00 OK

Memtest notes: valgrind

Check Details

Version: 1.7.0
Check: compiled code
Result: NOTE
    File ‘refGenome/libs/refGenome.so’:
     Found no call to: ‘R_useDynamicSymbols’
    
    It is good practice to register native routines and to disable symbol
    search.
    
    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 1.7.0
Check: files in ‘vignettes’
Result: WARN
    Files in the 'vignettes' directory newer than all files in 'inst/doc':
     ‘refGenome.Rnw’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64

Version: 1.7.0
Check: tests
Result: ERROR
     Running ‘test-all.R’ [2s/2s]
     Running ‘test_overlap_juncs.r’ [0s/0s]
    Running the tests in ‘tests/test_overlap_juncs.r’ failed.
    Last 13 lines of output:
     >
     >
     > ## 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)
     > res<-overlapJuncs(qry,junc)
     Error in overlapJuncs(qry, junc) : could not find function "overlapJuncs"
     Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.7.0
Check: tests
Result: ERROR
     Running ‘test-all.R’ [1s/2s]
     Running ‘test_overlap_juncs.r’ [0s/0s]
    Running the tests in ‘tests/test_overlap_juncs.r’ failed.
    Last 13 lines of output:
     >
     >
     > ## 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)
     > res<-overlapJuncs(qry,junc)
     Error in overlapJuncs(qry, junc) : could not find function "overlapJuncs"
     Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.7.0
Flags: --no-stop-on-test-error
Check: compiled code
Result: NOTE
    File ‘refGenome/libs/refGenome.so’:
     Found no call to: ‘R_useDynamicSymbols’
    
    It is good practice to register native routines and to disable symbol
    search.
    
    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-macos-x86_64-clang

Version: 1.7.0
Flags: --no-stop-on-test-error
Check: files in ‘vignettes’
Result: WARN
    Files in the 'vignettes' directory newer than all files in 'inst/doc':
     ‘refGenome.Rnw’
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-macos-x86_64-clang

Version: 1.7.0
Flags: --no-stop-on-test-error
Check: tests
Result: ERROR
     Running ‘test-all.R’
     Running ‘test_overlap_juncs.r’
     Running ‘test_read_gtf.r’
     Running ‘test_unify_juncs.r’
     Running ‘test_unify_ranges.r’
    Running the tests in ‘tests/test_overlap_juncs.r’ failed.
    Complete output:
     >
     >
     > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
     > # Requires: Initialized objects (as done by test-all.R header)
     > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
     >
     >
     > ## 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)
     > res<-overlapJuncs(qry,junc)
     Error in overlapJuncs(qry, junc) : could not find function "overlapJuncs"
     Execution halted
    Running the tests in ‘tests/test_read_gtf.r’ failed.
    Complete output:
     >
     > ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
     > ## Tests read.gtf features
     > ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
     >
     > ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
     > ## hs.ensembl.76.small.gtf
     > ## contains the first 100 lines of file
     > ## ftp://ftp.ensembl.org/pub/release-76/gtf/
     > ## homo_sapiens/Homo_sapiens.GRCh38.76.gtf.gz
     > ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
     >
     > ens76 <- system.file("extdata",
     + "hs.ensembl.76.small.gtf", package = "refGenome", mustWork=TRUE)
     >
     > en76 <- ensemblGenome()
     Error in ensemblGenome() : could not find function "ensemblGenome"
     Execution halted
    Running the tests in ‘tests/test_unify_juncs.r’ failed.
    Complete output:
     >
     > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
     > # Requires: Initialized objects (as done by test-all.R header)
     > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
     >
     > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
     > # Artificially added transcript_biotype data from ensembl version 80
     > # For transcript_id's which are not found idn ensembl 80,
     > # the transcript_biotype is manually set to "nonsense_mediated_decay".
     > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
     > # ensfile <- system.file("extdata", "hs.ensembl.62.small.RData",
     > # package = "refGenome", mustWork=TRUE)
     > # ens <- loadGenome(ensfile)
     > # jtn <- ens@ev$gtf$transcript_id
     > # mtc <- match(jtn, en80@ev$gtf$transcript_id)
     > # biot <- en80@ev$gtf$transcript_biotype[mtc]
     > # biot[is.na(biot)] <- "nonsense_mediated_decay"
     > # ens@ev$gtf$transcript_biotype <- biot
     > # saveGenome(ens,
     > # file="~/projects/R/refGenome/inst/extdata/hs.ensembl.62.small.RData",
     > # useBasedir=FALSE)
     > #
     > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
     >
     >
     > uj <- unifyJuncs(junc)
     Error in unifyJuncs(junc) : could not find function "unifyJuncs"
     Execution halted
    Running the tests in ‘tests/test_unify_ranges.r’ failed.
    Complete output:
     >
     >
     > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
     > # Output consistency of unify Ranges:
     > # Consecutive ranges must not ovelap.
     > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
     >
     > urg <- unifyRanges(enex)
     Error in unifyRanges(enex) : could not find function "unifyRanges"
     Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-macos-x86_64-clang

Version: 1.7.0
Check: running tests for arch ‘i386’
Result: ERROR
     Running 'test-all.R' [3s]
     Running 'test_overlap_juncs.r' [0s]
    Running the tests in 'tests/test_overlap_juncs.r' failed.
    Last 13 lines of output:
     >
     >
     > ## 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)
     > res<-overlapJuncs(qry,junc)
     Error in overlapJuncs(qry, junc) : could not find function "overlapJuncs"
     Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 1.7.0
Check: running tests for arch ‘x64’
Result: ERROR
     Running 'test-all.R' [3s]
     Running 'test_overlap_juncs.r' [1s]
    Running the tests in 'tests/test_overlap_juncs.r' failed.
    Last 13 lines of output:
     >
     >
     > ## 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)
     > res<-overlapJuncs(qry,junc)
     Error in overlapJuncs(qry, junc) : could not find function "overlapJuncs"
     Execution halted
Flavor: r-devel-windows-ix86+x86_64