CRAN Package Check Results for Package sim1000G

Last updated on 2018-02-07 10:52:27 CET.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	1.37	2.78	41.29	44.07	ERROR
r-devel-linux-x86_64-debian-gcc	1.37	2.08	33.26	35.34	ERROR
r-devel-linux-x86_64-fedora-clang	1.37			72.47	OK
r-devel-linux-x86_64-fedora-gcc	1.37			70.03	OK
r-devel-windows-ix86+x86_64	1.37	9.00	72.00	81.00	ERROR
r-patched-linux-x86_64	1.37	1.66	47.11	48.77	ERROR
r-patched-solaris-x86	1.37			112.50	OK
r-release-linux-x86_64	1.33	0.85	45.32	46.17	OK
r-release-windows-ix86+x86_64	1.37	6.00	65.00	71.00	ERROR
r-release-osx-x86_64	1.33				OK
r-oldrel-windows-ix86+x86_64	1.37	6.00	49.00	55.00	ERROR
r-oldrel-osx-x86_64	1.33				OK

Check Details

Version: 1.37
Check: examples
Result: ERROR
    Running examples in ‘sim1000G-Ex.R’ failed
    The error most likely occurred in:

    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: generateChromosomeRecombinationPositions
    > ### Title: Genetates a recombination vector arising from one meiotic event.
    > ### The origin of segments is coded as (0 - haplotype1 , 1 - haplotype2 )
    > ### Aliases: generateChromosomeRecombinationPositions
    >
    > ### ** Examples
    >
    >
    > library("sim1000G")
    >
    > readGeneticMap(4)
     -> Downloading genetic map from: https://github.com/adimitromanolakis/geneticMap-GRCh37/raw/master/genetic_map_GRCh37_chr4.txt.gz
     -> Saving genetic map to: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/sim1000G/datasets/genetic_map_GRCh37_chr4.txt.gz
    Warning in download.file(url, destfile = dest_path, quiet = TRUE) :
     URL https://github.com/adimitromanolakis/geneticMap-GRCh37/raw/master/genetic_map_GRCh37_chr4.txt.gz: cannot open destfile '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/sim1000G/datasets/genetic_map_GRCh37_chr4.txt.gz', reason 'Read-only file system'
    Warning in download.file(url, destfile = dest_path, quiet = TRUE) :
     download had nonzero exit status
    Error in readGeneticMapFromFile(fname) :
     Genetic map file /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/sim1000G/datasets/genetic_map_GRCh37_chr4.txt.gz not found
    Calls: readGeneticMap -> readGeneticMapFromFile
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.37
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Warning in gplots::heatmap.2(C, col = rev(heat.colors(100)), Rowv = F, Colv = F, :
     Discrepancy: Rowv is FALSE, while dendrogram is `both'. Omitting row dendogram.
    Warning in gplots::heatmap.2(C, col = rev(heat.colors(100)), Rowv = F, Colv = F, :
     Discrepancy: Colv is FALSE, while dendrogram is `column'. Omitting column dendogram.
    Warning in get_engine(options$engine) :
     Unknown language engine 'cpp' (must be registered via knit_engines$set()).
    Parsed with column specification:
    cols(
     .default = col_character(),
     `#CHROM` = col_integer(),
     POS = col_integer(),
     QUAL = col_integer()
    )
    See spec(...) for full column specifications.
    Warning in download.file(url, destfile = dest_path, quiet = TRUE) :
     URL https://github.com/adimitromanolakis/geneticMap-GRCh37/raw/master/genetic_map_GRCh37_chr4.txt.gz: cannot open destfile '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/sim1000G/datasets/genetic_map_GRCh37_chr4.txt.gz', reason 'Read-only file system'
    Warning in download.file(url, destfile = dest_path, quiet = TRUE) :
     download had nonzero exit status
    Warning in download.file(url, destfile = dest_path, quiet = TRUE) :
     URL https://github.com/adimitromanolakis/geneticMap-GRCh37/raw/master/genetic_map_GRCh37_chr4.txt.gz: cannot open destfile '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/sim1000G/datasets/genetic_map_GRCh37_chr4.txt.gz', reason 'Read-only file system'
    Warning in download.file(url, destfile = dest_path, quiet = TRUE) :
     download had nonzero exit status
    Quitting from lines 100-115 (SimulatingFamilyData.Rmd)
    Error: processing vignette ‘SimulatingFamilyData.Rmd’ failed with diagnostics:
    Genetic map file /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/sim1000G/datasets/genetic_map_GRCh37_chr4.txt.gz not found
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.37
Check: examples
Result: ERROR
    Running examples in ‘sim1000G-Ex.R’ failed
    The error most likely occurred in:

    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: generateChromosomeRecombinationPositions
    > ### Title: Genetates a recombination vector arising from one meiotic event.
    > ### The origin of segments is coded as (0 - haplotype1 , 1 - haplotype2 )
    > ### Aliases: generateChromosomeRecombinationPositions
    >
    > ### ** Examples
    >
    >
    > library("sim1000G")
    >
    > readGeneticMap(4)
     -> Downloading genetic map from: https://github.com/adimitromanolakis/geneticMap-GRCh37/raw/master/genetic_map_GRCh37_chr4.txt.gz
     -> Saving genetic map to: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/sim1000G/datasets/genetic_map_GRCh37_chr4.txt.gz
    Warning in download.file(url, destfile = dest_path, quiet = TRUE) :
     URL https://github.com/adimitromanolakis/geneticMap-GRCh37/raw/master/genetic_map_GRCh37_chr4.txt.gz: cannot open destfile '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/sim1000G/datasets/genetic_map_GRCh37_chr4.txt.gz', reason 'Read-only file system'
    Warning in download.file(url, destfile = dest_path, quiet = TRUE) :
     download had nonzero exit status
    Error in readGeneticMapFromFile(fname) :
     Genetic map file /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/sim1000G/datasets/genetic_map_GRCh37_chr4.txt.gz not found
    Calls: readGeneticMap -> readGeneticMapFromFile
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.37
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Warning in gplots::heatmap.2(C, col = rev(heat.colors(100)), Rowv = F, Colv = F, :
     Discrepancy: Rowv is FALSE, while dendrogram is `both'. Omitting row dendogram.
    Warning in gplots::heatmap.2(C, col = rev(heat.colors(100)), Rowv = F, Colv = F, :
     Discrepancy: Colv is FALSE, while dendrogram is `column'. Omitting column dendogram.
    Warning in get_engine(options$engine) :
     Unknown language engine 'cpp' (must be registered via knit_engines$set()).
    Parsed with column specification:
    cols(
     .default = col_character(),
     `#CHROM` = col_integer(),
     POS = col_integer(),
     QUAL = col_integer()
    )
    See spec(...) for full column specifications.
    Warning in download.file(url, destfile = dest_path, quiet = TRUE) :
     URL https://github.com/adimitromanolakis/geneticMap-GRCh37/raw/master/genetic_map_GRCh37_chr4.txt.gz: cannot open destfile '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/sim1000G/datasets/genetic_map_GRCh37_chr4.txt.gz', reason 'Read-only file system'
    Warning in download.file(url, destfile = dest_path, quiet = TRUE) :
     download had nonzero exit status
    Warning in download.file(url, destfile = dest_path, quiet = TRUE) :
     URL https://github.com/adimitromanolakis/geneticMap-GRCh37/raw/master/genetic_map_GRCh37_chr4.txt.gz: cannot open destfile '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/sim1000G/datasets/genetic_map_GRCh37_chr4.txt.gz', reason 'Read-only file system'
    Warning in download.file(url, destfile = dest_path, quiet = TRUE) :
     download had nonzero exit status
    Quitting from lines 100-115 (SimulatingFamilyData.Rmd)
    Error: processing vignette ‘SimulatingFamilyData.Rmd’ failed with diagnostics:
    Genetic map file /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/sim1000G/datasets/genetic_map_GRCh37_chr4.txt.gz not found
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.37
Check: examples
Result: ERROR
    Running examples in 'sim1000G-Ex.R' failed
    The error most likely occurred in:

    > ### Name: downloadGeneticMap
    > ### Title: Downloads a genetic map for a particular chromosome under GRCh37
    > ### coordinates for use with sim1000G.
    > ### Aliases: downloadGeneticMap
    >
    > ### ** Examples
    >
    >
    >
    >
    > downloadGeneticMap(22, dir=tempdir() )
    Warning in file(file, ifelse(append, "a", "w")) :
     cannot open file '/tmp/xxx': Permission denied
    Error in file(file, ifelse(append, "a", "w")) :
     cannot open the connection
    Calls: downloadGeneticMap -> cat -> file
    Execution halted
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.37
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Warning in file(file, ifelse(append, "a", "w")) :
     cannot open file '/tmp/samples1.txt': Permission denied
    Quitting from lines 32-51 (Example1.Rmd)
    Error: processing vignette 'Example1.Rmd' failed with diagnostics:
    cannot open the connection
    Execution halted
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.37
Check: examples
Result: ERROR
    Running examples in ‘sim1000G-Ex.R’ failed
    The error most likely occurred in:

    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: generateChromosomeRecombinationPositions
    > ### Title: Genetates a recombination vector arising from one meiotic event.
    > ### The origin of segments is coded as (0 - haplotype1 , 1 - haplotype2 )
    > ### Aliases: generateChromosomeRecombinationPositions
    >
    > ### ** Examples
    >
    >
    > library("sim1000G")
    >
    > readGeneticMap(4)
     -> Downloading genetic map from: https://github.com/adimitromanolakis/geneticMap-GRCh37/raw/master/genetic_map_GRCh37_chr4.txt.gz
     -> Saving genetic map to: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/sim1000G/datasets/genetic_map_GRCh37_chr4.txt.gz
    Warning in download.file(url, destfile = dest_path, quiet = TRUE) :
     URL https://github.com/adimitromanolakis/geneticMap-GRCh37/raw/master/genetic_map_GRCh37_chr4.txt.gz: cannot open destfile '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/sim1000G/datasets/genetic_map_GRCh37_chr4.txt.gz', reason 'Read-only file system'
    Warning in download.file(url, destfile = dest_path, quiet = TRUE) :
     download had nonzero exit status
    Error in readGeneticMapFromFile(fname) :
     Genetic map file /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/sim1000G/datasets/genetic_map_GRCh37_chr4.txt.gz not found
    Calls: readGeneticMap -> readGeneticMapFromFile
    Execution halted
Flavor: r-patched-linux-x86_64

Version: 1.37
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Warning in gplots::heatmap.2(C, col = rev(heat.colors(100)), Rowv = F, Colv = F, :
     Discrepancy: Rowv is FALSE, while dendrogram is `both'. Omitting row dendogram.
    Warning in gplots::heatmap.2(C, col = rev(heat.colors(100)), Rowv = F, Colv = F, :
     Discrepancy: Colv is FALSE, while dendrogram is `column'. Omitting column dendogram.
    Warning in get_engine(options$engine) :
     Unknown language engine 'cpp' (must be registered via knit_engines$set()).
    Parsed with column specification:
    cols(
     .default = col_character(),
     `#CHROM` = col_integer(),
     POS = col_integer(),
     QUAL = col_integer()
    )
    See spec(...) for full column specifications.
    Warning in download.file(url, destfile = dest_path, quiet = TRUE) :
     URL https://github.com/adimitromanolakis/geneticMap-GRCh37/raw/master/genetic_map_GRCh37_chr4.txt.gz: cannot open destfile '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/sim1000G/datasets/genetic_map_GRCh37_chr4.txt.gz', reason 'Read-only file system'
    Warning in download.file(url, destfile = dest_path, quiet = TRUE) :
     download had nonzero exit status
    Warning in download.file(url, destfile = dest_path, quiet = TRUE) :
     URL https://github.com/adimitromanolakis/geneticMap-GRCh37/raw/master/genetic_map_GRCh37_chr4.txt.gz: cannot open destfile '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/sim1000G/datasets/genetic_map_GRCh37_chr4.txt.gz', reason 'Read-only file system'
    Warning in download.file(url, destfile = dest_path, quiet = TRUE) :
     download had nonzero exit status
    Quitting from lines 100-115 (SimulatingFamilyData.Rmd)
    Error: processing vignette ‘SimulatingFamilyData.Rmd’ failed with diagnostics:
    Genetic map file /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/sim1000G/datasets/genetic_map_GRCh37_chr4.txt.gz not found
    Execution halted
Flavor: r-patched-linux-x86_64