Last updated on 2015-02-05 23:50:29.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.14 | 2.64 | 39.61 | 42.25 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 1.14 | 2.83 | 38.69 | 41.52 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 1.14 | 80.84 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 1.14 | 77.90 | NOTE | |||
| r-devel-osx-x86_64-clang | 1.14 | 82.05 | NOTE | |||
| r-devel-windows-ix86+x86_64 | 1.14 | 28.00 | 79.00 | 107.00 | NOTE | |
| r-patched-linux-x86_64 | 1.14 | 3.09 | 43.74 | 46.83 | NOTE | |
| r-patched-solaris-sparc | 1.14 | 556.00 | NOTE | |||
| r-patched-solaris-x86 | 1.14 | 115.20 | NOTE | |||
| r-release-linux-ix86 | 1.14 | 3.98 | 54.84 | 58.82 | NOTE | |
| r-release-linux-x86_64 | 1.14 | 3.13 | 44.37 | 47.50 | NOTE | |
| r-release-osx-x86_64-mavericks | 1.14 | ERROR | ||||
| r-release-osx-x86_64-snowleopard | 1.14 | ERROR | ||||
| r-release-windows-ix86+x86_64 | 1.14 | 28.00 | 99.00 | 127.00 | NOTE | |
| r-oldrel-windows-ix86+x86_64 | 1.14 | 18.00 | 100.00 | 118.00 | NOTE |
Version: 1.14
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking: ‘asreml’ ‘happy.hbrem’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64
Version: 1.14
Check: dependencies in R code
Result: NOTE
'library' or 'require' calls to packages already attached by Depends:
‘gdata’ ‘seriation’
Please remove these calls from your code.
'library' or 'require' calls in package code:
‘Heatplus’ ‘VPdtw’ ‘aod’ ‘asreml’ ‘happy.hbrem’ ‘lattice’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
‘gdata’ ‘seriation’ ‘wgaim’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
':::' call which should be '::': ‘qtl:::readMWril’
See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
‘qtl:::adjust.rf.ri’ ‘qtl:::plot.scanone’ ‘qtl:::ripple.perm1’
‘qtl:::ripple.perm2’ ‘qtl:::testchr’
See the note in ?`:::` about the use of this operator.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64
Version: 1.14
Check: foreign function calls
Result: NOTE
Foreign function calls to a different package:
.C("R_reorgRIgenoprob", ..., PACKAGE = "qtl")
.C(cfunc, ..., PACKAGE = "qtl")
.C(func, ..., PACKAGE = "qtl")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64
Version: 1.14
Check: R code for possible problems
Result: NOTE
CR_calcLD: no visible global function definition for ‘lowerTriangle’
fill: no visible global function definition for ‘upperTriangle<-’
fill: no visible global function definition for ‘lowerTriangle<-’
fill: no visible global function definition for ‘lowerTriangle’
fill: no visible global function definition for ‘upperTriangle’
findqtl2: no visible global function definition for ‘dilation’
fit.mpqtl: no visible global function definition for ‘wald.test’
mpIM: no visible global function definition for ‘stepAIC’
mpIM: no visible global function definition for ‘wald.test’
mpcalcld: no visible global function definition for ‘lowerTriangle<-’
mpcalcld: no visible global function definition for ‘upperTriangle<-’
mpcalcld: no visible global function definition for ‘upperTriangle’
mpestrf: no visible global function definition for ‘lowerTriangle<-’
mpestrf: no visible global function definition for ‘upperTriangle<-’
mpestrf: no visible global function definition for ‘upperTriangle’
mporder : <anonymous>: no visible global function definition for
‘seriate’
mporder: no visible binding for global variable ‘get_order’
mpprob: no visible global function definition for ‘happy’
mpprob: no visible global function definition for ‘hdesign’
plot.mapcomp: no visible global function definition for ‘xyplot’
plot.mpcross: no visible global function definition for
‘upperTriangle<-’
plot.mpcross: no visible global function definition for ‘upperTriangle’
plot.mpcross: no visible global function definition for
‘lowerTriangle<-’
plot.mpcross: no visible global function definition for ‘lowerTriangle’
plot.mpcross: no visible global function definition for ‘heatmap_2’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard, r-release-windows-ix86+x86_64
Version: 1.14
Check: Rd line widths
Result: NOTE
Rd file 'clean.mpcross.Rd':
\examples lines wider than 100 characters:
sim.dat <- sim.mpcross(map=map, pedigree=sim.ped, qtl=matrix(data=c(1, 45, .4, 0, 0, 0), nrow=1, ncol=6, byrow=TRUE),seed=1)
Rd file 'findqtl2.Rd':
\examples lines wider than 100 characters:
sim.dat <- sim.mpcross(map=sim.map, pedigree=sim.ped, qtl=matrix(data=c(1, 10, .4, 0, 0, 0, 1, 70, 0, .35, 0, 0), nrow=2, ncol=6, byrow ... [TRUNCATED]
Rd file 'fit.Rd':
\examples lines wider than 100 characters:
sim.dat <- sim.mpcross(map=sim.map, pedigree=sim.ped, qtl=matrix(data=c(1, 10, .4, 0, 0, 0, 1, 70, 0, .35, 0, 0), nrow=2, ncol=6, byrow ... [TRUNCATED]
Rd file 'mpIM.Rd':
\examples lines wider than 100 characters:
sim.dat <- sim.mpcross(map=sim.map, pedigree=sim.ped, qtl=matrix(data=c(1, 10, .4, 0, 0, 0, 1, 70, 0, .35, 0, 0), nrow=2, ncol=6, byrow ... [TRUNCATED]
Rd file 'mpcross.Rd':
\examples lines wider than 100 characters:
sim.dat <- sim.mpcross(map=map, pedigree=sim.ped, qtl=matrix(data=c(1, 10, .4, 0, 0, 0, 1, 70, 0, .35, 0, 0), nrow=2, ncol=6, byrow=TRU ... [TRUNCATED]
Rd file 'mpestrf.Rd':
\examples lines wider than 100 characters:
sim.dat <- sim.mpcross(map=map, pedigree=sim.ped, qtl=matrix(data=c(1, 50, .4, 0, 0, 0), nrow=1, ncol=6, byrow=TRUE), seed=1)
Rd file 'mporder.Rd':
\usage lines wider than 90 characters:
criterion = c("Path_length", "AR_events", "AR_deviations", "Gradient_raw", "Inertia", "Least_squares", "minXO", "lkhdsum"),
Rd file 'mpprob.Rd':
\examples lines wider than 100 characters:
sim.dat <- sim.mpcross(map=sim.map, pedigree=sim.ped, qtl=matrix(data=c(1, 50, .4, 0, 0, 0), nrow=1, ncol=6, byrow=TRUE), seed=1)
Rd file 'plot.mpcross.Rd':
\examples lines wider than 100 characters:
sim.dat <- sim.mpcross(map=sim.map, pedigree=sim.ped, qtl=matrix(data=c(1, 10, .4, 0, 0, 0, 1, 70, 0, .35, 0, 0), nrow=2, ncol=6, byrow ... [TRUNCATED]
Rd file 'plot.mpprob.Rd':
\examples lines wider than 100 characters:
sim.dat <- sim.mpcross(map=sim.map, pedigree=sim.ped, qtl=matrix(data=c(1, 10, .4, 0, 0, 0, 1, 70, 0, .35, 0, 0), nrow=2, ncol=6, byrow ... [TRUNCATED]
Rd file 'plot.mpqtl.Rd':
\examples lines wider than 100 characters:
sim.dat <- sim.mpcross(map=sim.map, pedigree=sim.ped, qtl=matrix(data=c(1, 10, .4, 0, 0, 0, 1, 70, 0, .35, 0, 0), nrow=2, ncol=6, byrow ... [TRUNCATED]
Rd file 'qtlmap.Rd':
\examples lines wider than 100 characters:
sim.dat <- sim.mpcross(map=sim.map, pedigree=sim.ped, qtl=matrix(data=c(1, 10, .4, 0, 0, 0, 1, 70, 0, .35, 0, 0), nrow=2, ncol=6, byrow ... [TRUNCATED]
Rd file 'sim.mpcross.Rd':
\examples lines wider than 100 characters:
sim.dat <- sim.mpcross(map=map, pedigree=sim.ped, qtl=matrix(data=c(1, 50, .4, 0, 0, 0), nrow=1, ncol=6, byrow=TRUE), seed=1)
Rd file 'subset.mpcross.Rd':
\examples lines wider than 100 characters:
sim.dat <- sim.mpcross(map=map, pedigree=ped, qtl=matrix(data=c(1, 10, .4, 0, 0, 0, 1, 70, 0, .35, 0, 0), nrow=2, ncol=6, byrow=TRUE), ... [TRUNCATED]
Rd file 'summary.mpcross.Rd':
\examples lines wider than 100 characters:
sim.dat <- sim.mpcross(map=sim.map, pedigree=sim.ped, qtl=matrix(data=c(1, 10, .4, 0, 0, 0, 1, 70, 0, .35, 0, 0), nrow=2, ncol=6, byrow ... [TRUNCATED]
Rd file 'summary.mpprob.Rd':
\examples lines wider than 100 characters:
sim.dat <- sim.mpcross(map=sim.map, pedigree=sim.ped, qtl=matrix(data=c(1, 10, .4, 0, 0, 0, 1, 70, 0, .35, 0, 0), nrow=2, ncol=6, byrow ... [TRUNCATED]
Rd file 'summary.mpqtl.Rd':
\examples lines wider than 100 characters:
sim.dat <- sim.mpcross(map=sim.map, pedigree=sim.ped, qtl=matrix(data=c(1, 10, .4, 0, 0, 0, 1, 70, 0, .35, 0, 0), nrow=2, ncol=6, byrow ... [TRUNCATED]
Rd file 'supportinterval.Rd':
\examples lines wider than 100 characters:
sim.dat <- sim.mpcross(map=map, pedigree=sim.ped, qtl=matrix(data=c(1, 10, .4, 0, 0, 0, 1, 70, 0, .35, 0, 0), nrow=2, ncol=6, byrow=TRU ... [TRUNCATED]
These lines will be truncated in the PDF manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-ix86, r-release-linux-x86_64
Version: 1.14
Check: dependencies in R code
Result: NOTE
'library' or 'require' calls to packages already attached by Depends:
‘gdata’ ‘seriation’
Please remove these calls from your code.
Packages in Depends field not imported from:
‘gdata’ ‘seriation’ ‘wgaim’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
':::' call which should be '::': ‘qtl:::readMWril’
See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
‘qtl:::adjust.rf.ri’ ‘qtl:::plot.scanone’ ‘qtl:::ripple.perm1’
‘qtl:::ripple.perm2’ ‘qtl:::testchr’
See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
Flavors: r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64
Version: 1.14
Check: foreign function calls
Result: NOTE
Foreign function calls to a different package:
.C("R_reorgRIgenoprob", ..., PACKAGE = "qtl")
.C(cfunc, ..., PACKAGE = "qtl")
.C(func, ..., PACKAGE = "qtl")
See the chapter ‘System and foreign language interfaces’ of the
‘Writing R Extensions’ manual.
Flavors: r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64
Version: 1.14
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking:
‘asreml’ ‘happy.hbrem’ ‘Heatplus’
Flavors: r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard
Version: 1.14
Check: Rd cross-references
Result: NOTE
Package unavailable to check Rd xrefs: ‘Heatplus’
Flavors: r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard
Version: 1.14
Check: examples
Result: ERROR
Running examples in ‘mpMap-Ex.R’ failed
The error most likely occurred in:
> ### Name: mpestrf
> ### Title: Estimate pairwise recombination fractions between markers
> ### Aliases: mpestrf
>
> ### ** Examples
>
> map <- sim.map(len=100, n.mar=11, eq.spacing=TRUE, include.x=FALSE)
> sim.ped <- sim.mpped(4, 1, 500, 6, 1)
> sim.dat <- sim.mpcross(map=map, pedigree=sim.ped, qtl=matrix(data=c(1, 50, .4, 0, 0, 0), nrow=1, ncol=6, byrow=TRUE), seed=1)
> dat.rf <- mpestrf(sim.dat)
> plot(dat.rf)
Loading required package: Heatplus
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘Heatplus’
Error in plot.mpcross(dat.rf) : could not find function "heatmap_2"
Calls: plot -> plot.mpcross
Execution halted
Flavors: r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard
Version: 1.14
Check: R code for possible problems
Result: NOTE
mpprob: no visible global function definition for 'happy'
mpprob: no visible global function definition for 'hdesign'
Flavor: r-oldrel-windows-ix86+x86_64