CRAN Package Check Results for Maintainer ‘Thomas Lumley <tlumley at u.washington.edu>’

Last updated on 2014-10-10 15:50:02.

Package ERROR WARN NOTE OK
biglm 14
ConvCalendar 6 8
dichromat 14
leaps 14
odfWeave.survey 15
randaes 6 8
rmeta 14

Package biglm

Current CRAN status: NOTE: 14

Version: 0.9-1
Check: top-level files
Result: NOTE
    Non-standard file/directory found at top level:
     ‘test’
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-x86_64

Version: 0.9-1
Check: dependencies in R code
Result: NOTE
    Packages in Depends field not imported from:
     ‘DBI’ ‘methods’
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
    See the information on DESCRIPTION files in the chapter ‘Creating R
    packages’ of 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, 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-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.9-1
Check: foreign function calls
Result: NOTE
    Call with DUP:
     .Fortran("regcf", as.integer(p), as.integer(p * p/2), bigQR$D,
     bigQR$rbar, bigQR$thetab, bigQR$tol, beta = numeric(p), nreq = as.integer(nvar),
     ier = integer(1), DUP = FALSE)
    DUP is no longer supported and will be ignored.
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: 0.9-1
Check: R code for possible problems
Result: NOTE
    bigglm.RODBC: no visible global function definition for ‘odbcQuery’
    bigglm.RODBC : chunk: no visible global function definition for
     ‘odbcQuery’
    bigglm.RODBC : chunk: no visible global function definition for
     ‘sqlGetResults’
    
    Found the following calls to data() loading into the global environment:
    File ‘biglm/R/bigglm.R’:
     data(reset = TRUE)
     data(reset = FALSE)
    See section ‘Good practice’ in ‘?data’.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-osx-x86_64-clang

Version: 0.9-1
Check: R code for possible problems
Result: NOTE
    bigglm.RODBC: no visible global function definition for ‘odbcQuery’
    bigglm.RODBC : chunk: no visible global function definition for
     ‘odbcQuery’
    bigglm.RODBC : chunk: no visible global function definition for
     ‘sqlGetResults’
Flavors: r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-release-osx-x86_64-mavericks

Version: 0.9-1
Check: foreign function calls
Result: NOTE
    Call with DUP != TRUE:
     .Fortran("regcf", as.integer(p), as.integer(p * p/2), bigQR$D,
     bigQR$rbar, bigQR$thetab, bigQR$tol, beta = numeric(p), nreq = as.integer(nvar),
     ier = integer(1), DUP = FALSE)
    DUP = FALSE is deprecated and will be disabled in future versions of R.
Flavors: r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86

Version: 0.9-1
Check: R code for possible problems
Result: NOTE
    Found the following calls to data() loading into the global environment:
    File ‘biglm/R/bigglm.R’:
     data(reset = TRUE)
     data(reset = FALSE)
    See section ‘Good practice’ in ‘?data’.
Flavors: r-patched-linux-x86_64, r-release-linux-ix86, r-release-linux-x86_64

Version: 0.9-1
Check: foreign function calls
Result: NOTE
    Call with DUP = FALSE:
     .Fortran("regcf", as.integer(p), as.integer(p * p/2), bigQR$D,
     bigQR$rbar, bigQR$thetab, bigQR$tol, beta = numeric(p), nreq = as.integer(nvar),
     ier = integer(1), DUP = FALSE)
    DUP = FALSE is deprecated and may be disabled in future versions of R.
Flavors: r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64

Version: 0.9-1
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘RODBC’
Flavor: r-release-osx-x86_64-mavericks

Package ConvCalendar

Current CRAN status: NOTE: 6, OK: 8

Version: 1.2
Check: top-level files
Result: NOTE
    Non-standard file/directory found at top level:
     ‘COPYRIGHTS’
    Copyright information should be in file inst/COPYRIGHTS
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-x86_64

Package dichromat

Current CRAN status: OK: 14

Package leaps

Current CRAN status: NOTE: 14

Version: 2.9
Check: foreign function calls
Result: NOTE
    Call with DUP:
     .Fortran("makeqr", np = as.integer(np), nn = as.integer(nn),
     wt = as.double(wt), tx = t(xx), y = as.double(y), d = numeric(np),
     rbar = numeric(nrbar), thetab = numeric(np), sserr = numeric(1),
     ier = as.integer(0), PACKAGE = "leaps", DUP = FALSE)
    DUP is no longer supported and will be ignored.
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: 2.9
Check: Rd line widths
Result: NOTE
    Rd file 'leaps.Rd':
     \usage lines wider than 90 characters:
     leaps(x=, y=, wt=rep(1, NROW(x)), int=TRUE, method=c("Cp", "adjr2", "r2"), nbest=10, names=NULL, df=NROW(x), strictly.compatible=TRUE)
    
    Rd file 'leaps.setup.Rd':
     \usage lines wider than 90 characters:
     leaps.setup(x,y,wt=rep(1,length(y)),force.in=NULL,force.out=NULL,intercept=TRUE,nvmax=8,nbest=1,warn.dep=TRUE)
    
    Rd file 'plot.regsubsets.Rd':
     \usage lines wider than 90 characters:
     plot(x, labels=obj$xnames, main=NULL, scale=c("bic", "Cp", "adjr2", "r2"), col=gray(seq(0, 0.9, length = 10)),...)
    
    Rd file 'regsubsets.Rd':
     \usage lines wider than 90 characters:
     regsubsets(x=, data=, weights=NULL, nbest=1, nvmax=8, force.in=NULL, force.out=NULL, intercept=TRUE, method=c("exhaustive", "backward", ... [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-x86_64

Version: 2.9
Check: compiled code
Result: NOTE
    File ‘leaps/libs/leaps.so’:
     Found ‘_gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
     (Fortran)
     Object: ‘leaps.o’
    
    Compiled code should not call entry points which might terminate R nor
    write to stdout/stderr instead of to the console, nor the C RNG.
    
    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, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 2.9
Check: compiled code
Result: NOTE
    File ‘leaps/libs/leaps.so’:
     Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
     (Fortran)
     Object: ‘leaps.o’
    
    Compiled code should not call entry points which might terminate R nor
    write to stdout/stderr instead of to the console, nor the C RNG.
    
    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavor: r-devel-osx-x86_64-clang

Version: 2.9
Check: compiled code
Result: NOTE
    File 'leaps/libs/i386/leaps.dll':
     Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
     (Fortran)
     Object: 'leaps.o'
    File 'leaps/libs/x64/leaps.dll':
     Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
     (Fortran)
     Object: 'leaps.o'
    
    Compiled code should not call entry points which might terminate R nor
    write to stdout/stderr instead of to the console, nor the C RNG.
    
    See 'Writing portable packages' in the 'Writing R Extensions' manual.
Flavor: r-devel-windows-ix86+x86_64

Version: 2.9
Check: foreign function calls
Result: NOTE
    Call with DUP != TRUE:
     .Fortran("makeqr", np = as.integer(np), nn = as.integer(nn),
     wt = as.double(wt), tx = t(xx), y = as.double(y), d = numeric(np),
     rbar = numeric(nrbar), thetab = numeric(np), sserr = numeric(1),
     ier = as.integer(0), PACKAGE = "leaps", DUP = FALSE)
    DUP = FALSE is deprecated and will be disabled in future versions of R.
Flavors: r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86

Version: 2.9
Check: compiled code
Result: NOTE
    File ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/leaps/libs/leaps.so’:
     Found ‘_gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
     (Fortran)
     Object: ‘leaps.o’
    
    Compiled code should not call entry points which might terminate R nor
    write to stdout/stderr instead of to the console.
    
    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavor: r-patched-linux-x86_64

Version: 2.9
Check: compiled code
Result: NOTE
    File ‘/home/ripley/R/Lib32/leaps/libs/leaps.so’:
     Found ‘__f90_esfw’, possibly from ‘print’ (Fortran), ‘write’
     (Fortran)
     Object: ‘leaps.o’
     Found ‘__f90_eslw’, possibly from ‘print’ (Fortran), ‘write’
     (Fortran)
     Object: ‘leaps.o’
    
    Compiled code should not call entry points which might terminate R nor
    write to stdout/stderr instead of to the console.
    
    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-patched-solaris-sparc, r-patched-solaris-x86

Version: 2.9
Check: foreign function calls
Result: NOTE
    Call with DUP = FALSE:
     .Fortran("makeqr", np = as.integer(np), nn = as.integer(nn),
     wt = as.double(wt), tx = t(xx), y = as.double(y), d = numeric(np),
     rbar = numeric(nrbar), thetab = numeric(np), sserr = numeric(1),
     ier = as.integer(0), PACKAGE = "leaps", DUP = FALSE)
    DUP = FALSE is deprecated and may be disabled in future versions of R.
Flavors: r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64

Version: 2.9
Check: compiled code
Result: NOTE
    File ‘/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/leaps/libs/leaps.so’:
     Found ‘_gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
     (Fortran)
     Object: ‘leaps.o’
    
    Compiled code should not call entry points which might terminate R nor
    write to stdout/stderr instead of to the console.
    
    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-release-linux-ix86, r-release-linux-x86_64

Version: 2.9
Check: compiled code
Result: NOTE
    File ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.1/leaps.Rcheck/leaps/libs/leaps.so’:
     Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
     (Fortran)
     Object: ‘leaps.o’
    
    Compiled code should not call entry points which might terminate R nor
    write to stdout/stderr instead of to the console.
    
    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavor: r-release-osx-x86_64-mavericks

Version: 2.9
Check: compiled code
Result: NOTE
    File 'd:/Rcompile/CRANpkg/lib/3.1/leaps/libs/i386/leaps.dll':
     Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
     (Fortran)
     Object: 'leaps.o'
    File 'd:/Rcompile/CRANpkg/lib/3.1/leaps/libs/x64/leaps.dll':
     Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
     (Fortran)
     Object: 'leaps.o'
    
    Compiled code should not call entry points which might terminate R nor
    write to stdout/stderr instead of to the console.
    
    See 'Writing portable packages' in the 'Writing R Extensions' manual.
Flavor: r-release-windows-ix86+x86_64

Version: 2.9
Check: compiled code
Result: NOTE
    File 'd:/Rcompile/CRANpkg/lib/3.0/leaps/libs/i386/leaps.dll':
     Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
     (Fortran)
     Object: 'leaps.o'
    File 'd:/Rcompile/CRANpkg/lib/3.0/leaps/libs/x64/leaps.dll':
     Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
     (Fortran)
     Object: 'leaps.o'
    
    Compiled code should not call entry points which might terminate R nor
    write to stdout/stderr instead of to the console.
    
    See 'Writing portable packages' in the 'Writing R Extensions' manual.
Flavor: r-oldrel-windows-ix86+x86_64

Package odfWeave.survey

Current CRAN status: OK: 15

Package randaes

Current CRAN status: NOTE: 6, OK: 8

Version: 0.3
Check: top-level files
Result: NOTE
    Non-standard file/directory found at top level:
     ‘COPYRIGHTS’
    Copyright information should be in file inst/COPYRIGHTS
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-x86_64

Package rmeta

Current CRAN status: NOTE: 14

Version: 2.16
Check: dependencies in R code
Result: NOTE
    'library' or 'require' call to ‘grid’ which was already attached by Depends.
     Please remove these calls from your code.
    See the information on DESCRIPTION files in the chapter ‘Creating R
    packages’ of 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, 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-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.16
Check: R code for possible problems
Result: NOTE
    plot.meta.cum: warning in qnorm((1 - conf.level)/2, s = ses[m]):
     partial argument match of ‘s’ to ‘sd’
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-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.16
Check: Rd files
Result: NOTE
    prepare_Rd: meta.MH.Rd:55: Dropping empty section \references
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-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.16
Check: Rd line widths
Result: NOTE
    Rd file 'forestplot.Rd':
     \examples lines wider than 100 characters:
     c("","OR",format(exp(steroid$logOR),digits=2),NA,format(exp(steroid$logMH),digits=2))
    
    Rd file 'meta.cum.Rd':
     \usage lines wider than 90 characters:
     NULL, subset = NULL, na.action = na.fail, method = c("meta.MH", "meta.DSL"), statistic = "OR")
     cummeta.summaries(effects,stderrs, conf.level = 0.95, names = NULL,weights=NULL, data= NULL, subset = NULL, na.action = get(getOption(" ... [TRUNCATED]
     summary.line = TRUE, summary.conf = FALSE, main="Cumulative meta-analysis", lwd=1, ...)
     \examples lines wider than 100 characters:
     steroid<-cummeta(n.trt,n.ctrl,ev.trt,ev.ctrl,names=name,data=cochrane,statistic="RR",method="meta.MH")
    
    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-x86_64