- using R Under development (unstable) (2012-02-23 r58468)
- using platform: i686-pc-linux-gnu (32-bit)
- using session charset: UTF-8
- checking for file ‘GWAF/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘GWAF’ version ‘1.2’
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... NOTE
As from R 2.14.0 all packages need a namespace.
One will be generated on installation, but it is better to handcraft a
NAMESPACE file: R CMD build will produce a suitable starting point.
- checking for executable files ... OK
- checking whether package ‘GWAF’ can be installed ... OK
- checking installed package size ... OK
- checking package directory ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking R files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... OK
- checking whether the package can be loaded with stated dependencies ... OK
- checking whether the package can be unloaded cleanly ... OK
- checking for unstated dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... NOTE
GWplot: warning in bitmap(outfile, w = 12, h = 8): partial argument
match of 'h' to 'height'
GWplot: warning in bitmap(outfile, w = 12, h = 8): partial argument
match of 'w' to 'width'
auto: warning in write(cmds, paste(phen, ".lme.", when, ".", j, ".R",
sep = ""), ncol = 1): partial argument match of 'ncol' to 'ncolumns'
auto: warning in write(paste("qsub -cwd ", phen, ".lme.", when, ".", j,
".sh", sep = ""), paste(phen, ".lme.", when, ".lst", sep = ""), ncol
= 1, append = T): partial argument match of 'ncol' to 'ncolumns'
auto: warning in write(c("phen", "snp", "n0", "n1", "n2", "h2q",
"beta", "se", "chisq", "df", "model", "pval"), outfile, sep = ",",
ncol = 12): partial argument match of 'ncol' to 'ncolumns'
auto: warning in write(c("phen", "snp", "n0", "n1", "n2", "h2q",
"beta10", "beta20", "beta21", "se10", "se20", "se21", "chisq", "df",
"model", "pval"), outfile, ncol = 16, sep = ","): partial argument
match of 'ncol' to 'ncolumns'
auto: warning in write(cmds, paste(phen, ".lme.imputed.", when, ".", j,
".R", sep = ""), ncol = 1): partial argument match of 'ncol' to
'ncolumns'
auto: warning in write(paste("qsub -cwd ", phen, ".lme.imputed.", when,
".", j, ".sh", sep = ""), paste(phen, ".lme.imputed.", when, ".lst",
sep = ""), ncol = 1, append = T): partial argument match of 'ncol' to
'ncolumns'
auto: warning in write(c("phen", "snp", "N", "AF", "h2q", "beta", "se",
"pval"), outfile, ncol = 8, sep = ","): partial argument match of
'ncol' to 'ncolumns'
auto: warning in write(cmds, paste(phen, ".gee.", when, ".", j, ".R",
sep = ""), ncol = 1): partial argument match of 'ncol' to 'ncolumns'
auto: warning in write(paste("qsub -cwd ", phen, ".gee.", when, ".", j,
".sh", sep = ""), paste(phen, ".gee.", when, ".lst", sep = ""), ncol
= 1, append = T): partial argument match of 'ncol' to 'ncolumns'
auto: warning in write(c("phen", "snp", "n0", "n1", "n2", "nd0", "nd1",
"nd2", "miss.0", "miss.1", "miss.diff.p", "beta", "se", "chisq",
"df", "model", "remark", "pval"), outfile, sep = ",", ncol = 18):
partial argument match of 'ncol' to 'ncolumns'
auto: warning in write(c("phen", "snp", "n0", "n1", "n2", "nd0", "nd1",
"nd2", "miss.0", "miss.1", "miss.diff.p", "beta10", "beta20",
"beta21", "se10", "se20", "se21", "chisq", "df", "model", "remark",
"pval"), outfile, sep = ",", ncol = 22): partial argument match of
'ncol' to 'ncolumns'
auto: warning in write(cmds, paste(phen, ".gee.imputed.", when, ".", j,
".R", sep = ""), ncol = 1): partial argument match of 'ncol' to
'ncolumns'
auto: warning in write(paste("qsub -cwd ", phen, ".gee.imputed.", when,
".", j, ".sh", sep = ""), paste(phen, ".gee.imputed.", when, ".lst",
sep = ""), ncol = 1, append = T): partial argument match of 'ncol' to
'ncolumns'
auto: warning in write(c("phen", "snp", "N", "Nd", "AF", "AFd", "beta",
"se", "remark", "pval"), outfile, ncol = 10, sep = ","): partial
argument match of 'ncol' to 'ncolumns'
gee.lgst.batch : read.in.data: warning in read.table(gzfile(genfile),
header = TRUE, na.string = "", sep = sep.gen): partial argument match
of 'na.string' to 'na.strings'
gee.lgst.batch.imputed : read.in.data: warning in
read.table(gzfile(genfile), header = TRUE, na.string = "", sep =
sep.gen): partial argument match of 'na.string' to 'na.strings'
lme.batch : read.in.data: warning in read.table(gzfile(genfile), header
= TRUE, na.string = "", sep = sep.gen): partial argument match of
'na.string' to 'na.strings'
lme.batch: warning in assign("phen", phen, env = .GlobalEnv, inherits =
T): partial argument match of 'env' to 'envir'
lme.batch: warning in assign("test.dat", test.dat, env = .GlobalEnv,
inherits = T): partial argument match of 'env' to 'envir'
lme.batch: warning in assign("i", i, env = .GlobalEnv, inherits = T):
partial argument match of 'env' to 'envir'
lme.batch: warning in assign("x.covar", x.covar, env = .GlobalEnv,
inherits = T): partial argument match of 'env' to 'envir'
lme.batch: warning in assign("test2.dat", test2.dat, env = .GlobalEnv,
inherits = T): partial argument match of 'env' to 'envir'
lme.batch: warning in assign("id", id, env = .GlobalEnv, inherits = T):
partial argument match of 'env' to 'envir'
lme.batch: no visible binding for global variable ‘kmat’
lme.batch: warning in assign("snp.i", snp.i, env = .GlobalEnv, inherits
= T): partial argument match of 'env' to 'envir'
lme.batch.imputed : read.in.data: warning in
read.table(gzfile(genfile), header = TRUE, na.string = "", sep =
sep.gen): partial argument match of 'na.string' to 'na.strings'
lme.batch.imputed: warning in assign("phen", phen, env = .GlobalEnv,
inherits = T): partial argument match of 'env' to 'envir'
lme.batch.imputed: warning in assign("test.dat", test.dat, env =
.GlobalEnv, inherits = T): partial argument match of 'env' to 'envir'
lme.batch.imputed: warning in assign("xcovar", xcovar, env =
.GlobalEnv, inherits = T): partial argument match of 'env' to 'envir'
lme.batch.imputed: warning in assign("test1.dat", test1.dat, env =
.GlobalEnv, inherits = T): partial argument match of 'env' to 'envir'
lme.batch.imputed: warning in assign("id", id, env = .GlobalEnv,
inherits = T): partial argument match of 'env' to 'envir'
lme.batch.imputed: no visible binding for global variable ‘kmat’
lme.batch.imputed: warning in assign("i", i, env = .GlobalEnv, inherits
= T): partial argument match of 'env' to 'envir'
lme.batch.imputed: warning in assign("x.covar", x.covar, env =
.GlobalEnv, inherits = T): partial argument match of 'env' to 'envir'
lme.batch.imputed: warning in assign("test2.dat", test2.dat, env =
.GlobalEnv, inherits = T): partial argument match of 'env' to 'envir'
qq: warning in bitmap(outfile, w = 8, h = 8): partial argument match of
'h' to 'height'
qq: warning in bitmap(outfile, w = 8, h = 8): partial argument match of
'w' to 'width'
- checking Rd files ... OK
- checking Rd metadata ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking sizes of PDF files under ‘inst/doc’ ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking examples ... NONE
- checking PDF version of manual ... OK
NOTE: There were 2 notes.
See
‘/home/hornik/tmp/R.check/r-devel/Work/PKGS/GWAF.Rcheck/00check.log’
for details.