- using R Under development (unstable) (2012-05-22 r59396)
- using platform: x86_64-unknown-linux-gnu (64-bit)
- using session charset: UTF-8
- checking for file ‘Geneclust/DESCRIPTION’ ... OK
- this is package ‘Geneclust’ version ‘1.0.1’
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... WARNING
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.
CRAN requires a NAMESPACE file for all submissions.
- checking for executable files ... OK
- checking whether package ‘Geneclust’ can be installed ... WARNING
Found the following significant warnings:
Warning: Rank mismatch in argument 'nall' at (1) (scalar and rank-1)
See ‘/data/gannet/tmp/ripley/R/packages/tests-devel/Geneclust.Rcheck/00install.out’ for details.
- 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 loading without being on the library search path ... 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
File ‘Geneclust/R/zzz.R’:
.First.lib calls:
cat("**********************************************************", fill = TRUE)
cat("* Geneclust 1.0.1 is loaded *", fill = TRUE)
cat("* *", fill = TRUE)
cat("* Use help(Geneclust) for a quick overview. *", fill = TRUE)
cat("* *", fill = TRUE)
cat("**********************************************************", fill = TRUE)
require(spatial)
Package startup functions should not change the search path.
Package startup functions should use ‘packageStartupMessage’ to
generate messages.
See section ‘Good practice’ in ?.onAttach.
Fst: warning in matrix(nr = npopmax, nc = npopmax, 0): partial argument
match of 'nr' to 'nrow'
Fst: warning in matrix(nr = npopmax, nc = npopmax, 0): partial argument
match of 'nc' to 'ncol'
Fst: warning in matrix(nr = nindivtmp, nc = 2, data = -999): partial
argument match of 'nr' to 'nrow'
Fst: warning in matrix(nr = nindivtmp, nc = 2, data = -999): partial
argument match of 'nc' to 'ncol'
mcmcgeneclust: warning in write.table(param, file = paste(path.mcmc,
"paraminfer.txt", sep = ""), quote = FALSE, row.name = FALSE,
col.name = FALSE): partial argument match of 'row.name' to
'row.names'
mcmcgeneclust: warning in write.table(param, file = paste(path.mcmc,
"paraminfer.txt", sep = ""), quote = FALSE, row.name = FALSE,
col.name = FALSE): partial argument match of 'col.name' to
'col.names'
postclassif: warning in matrix(nr = nindiv, byrow = FALSE, data =
updatelabel): partial argument match of 'nr' to 'nrow'
postclassif: warning in matrix(1:2, nr = 1, ncol = 2): partial argument
match of 'nr' to 'nrow'
simpatch: warning in matrix(nr = nindiv, nc = nloc * 2): partial
argument match of 'nr' to 'nrow'
simpatch: warning in matrix(nr = nindiv, nc = nloc * 2): partial
argument match of 'nc' to 'ncol'
simpatch: warning in write.table(param, file = paste(file,
"paramsimu.txt", sep = ""), quote = FALSE, row.name = FALSE, col.name
= FALSE): partial argument match of 'row.name' to 'row.names'
simpatch: warning in write.table(param, file = paste(file,
"paramsimu.txt", sep = ""), quote = FALSE, row.name = FALSE, col.name
= FALSE): partial argument match of 'col.name' to 'col.names'
simpottsdir: warning in matrix(recup, nr = nindiv, byrow = FALSE):
partial argument match of 'nr' to 'nrow'
- checking Rd files ... NOTE
prepare_Rd: FormatGenotypes.Rd:35: Dropping empty section \keyword
prepare_Rd: FormatGenotypes.Rd:30: Dropping empty section \seealso
prepare_Rd: Fst.Rd:36: Dropping empty section \keyword
prepare_Rd: Geneclust-package.Rd:138: Dropping empty section \keyword
prepare_Rd: Geneclust-package.Rd:141-144: Dropping empty section \examples
prepare_Rd: geneclust.Rd:176: Dropping empty section \keyword
prepare_Rd: geneclust.Rd:178-180: Dropping empty section \examples
prepare_Rd: mcmcgeneclust.Rd:116: Dropping empty section \keyword
prepare_Rd: postclassif.Rd:43: Dropping empty section \keyword
prepare_Rd: postfis.Rd:31: Dropping empty section \keyword
prepare_Rd: postpsi.Rd:24: Dropping empty section \keyword
prepare_Rd: setplot.Rd:24: Dropping empty section \keyword
prepare_Rd: simpatch.Rd:61: Dropping empty section \keyword
prepare_Rd: simpatch.Rd:57: Dropping empty section \seealso
prepare_Rd: simpottsdir.Rd:55: Dropping empty section \keyword
prepare_Rd: subsample.Rd:29: Dropping empty section \keyword
prepare_Rd: tablecst.Rd:67: Dropping empty section \keyword
- 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 line endings in C/C++/Fortran sources/headers ... OK
- checking line endings in Makefiles ... OK
- checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
- checking compiled code ... NOTE
File ‘/data/gannet/tmp/ripley/R/packages/tests-devel/Geneclust.Rcheck/Geneclust/libs/Geneclust.so’:
Found ‘_gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
(Fortran)
Objects: ‘main.o’, ‘mainpotts.o’
Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
- checking examples ... OK
- checking PDF version of manual ... OK
WARNING: There were 2 warnings.
NOTE: There were 3 notes.
See
‘/data/gannet/tmp/ripley/R/packages/tests-devel/Geneclust.Rcheck/00check.log’
for details.