Check results for 'mvbutils'

using R Under development (unstable) (2012-02-06 r58287)
using platform: i686-pc-linux-gnu (32-bit)
using session charset: UTF-8
checking for file ‘mvbutils/DESCRIPTION’ ... OK
this is package ‘mvbutils’ version ‘2.5.101’
checking package namespace information ... OK
checking package dependencies ... OK
checking if this is a source package ... OK
checking if there is a namespace ... OK
checking for executable files ... OK
checking whether package ‘mvbutils’ 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 whether the namespace can be loaded with stated dependencies ... OK
checking whether the namespace 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
%where.warn%: warning in deparse(substitute(cond), nlines = 1, width =
50): partial argument match of 'width' to 'width.cutoff'
%where.warn%: warning in deparse(substitute(x), nlines = 1, width =
20): partial argument match of 'width' to 'width.cutoff'
.Last.lib: warning in ls(s, patt = "^base\\."): partial argument match
of 'patt' to 'pattern'
.onLoad: warning in evalq({: partial argument match of 'env' to 'envir'
.onLoad: warning in maintained.packages <- originals.mp <-
dont.lock.envs <- presave.hooks <- list(): partial argument match of
'env' to 'envir'
.onLoad: warning in fix.list <- empty.data.frame(name = , file = ,
where = , where.type = , dataclass = "", has.source = FALSE,
file.time = 0): partial argument match of 'env' to 'envir'
.onLoad: warning in dont.lock.envnames <- character(0): partial
argument match of 'env' to 'envir'
.onLoad: warning in }, env = nsenv): partial argument match of 'env' to
'envir'
.onLoad : f: no visible binding for global variable ‘blah’
.onLoad: no visible binding for global variable ‘package’
.onLoad: no visible binding for global variable ‘tasks’
.onLoad: no visible binding for global variable ‘ROOT’
.onLoad: no visible binding for global variable ‘mvbutils’
.onLoad: no visible binding for global variable ‘head.default’
.onLoad: no visible binding for global variable ‘tail.default’
FF: no visible binding for global variable ‘w’
FF: no visible binding for global variable ‘mods.in.packages’
FF: no visible binding for global variable ‘mods.in.tasks’
FF: no visible binding for global variable ‘tracees’
FF: no visible binding for global variable ‘mtrace’
Save.pos: no visible global function definition for ‘warn’
Save.pos: no visible global function definition for ‘check.for.tracees’
Save.pos: no visible binding for global variable ‘tracees’
Save.pos: no visible binding for global variable ‘mtrace’
autoedit: warning in exists("autoedit.callback", env = s, inherits =
FALSE): partial argument match of 'env' to 'envir'
autoedit: warning in assign("autoedit.callback",
addTaskCallback(function(...) {: partial argument match of 'env' to
'envir'
autoedit: warning in try(FF()): partial argument match of 'env' to
'envir'
autoedit: warning in TRUE: partial argument match of 'env' to 'envir'
autoedit: warning in }), env = s): partial argument match of 'env' to
'envir'
called.by: warning in unlist(lapply(where, exists, x = fname), use =
FALSE): partial argument match of 'use' to 'use.names'
cd: no visible binding for global variable ‘last.warning’
cd: no visible binding for global variable ‘.Traceback’
cd: no visible binding for global variable ‘.Saved.plots’
cd: no visible binding for global variable ‘.’
cd: warning in load.mvb(file.path(orig.path, ".RData"),
names(orig.path), pos = 2, attach = TRUE, path = orig.path): partial
argument match of 'attach' to 'attach.new'
cd..: no visible binding for global variable ‘execute.Last’
cd..: no visible binding for global variable ‘orig.path’
cd.load: warning in save.refdb(file = filename, env =
maintained.packages[[taskname]]): partial argument match of 'env' to
'envir'
cd.load: no visible binding for global variable ‘.’
cd.load: no visible binding for global variable ‘execute.First’
cd.write.mvb.tasks: no visible binding for global variable ‘.’
cd.write.mvb.tasks.guts: warning in exists("tasks", env = env, inherits
= FALSE): partial argument match of 'env' to 'envir'
cdfind: no visible binding for global variable ‘.’
cditerate: warning in assign("[[", my.index, env =
sys.frame(sys.nframe())): partial argument match of 'env' to 'envir'
cditerate: warning in assign("[[<-", my.index.assign, env =
sys.frame(sys.nframe())): partial argument match of 'env' to 'envir'
cditerate: warning in exists.mvb("tasks", env = env): partial argument
match of 'env' to 'envir'
cditerate: warning in get("tasks", env = env): partial argument match
of 'env' to 'envir'
cdregexpr: no visible binding for global variable ‘.’
cdtree: no visible binding for global variable ‘.’
cdtree: no visible binding for global variable ‘x’
check.pkg: no visible binding for global variable ‘subdir’
copy.ns.objects : icns : f: no visible binding for global variable
‘blah’
create.backups: no visible binding for global variable ‘.’
deal.with.backups: no visible global function definition for ‘warn’
demlazy: no visible binding for global variable ‘.’
discard.mouldering.backups: no visible binding for global variable
‘backup.fix’
doc2Rd: no visible binding for global variable ‘.’
doc2Rd: no visible binding for global variable ‘docType’
doc2Rd: no visible binding for global variable ‘author’
dont.save: no visible binding for global variable ‘.SavedPlots’
dont.save: no visible binding for global variable ‘last.warning’
dont.save: no visible binding for global variable ‘.Traceback’
expand.match: warning in pmatch(toupper(short), toupper(long), dup =
TRUE): partial argument match of 'dup' to 'duplicates.ok'
expand.match: warning in pmatch(short, long, dup = TRUE): partial
argument match of 'dup' to 'duplicates.ok'
find.and.get: no visible binding for global variable ‘name’
find.and.get: no visible binding for global variable ‘fixing’
find.and.get: no visible binding for global variable ‘tracees’
find.and.get: no visible binding for global variable ‘what’
find.derefs: no visible binding for global variable ‘.’
find.docholder: no visible binding for global variable ‘funs’
find.documented : findo: no visible binding for global variable ‘.’
find.funs: warning in unlist(lapply(pos, findo), use = FALSE): partial
argument match of 'use' to 'use.names'
find.path : get.tasks.if.present: warning in exists.mvb("tasks", env =
env.or.pos): partial argument match of 'env' to 'envir'
find.path : get.tasks.if.present: warning in get("tasks", env =
env.or.pos): partial argument match of 'env' to 'envir'
find.path: warning in objects(env = env, all = TRUE): partial argument
match of 'env' to 'envir'
find.path: warning in objects(env = env, all = TRUE): partial argument
match of 'all' to 'all.names'
find.web: no visible binding for global variable ‘generics’
find.web: no visible binding for global variable ‘where’
find.web: no visible binding for global variable ‘textcolor’
find.web: no visible binding for global variable ‘prune’
find.web: no visible binding for global variable ‘highlight’
fixr: warning in deparse(substitute(x), width = 30, nlines = 1):
partial argument match of 'width' to 'width.cutoff'
fixr: no visible binding for global variable ‘load.from’
fixr: no visible binding for global variable ‘name.load.from’
fixr: no visible binding for global variable ‘trace.was.on’
fixr: no visible global function definition for ‘mtrace’
fixr: no visible binding for global variable ‘type.load.from’
fixr: no visible binding for global variable ‘package’
fixr: no visible binding for global variable ‘task’
fixr.guts: no visible binding for global variable ‘tracees’
fixr.guts: no visible global function definition for ‘mtrace’
fixup.DLLs: warning in dir(rpath, patt = suffix): partial argument
match of 'patt' to 'pattern'
fixup.DLLs: warning in dir(file.path(rpath, "inst", libs), patt =
suffix): partial argument match of 'patt' to 'pattern'
fixup.DLLs: warning in dir(ipath.libs, patt = suffix): partial argument
match of 'patt' to 'pattern'
fixup.DLLs: warning in dir(file.path(rpath, "src"), patt =
"[.](c|cc|cpp|C|f|f90|f95|m|mm|M)$"): partial argument match of
'patt' to 'pattern'
fixup.exports: no visible binding for global variable ‘.’
fixup.help: no visible binding for global variable ‘spath’
fixup.help: warning in dir(manpath, patt = "[.]Rd$"): partial argument
match of 'patt' to 'pattern'
fixup.help: no visible binding for global variable ‘ipath’
fixup.help: no visible binding for global variable ‘force.all.docs’
fixup.help: no visible binding for global variable ‘dynamic.help’
fixup.help: no visible binding for global variable ‘pkg’
fixup.help: no visible binding for global variable ‘is.Rd2’
foodweb: no visible binding for global variable ‘level’
foodweb: no visible binding for global variable ‘funmat’
foodweb: no visible binding for global variable ‘x’
generic.dll.loader: warning in dir(dll.path, pattern = this.ext, full =
FALSE, ignore.case = .Platform$OS.type == "windows"): partial
argument match of 'full' to 'full.names'
get.new.file.numbers: no visible binding for global variable ‘.’
help2flatdoc: no visible binding for global variable ‘.’
help2flatdoc: no visible binding for global variable ‘USAGE’
help2flatdoc: no visible binding for global variable ‘EXAMPLES’
hook.set.already: no visible binding for global variable ‘prepend’
internal.copy.ns.objects : f: no visible binding for global variable
‘blah’
load.live.package: no visible binding for '<<-' assignment to
‘live.packages’
load.live.package: no visible binding for global variable
‘live.packages’
load.maintained.package: no visible binding for global variable
‘mvb.session.info’
load.mvb: warning in load.refdb(filename, env = envir, fpath = path):
partial argument match of 'env' to 'envir'
make.NAMESPACE : <anonymous>: warning in get(x, env = env): partial
argument match of 'env' to 'envir'
make.NAMESPACE: no visible binding for global variable ‘.’
methodize.USAGE: no visible binding for global variable ‘overall.name’
mlazy: no visible binding for global variable ‘.’
mlibrary2: no visible binding for global variable ‘tasks’
mlocal: warning in exists.mvb(i, env = nlocal.env): partial argument
match of 'env' to 'envir'
mlocal: no visible binding for global variable ‘override.answer’
move: warning in find.path(char = to): partial argument match of 'char'
to 'char.rel.path'
move: warning in find.path(char = from): partial argument match of
'char' to 'char.rel.path'
move: no visible binding for global variable ‘.’
move: warning in get(i, env = from$env): partial argument match of
'env' to 'envir'
move.fix.list: no visible binding for global variable ‘what’
move.fix.list: no visible binding for global variable ‘to’
move.to.mcache: no visible binding for global variable ‘.’
mp.synch: no visible binding for global variable ‘exports.have.changed’
mtidy: no visible binding for global variable ‘.’
mupdate.mcache: no visible binding for global variable ‘.’
mvb.sys.on.exit: no visible global function definition for
‘find.debug.HQ’
not.for.packaging: no visible binding for global variable ‘tasks’
not.for.packaging: no visible binding for global variable ‘.Traceback’
not.for.packaging: no visible binding for global variable
‘last.warning’
not.for.packaging: no visible binding for global variable ‘.SavedPlots’
organize.web.display: no visible binding for global variable ‘n’
organize.web.display: no visible binding for global variable ‘funs’
organize.web.display: no visible binding for global variable ‘funmat’
organize.web.display: no visible binding for global variable ‘minstrl’
patch.installed: no visible binding for global variable ‘dir.’
patch.installed: no visible binding for global variable ‘subdir’
patch.installed: possible error in loadNamespace(pkg, partial = TRUE,
declarativeOnly = TRUE): unused argument(s) (declarativeOnly = TRUE)
patch.installed: warning in load(from, env = e): partial argument match
of 'env' to 'envir'
patch.installed: warning in load(from.nonfuns, env = e): partial
argument match of 'env' to 'envir'
patch.package: no visible binding for global variable ‘.’
patch.package: no visible global function definition for ‘rm.from.pkg’
patch.package: no visible binding for global variable ‘doc’
patch.package: no visible binding for global variable ‘export.me’
pre.install: no visible binding for global variable ‘subdir’
pre.install: no visible binding for global variable ‘dir.’
pre.install: warning in dir(mlazy.temp.dir, patt = "^obj[0-9]+.rda$"):
partial argument match of 'patt' to 'pattern'
pre.install: warning in dir(mlazy.inst.dir, patt = "^obj[0-9]+.rda$"):
partial argument match of 'patt' to 'pattern'
pre.install: no visible binding for global variable ‘R’
pre.install: no visible binding for global variable ‘man’
pre.install: no visible binding for global variable ‘inst’
pre.install: no visible binding for global variable ‘ewhere’
pre.install: warning in dir(dir., patt = "^Makefile"): partial argument
match of 'patt' to 'pattern'
pre.install : get.nondirs: no visible binding for global variable
‘dir.’
pre.install : get.nondirs: warning in list.files(cdir, all.files =
TRUE, full = FALSE, recursive = recursive): partial argument match of
'full' to 'full.names'
pre.install: no visible binding for global variable ‘src’
pre.install: no visible binding for global variable ‘exec’
pre.install: no visible binding for global variable ‘tests’
pre.install: no visible binding for global variable ‘.’
pre.install : <anonymous>: no visible binding for global variable
‘ewhere’
pre.install: no visible binding for global variable ‘dll.paths’
pre.install: no visible binding for global variable ‘.required’
pre.install: no visible binding for global variable ‘tasks’
pre.install: no visible binding for global variable ‘.Traceback’
pre.install: no visible binding for global variable ‘last.warning’
pre.install: no visible binding for global variable ‘.SavedPlots’
pre.install: no visible binding for global variable ‘task.path’
pre.install: no visible binding for global variable ‘env’
pre.install: no visible binding for global variable ‘..’
pre.install: warning in dir(demo.dir, patt = "\\.(r|R)$"): partial
argument match of 'patt' to 'pattern'
pre.install: no visible binding for global variable ‘exclude.funs’
pre.install: no visible binding for global variable ‘exclude.data’
pre.install: warning in source.mvb(rfile, env = e): partial argument
match of 'env' to 'envir'
pre.install: warning in dir(Rd.dir, patt = "\\.Rd$", all.files = TRUE):
partial argument match of 'patt' to 'pattern'
pre.install : provisionally.add.man.file: no visible binding for global
variable ‘subdir’
pre.install : Rdconv.internals: no visible binding for global variable
‘ewhere’
pre.install: no visible binding for global variable ‘.First.lib’
pre.install: no visible binding for global variable ‘.onAttach’
promote.2.to.1: warning in load.mvb(file = file.path(full.path,
".RData"), name = names(full.path), pos = 1, path = full.path):
partial argument match of 'file' to 'filename'
rcmdgeneric.pkg: no visible binding for global variable ‘dir.’
rcmdgeneric.pkg: no visible binding for global variable ‘subdir’
rcmdgeneric.pkg: no visible binding for global variable ‘ewhere’
reattach.placeholder: no visible global function definition for
‘get.image.filename’
restore.all.backups: no visible global function definition for
‘replace.underscores’
save.mchanged: no visible binding for global variable ‘.’
save.refdb: no visible binding for global variable ‘.’
save.refdb: no visible binding for global variable ‘name’
save.refdb: no visible binding for global variable ‘task.tree’
set.pkg.and.dir: no visible binding for global variable
‘character.only’
set.pkg.and.dir: no visible binding for global variable
‘dir.above.source’
set.rcmd.vars: no visible binding for global variable ‘sep’
setup.dontruns: no visible binding for global variable ‘.’
setup.mcache: no visible binding for global variable ‘.’
subco: no visible binding for global variable ‘Rd.version’
unpackage: warning in dir(x, all = TRUE): partial argument match of
'all' to 'all.files'
unpackage : filecop: warning in dir(file.path(spath, fname), all =
TRUE): partial argument match of 'all' to 'all.files'
unpackage: warning in dir(spath, all = TRUE): partial argument match of
'all' to 'all.files'
unpackage: no visible binding for global variable ‘.’
unpackage: no visible binding for global variable ‘CONTENTS’
unpackage: no visible binding for global variable ‘INDEX’
unpackage: no visible binding for global variable ‘MD5’
unpackage: no visible binding for global variable ‘NAMESPACE’
unpackage: no visible binding for global variable ‘..’
unpackage: no visible binding for global variable ‘src’
unpackage: no visible binding for global variable ‘chtml’
unpackage: no visible binding for global variable ‘html’
unpackage: no visible binding for global variable ‘latex’
unpackage: no visible binding for global variable ‘meta’
unpackage: no visible binding for global variable ‘R’
unpackage: no visible binding for global variable ‘libs’
unpackage: warning in dir(file.path(spath, "R"), patt = "[.][RrSsq]$",
full = TRUE): partial argument match of 'patt' to 'pattern'
unpackage: warning in dir(file.path(spath, "R"), patt = "[.][RrSsq]$",
full = TRUE): partial argument match of 'full' to 'full.names'
unpackage: warning in dir(datdir, patt =
"[.](R|r|rda|Rdata|txt|TXT|tab|csv|CSV)$"): partial argument match of
'patt' to 'pattern'
unpackage: warning in dir(file.path(spath, "man"), patt = "Rd$", full =
TRUE): partial argument match of 'patt' to 'pattern'
unpackage: warning in dir(file.path(spath, "man"), patt = "Rd$", full =
TRUE): partial argument match of 'full' to 'full.names'
unpackage.installed: warning in dir(x, all = TRUE): partial argument
match of 'all' to 'all.files'
unpackage.installed : filecop: warning in dir(file.path(ipath, fname),
all = TRUE): partial argument match of 'all' to 'all.files'
unpackage.installed: warning in dir(ipath, all = TRUE): partial
argument match of 'all' to 'all.files'
unpackage.installed: no visible binding for global variable ‘.’
unpackage.installed: no visible binding for global variable
‘DESCRIPTION’
unpackage.installed: no visible binding for global variable ‘CONTENTS’
unpackage.installed: no visible binding for global variable ‘INDEX’
unpackage.installed: no visible binding for global variable ‘MD5’
unpackage.installed: no visible binding for global variable ‘..’
unpackage.installed: no visible binding for global variable ‘src’
unpackage.installed: no visible binding for global variable ‘chtml’
unpackage.installed: no visible binding for global variable ‘html’
unpackage.installed: no visible binding for global variable ‘latex’
unpackage.installed: no visible binding for global variable ‘meta’
unpackage.installed: no visible binding for global variable ‘R’
unpackage.installed: no visible binding for global variable
‘file.with.source’
unpackage.installed: warning in dir(datdir, patt =
"[.](R|r|rda|Rdata|txt|TXT|tab|csv|CSV)$"): partial argument match of
'patt' to 'pattern'
update.installed.dir: warning in list.files(fp(opath, source), full =
TRUE, recursive = TRUE): partial argument match of 'full' to
'full.names'
update.installed.dir: warning in list.files(fp(ipath, installed), full
= TRUE, recursive = TRUE): partial argument match of 'full' to
'full.names'
update.loaded.pkg: no visible binding for global variable ‘doc’
update.loaded.pkg: no visible binding for global variable ‘export.me’
update.maintained.package: warning in load.refdb(env = mp): partial
argument match of 'env' to 'envir'
write.mvb.tasks: warning in get("tasks", env = env): partial argument
match of 'env' to 'envir'
write.sourceable.function: no visible binding for global variable
‘bug.position’
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 R/sysdata.rda ... OK
checking examples ... [9s/9s] OK
checking PDF version of manual ... OK
NOTE: There was 1 note.
See
‘/home/hornik/tmp/R.check/r-devel/Work/PKGS/mvbutils.Rcheck/00check.log’
for details.