dyebiasexamples 1.0.12
Philip Lijnzaad
| Snapshot Date: 2014-04-04 06:15:32 -0700 (Fri, 04 Apr 2014) | | URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_2_13/experiment/pkgs/dyebiasexamples | | Last Changed Rev: 2557 / Revision: 2768 | | Last Changed Date: 2013-11-01 13:36:05 -0700 (Fri, 01 Nov 2013) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | WARNINGS | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | [ WARNINGS ] | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | WARNINGS | OK |
* using log directory 'D:/biocbld/bbs-2.13-data-experiment/meat/dyebiasexamples.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'dyebiasexamples/DESCRIPTION' ... OK
* this is package 'dyebiasexamples' version '1.0.12'
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'dyebiasexamples' can be installed ... OK
* checking installed package size ... NOTE
installed size is 40.2Mb
sub-directories of 1Mb or more:
data 5.3Mb
extradata 34.8Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
'GEOquery' 'marray'
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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... WARNING
checkRd: (3) dyebias.geo2marray.Rd:10-17: \synopsis will be removed in R 3.1.0
checkRd: (3) dyebias.umcu.proper.estimators.Rd:11-13: \synopsis will be removed in R 3.1.0
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'dyebias.geo2marray':
dyebias.geo2marray
Code: function(gse, slide.ids = NULL, type = "norm", gene.selector =
function(table) { T}, reporterid.name, cy3.name,
cy5.name, R.name = NULL, G.name = NULL, M.name = NULL,
A.name = NULL, Rf.name = NULL, Gf.name = NULL, Rb.name
= NULL, Gb.name = NULL)
Docs: function(gse, slide.ids = NULL, type = "norm", gene.selector =
function(table) { TRUE}, reporterid.name, cy3.name,
cy5.name, R.name = NULL, G.name = NULL, M.name = NULL,
A.name = NULL, Rf.name = NULL, Gf.name = NULL, Rb.name
= NULL, Gb.name = NULL)
Mismatches in argument default values:
Name: 'gene.selector'
Code: function(table) {
T
}
Docs: function(table) {
TRUE
}
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... WARNING
Files not of a type allowed in a 'data' directory:
'README'
Please use e.g. 'inst/extdata' for non-R data files
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... WARNING
Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
data.norm.rda 2.1Mb 1.5Mb xz
data.raw.rda 3.2Mb 2.2Mb xz
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [6s] OK
** running examples for arch 'x64' ... [7s] OK
* checking PDF version of manual ... OK
WARNING: There were 4 warnings.
NOTE: There were 3 notes.
See
'D:/biocbld/bbs-2.13-data-experiment/meat/dyebiasexamples.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'dyebiasexamples' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'dyebiasexamples' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'dyebiasexamples' as dyebiasexamples_1.0.12.zip
* DONE (dyebiasexamples)