Repitools 1.3.0
Mark Robinson
| Snapshot Date: 2012-06-20 15:22:40 -0700 (Wed, 20 Jun 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Repitools | | Last Changed Rev: 65577 / Revision: 66885 | | Last Changed Date: 2012-04-29 09:27:44 -0700 (Sun, 29 Apr 2012) |
| lamb1 | Linux (openSUSE 12.1) / x86_64 | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | [ OK ] | OK |
| perceval | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/Repitools.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'Repitools/DESCRIPTION' ... OK
* this is package 'Repitools' version '1.3.0'
* 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 whether package 'Repitools' 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
.fdrTable: warning in matrix(, nr = length(cuts), nc = 4): partial
argument match of 'nr' to 'nrow'
.fdrTable: warning in matrix(, nr = length(cuts), nc = 4): partial
argument match of 'nc' to 'ncol'
.regionStats: warning in matrix(, nr = nrow(diffs), nc = ncol(diffs)):
partial argument match of 'nr' to 'nrow'
.regionStats: warning in matrix(, nr = nrow(diffs), nc = ncol(diffs)):
partial argument match of 'nc' to 'ncol'
.regionStats : <anonymous>: warning in matrix(NA, nr = nrow(diffs), nc
= n.perm): partial argument match of 'nr' to 'nrow'
.regionStats : <anonymous>: warning in matrix(NA, nr = nrow(diffs), nc
= n.perm): partial argument match of 'nc' to 'ncol'
.regionStats : <anonymous>: warning in .fdrTable(tmeanReal[, col], u,
ch, sp, 40, min.probes, max.gap, two.sides, maxCut = mx, verbose =
verbose): partial argument match of 'maxCut' to 'maxCutoff'
multiHeatmap: warning in viewport(x = start[i], y = ystarts[1], w =
(end[i] - start[i]), h = diff(ystarts[1:2]), just = c("left",
"bottom"), name = "vp1"): partial argument match of 'w' to 'width'
multiHeatmap: warning in viewport(x = start[i], y = ystarts[1], w =
(end[i] - start[i]), h = diff(ystarts[1:2]), just = c("left",
"bottom"), name = "vp1"): partial argument match of 'h' to 'height'
multiHeatmap: warning in viewport(x = end[i], y = ystarts[3], w =
min(cwidth * nc/tw), h = diff(ystarts[3:4]), just = c("right",
"bottom"), name = "vp2"): partial argument match of 'w' to 'width'
multiHeatmap: warning in viewport(x = end[i], y = ystarts[3], w =
min(cwidth * nc/tw), h = diff(ystarts[3:4]), just = c("right",
"bottom"), name = "vp2"): partial argument match of 'h' to 'height'
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... NOTE
The following files are already in R: 'Sweave.sty'
Please remove them from your package.
The following files should probably not be installed:
'analyses1.tex', 'analyses2.tex', 'datasets.tex', 'qc.tex',
'sInfo.tex', 'utilities.tex', 'visualisations.tex'
Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running 'tests.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK
NOTE: There were 2 notes.
See
'/Users/biocbuild/bbs-2.11-bioc/meat/Repitools.Rcheck/00check.log'
for details.