GLAD 2.26.0
Philippe Hupe
| Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/GLAD | | Last Changed Rev: 81642 / Revision: 88450 | | Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | [ OK ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/GLAD.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GLAD/DESCRIPTION’ ... OK
* this is package ‘GLAD’ version ‘2.26.0’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GLAD’ can be installed ... [7s/7s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* 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
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘GLAD/R/zzz.R’:
.onLoad calls:
packageStartupMessage("\n")
packageStartupMessage("######################################################################################\n")
packageStartupMessage("\n")
packageStartupMessage("Have fun with GLAD\n")
packageStartupMessage("\n")
packageStartupMessage("For smoothing it is possible to use either\n")
packageStartupMessage("the AWS algorithm (Polzehl and Spokoiny, 2002)\n")
packageStartupMessage("or the HaarSeg algorithm (Ben-Yaacov and Eldar, Bioinformatics, 2008)\n")
packageStartupMessage("\n")
packageStartupMessage("If you use the package with AWS, please cite:\n")
packageStartupMessage("Hupe et al. (Bioinformatics, 2004) and Polzehl and Spokoiny (2002)\n")
packageStartupMessage("\n")
packageStartupMessage("If you use the package with HaarSeg, please cite:\n")
packageStartupMessage("Hupe et al. (Bioinformatics, 2004) and (Ben-Yaacov and Eldar, Bioinformatics, 2008)\n")
packageStartupMessage("\n")
packageStartupMessage("For fast computation it is recommanded to use\n")
packageStartupMessage("the daglad function with smoothfunc=haarseg\n")
packageStartupMessage("\n")
packageStartupMessage("######################################################################################\n")
packageStartupMessage("\n")
packageStartupMessage("New options are available in daglad: see help for details.")
packageStartupMessage("\n")
See section ‘Good practice’ in '?.onAttach'.
arrayPersp.arrayCGH: warning in layout(matrix(c(1, 2), 1, 2), width =
c(9, 1)): partial argument match of 'width' to 'widths'
arrayPersp.arrayCGH: warning in matrix("green", nr = nrow(z), nc =
ncol(z)): partial argument match of 'nr' to 'nrow'
arrayPersp.arrayCGH: warning in matrix("green", nr = nrow(z), nc =
ncol(z)): partial argument match of 'nc' to 'ncol'
arrayPersp.default: warning in layout(matrix(c(1, 2), 1, 2), width =
c(9, 1)): partial argument match of 'width' to 'widths'
arrayPersp.default: warning in matrix("green", nr = nrow(z), nc =
ncol(z)): partial argument match of 'nr' to 'nrow'
arrayPersp.default: warning in matrix("green", nr = nrow(z), nc =
ncol(z)): partial argument match of 'nc' to 'ncol'
chrBreakpoints.profileCGH: no visible global function definition for
‘laws’
chrBreakpoints.profileCGH: possible error in aws(y =
subsetdata[["LogRatio"]], x = x, hinit = hinit, hmax = hmax, sigma2 =
sigma, NN = FALSE, symmetric = TRUE, ...): unused arguments (x = x,
hinit = hinit, NN = FALSE, symmetric = TRUE)
chrBreakpoints.profileCGH: possible error in aws(y =
subsetdata[["LogRatio"]], hinit = hinit, hmax = hmax, sigma2 = sigma,
symmetric = TRUE, ...): unused arguments (hinit = hinit, symmetric =
TRUE)
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘/home/biocbuild/bbs-2.13-bioc/meat/GLAD.Rcheck/GLAD/libs/GLAD.so’:
Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
Object: ‘glad-utils.o’
Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
Objects: ‘OutliersGNL.o’, ‘chrBreakpoints.o’, ‘findCluster.o’,
‘glad-utils.o’, ‘hclust.o’
Compiled code should not call entry points 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 installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
‘GLAD.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [4s/4s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
NOTE: There were 3 notes.
See
‘/home/biocbuild/bbs-2.13-bioc/meat/GLAD.Rcheck/00check.log’
for details.