aCGH 1.36.0
Peter Dimitrov
| Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/aCGH | | Last Changed Rev: 70050 / Revision: 74773 | | Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012) |
| lamb1 | Linux (openSUSE 12.1) / x86_64 | OK | [ OK ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| perceval | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/aCGH.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘aCGH/DESCRIPTION’ ... OK
* this is package ‘aCGH’ version ‘1.36.0’
* 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 ‘aCGH’ 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 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 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
aCGH.read.Sprocs: warning in read.table(fnames[1], h = TRUE, sep =
"\t", quote = "", comment.char = "", fill = TRUE, blank.lines.skip =
FALSE): partial argument match of 'h' to 'header'
aCGH.read.Sprocs: warning in read.table(latest.mapping.file, sep =
"\t", h = TRUE, quote = "", comment.char = ""): partial argument
match of 'h' to 'header'
plotCGH.func: warning in close.screen(all = TRUE): partial argument
match of 'all' to 'all.screens'
plotCGH.hmm.func: warning in close.screen(all = TRUE): partial argument
match of 'all' to 'all.screens'
plotFreqStat: warning in axis(side = 1, at = kb.loc[ind][1], label =
"", tick = FALSE): partial argument match of 'label' to 'labels'
plotGenome: warning in axis(side = 1, at = clone.genomepos[1]/1000,
label = "", tick = FALSE): partial argument match of 'label' to
'labels'
read.Sproc.files : <anonymous>: warning in read.table(fname, h = TRUE,
sep = "\t", quote = "", comment.char = "", fill = TRUE,
blank.lines.skip = FALSE, dec = "."): partial argument match of 'h'
to 'header'
states.hmm.func: warning in matrix(res$filtered.cond.probs, nr = k):
partial argument match of 'nr' to 'nrow'
states.hmm.func: warning in matrix(res$gamma, nr = k): partial argument
match of 'nr' to 'nrow'
plotSummaryProfile: no visible binding for global variable
‘numchromgain’
plotSummaryProfile: no visible binding for global variable
‘numchromloss’
plotSummaryProfile: no visible binding for global variable ‘numtrans’
plotSummaryProfile: no visible binding for global variable
‘numtrans.binary’
plotSummaryProfile: no visible binding for global variable ‘numaber’
plotSummaryProfile: no visible binding for global variable ‘numamplif’
plotSummaryProfile: no visible binding for global variable
‘numamplif.binary’
plotSummaryProfile: no visible binding for global variable
‘numamplicon’
plotSummaryProfile: no visible binding for global variable
‘sizeamplicon’
* 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 for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotFreqStat 6.169 0.016 6.201
* 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 was 1 note.
See
‘/loc/home/biocbuild/bbs-2.11-bioc/meat/aCGH.Rcheck/00check.log’
for details.
* installing *source* package ‘aCGH’ ...
** libs
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -g3 -I/usr/local/include -fpic -g -O2 -Wall -c hmm.cpp -o hmm.o
g++ -shared -L/usr/local/lib64 -o aCGH.so hmm.o -lm -L/home/biocbuild/bbs-2.11-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.11-bioc/meat/aCGH.Rcheck/aCGH/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
‘aCGH.Rnw’
** testing if installed package can be loaded
* DONE (aCGH)