ADaCGH2 1.9.0
Ramon Diaz-Uriarte
| Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ADaCGH2 | | Last Changed Rev: 74736 / Revision: 74774 | | Last Changed Date: 2013-03-23 04:33:47 -0700 (Sat, 23 Mar 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | [ OK ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/ADaCGH2.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ADaCGH2/DESCRIPTION’ ... OK
* this is package ‘ADaCGH2’ version ‘1.9.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
‘Rmpi’ ‘multicore’
* 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 ‘ADaCGH2’ can be installed ... [27s/29s] OK
* checking installed package size ... OK
* checking package 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function calls with ‘PACKAGE’ argument in a different package:
.Fortran("fndcpt", ..., PACKAGE = "DNAcopy")
.Fortran("wfindcpt", ..., PACKAGE = "DNAcopy")
See the chapter ‘System and foreign language interfaces’ of the
‘Writing R Extensions’ manual.
* checking R code for possible problems ... NOTE
mpi.clean.quit.Web: no visible global function definition for
‘mpi.comm.size’
mpi.clean.quit.Web: no visible global function definition for
‘mpi.close.Rslaves’
mpi.clean.quit.Web: no visible global function definition for
‘mpi.exit’
snowfallInit: no visible global function definition for
‘mpi.universe.size’
* 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 use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [26s/126s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
pSegment 3.524 0.148 33.303
outputToCGHregions 3.285 0.104 24.901
pChromPlot 2.936 0.084 25.190
inputDataToADaCGHData 2.628 0.032 9.681
snowfallInit 0.128 0.056 19.504
* 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 3 notes.
See
‘/home/biocbuild/bbs-2.12-bioc/meat/ADaCGH2.Rcheck/00check.log’
for details.
* installing *source* package ‘ADaCGH2’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c r_haarseg.c -o r_haarseg.o
r_haarseg.c: In function ‘ad_HaarConv’:
r_haarseg.c:65:12: warning: unused variable ‘totalNorm’ [-Wunused-variable]
r_haarseg.c: In function ‘ad_FindLocalPeaks’:
r_haarseg.c:152:8: warning: "/*" within comment [-Wcomment]
r_haarseg.c:176:8: warning: "/*" within comment [-Wcomment]
r_haarseg.c:128:9: warning: unused variable ‘j’ [-Wunused-variable]
r_haarseg.c: In function ‘ad_HaarConv’:
r_haarseg.c:97:27: warning: ‘highNonNormed’ may be used uninitialized in this function [-Wuninitialized]
r_haarseg.c:96:26: warning: ‘lowNonNormed’ may be used uninitialized in this function [-Wuninitialized]
r_haarseg.c:99:27: warning: ‘highWeightSum’ may be used uninitialized in this function [-Wuninitialized]
r_haarseg.c:98:26: warning: ‘lowWeightSum’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -shared -L/usr/local/lib -o ADaCGH2.so r_haarseg.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-bioc/meat/ADaCGH2.Rcheck/ADaCGH2/libs
** R
** data
** inst
** preparing package for lazy loading
'.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
'.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
'.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
Setting adacgh_changepoints to DNAcopy:::changepoints
Setting adacgh_trimmed.variance to DNAcopy:::trimmed.variance
** help
*** installing help indices
** building package indices
** installing vignettes
‘ADaCGH2.Rnw’ using ‘latin1’
** testing if installed package can be loaded
'.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
'.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
'.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
* DONE (ADaCGH2)