ADaCGH2 1.8.0
Ramon Diaz-Uriarte
| 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/ADaCGH2 | | 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 '/Users/biocbuild/bbs-2.11-bioc/meat/ADaCGH2.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'ADaCGH2/DESCRIPTION' ... OK
* this is package 'ADaCGH2' version '1.8.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'multicore'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'ADaCGH2' 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 ... 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
caughtError: warning in exists(".__ADaCGH_WEB_APPL", env = .GlobalEnv):
partial argument match of 'env' to 'envir'
caughtError: warning in exists(".__ADaCGH_SERVER_APPL", env =
.GlobalEnv): partial argument match of 'env' to 'envir'
caughtOtherError: warning in exists(".__ADaCGH_WEB_APPL", env =
.GlobalEnv): partial argument match of 'env' to 'envir'
caughtOtherError: warning in exists(".__ADaCGH_SERVER_APPL", env =
.GlobalEnv): partial argument match of 'env' to 'envir'
caughtOurError2: warning in exists(".__ADaCGH_SERVER_APPL", env =
.GlobalEnv): partial argument match of 'env' to 'envir'
caughtUserError2: warning in exists(".__ADaCGH_SERVER_APPL", env =
.GlobalEnv): partial argument match of 'env' to 'envir'
getffObj: warning in load(RDataName, env = parent.frame()): partial
argument match of 'env' to 'envir'
imagemap3: warning in png(file = paste(filename, ".png", sep = ""),
width = width, height = height, pointsize = ps): partial argument
match of 'file' to 'filename'
inputDataToADaCGHData: warning in exists(".__ADaCGH_SERVER_APPL", env =
.GlobalEnv): partial argument match of 'env' to 'envir'
sizesobj: warning in ls(env = parent.frame(n = n)): partial argument
match of 'env' to 'envir'
sizesobj: warning in get(l1[i], env = parent.frame(n = n)): partial
argument match of 'env' to 'envir'
snowfallInit: warning in ls(env = .GlobalEnv): partial argument match
of 'env' to 'envir'
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'
Found .Internal call in the following function:
'warningsForUsers'
with calls to .Internal functions
'.dfltWarn' '.signalCondition' 'warning'
Packages should not call .Internal(): it is not part of the API, for
use only by R itself and subject to change without notice.
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
outputToCGHregions 1.848 0.160 18.967
pSegment 1.623 0.212 22.599
pChromPlot 1.409 0.131 17.901
inputDataToADaCGHData 1.047 0.028 8.082
snowfallInit 0.079 0.069 14.216
* 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
'/Users/biocbuild/bbs-2.11-bioc/meat/ADaCGH2.Rcheck/00check.log'
for details.
* installing *source* package 'ADaCGH2' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c r_haarseg.c -o r_haarseg.o
r_haarseg.c: In function 'ad_HaarConv':
r_haarseg.c:65: warning: unused variable 'totalNorm'
r_haarseg.c:152:8: warning: "/*" within comment
r_haarseg.c:176:8: warning: "/*" within comment
r_haarseg.c: In function 'ad_FindLocalPeaks':
r_haarseg.c:128: warning: unused variable 'j'
r_haarseg.c: In function 'ad_HaarConv':
r_haarseg.c:64: warning: 'highNonNormed' may be used uninitialized in this function
r_haarseg.c:63: warning: 'lowNonNormed' may be used uninitialized in this function
r_haarseg.c:60: warning: 'highWeightSum' may be used uninitialized in this function
r_haarseg.c:59: warning: 'lowWeightSum' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o ADaCGH2.so r_haarseg.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/ADaCGH2.Rcheck/ADaCGH2/libs/i386
** R
** data
** inst
** preparing package for lazy loading
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
* DONE (ADaCGH2)