ADaCGH2 1.6.0
Ramon Diaz-Uriarte
| Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/ADaCGH2 | | Last Changed Rev: 64678 / Revision: 69725 | | Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012) |
| lamb2 | Linux (openSUSE 11.4) / 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 | OK | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/ADaCGH2.Rcheck’
* using R version 2.15.1 (2012-06-22)
* 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 ‘1.6.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘Rmpi’
* 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 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
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 installed files from ‘inst/doc’ ... OK
* checking examples ... 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
‘/loc/home/biocbuild/bbs-2.10-bioc/meat/ADaCGH2.Rcheck/00check.log’
for details.
* installing *source* package ‘ADaCGH2’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-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’
r_haarseg.c: In function ‘ad_FindLocalPeaks’:
r_haarseg.c:152:8: warning: "/*" within comment
r_haarseg.c:176:8: warning: "/*" within comment
r_haarseg.c:128:9: warning: unused variable ‘j’
r_haarseg.c: In function ‘ad_HaarConv’:
r_haarseg.c:59:12: warning: ‘lowWeightSum’ may be used uninitialized in this function
r_haarseg.c:60:12: warning: ‘highWeightSum’ may be used uninitialized in this function
r_haarseg.c:63:12: warning: ‘lowNonNormed’ may be used uninitialized in this function
r_haarseg.c:64:12: warning: ‘highNonNormed’ may be used uninitialized in this function
gcc -std=gnu99 -shared -L/usr/local/lib64 -o ADaCGH2.so r_haarseg.o -L/home/biocbuild/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.10-bioc/meat/ADaCGH2.Rcheck/ADaCGH2/libs
** 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)