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Package 2/444HostnameOS / ArchBUILDCHECKBUILD BIN
aCGH 1.29.1
Peter Dimitrov
Snapshot Date: 2011-03-17 11:16:30 -0700 (Thu, 17 Mar 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/aCGH
Last Changed Rev: 52465 / Revision: 53825
Last Changed Date: 2011-02-04 15:18:23 -0800 (Fri, 04 Feb 2011)
lamb1 Linux (openSUSE 11.3) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.6) / i386  OK [ OK ] OK 

Summary

Package: aCGH
Version: 1.29.1
Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch aCGH_1.29.1.tar.gz
StartedAt: 2011-03-17 15:21:05 -0700 (Thu, 17 Mar 2011)
EndedAt: 2011-03-17 15:22:37 -0700 (Thu, 17 Mar 2011)
EllapsedTime: 92.1 seconds
RetCode: 0
Status:  OK 
CheckDir: aCGH.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/aCGH.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'aCGH/DESCRIPTION' ... OK
* this is package 'aCGH' version '1.29.1'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'aCGH' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.6Mb
  sub-directories of 1Mb or more:
    data       4.4Mb
    doc        3.7Mb
    examples   1.2Mb
* 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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
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 examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

aCGH.Rcheck/00install.out:

* installing *source* package 'aCGH' ...
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -g3 -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c hmm.cpp -o hmm.o
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o aCGH.so hmm.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/aCGH.Rcheck/aCGH/libs/i386
** R
** data
** demo
** inst
** preparing package for lazy loading
Loading required package: splines
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (aCGH)

aCGH.Rcheck/aCGH-Ex.timings:

nameusersystemelapsed
aCGH4.0920.1474.239
aCGH.process0.1160.0020.117
aCGH.read.Sprocs0.6370.0070.643
clusterGenome1.8680.1211.996
colorectal0.7920.0280.819
fga.func0.8750.0240.898
find.hmm.states1.2050.0241.229
gainLoss1.7570.0651.823
heatmap0.9140.0340.950
impute.HMM0.8870.0060.892
impute.lowess0.1870.0080.195
mergeLevels0.1190.0020.120
plotFreqStat8.3780.0628.441
plotGenome1.4200.0601.487
plotHmmStates0.6420.0210.798
plotSummaryProfile2.1720.0822.284
summarize.clones0.8410.0310.871
threshold.func0.5770.0290.606