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Package 8/516HostnameOS / ArchBUILDCHECKBUILD BIN
aCGH 1.32.0
Peter Dimitrov
Snapshot Date: 2012-01-08 18:22:44 -0800 (Sun, 08 Jan 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/aCGH
Last Changed Rev: 59920 / Revision: 61898
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: aCGH
Version: 1.32.0
Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch aCGH_1.32.0.tar.gz
StartedAt: 2012-01-09 00:49:01 -0800 (Mon, 09 Jan 2012)
EndedAt: 2012-01-09 00:50:44 -0800 (Mon, 09 Jan 2012)
EllapsedTime: 102.8 seconds
RetCode: 0
Status:  OK  
CheckDir: aCGH.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/aCGH.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'aCGH/DESCRIPTION' ... OK
* this is package 'aCGH' version '1.32.0'
* 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 ... NOTE
  installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data       4.4Mb
    examples   1.2Mb
* checking package directory ... OK
* checking for portable file names ... 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
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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                 old_size new_size compress
  colorectal.rda    4.4Mb    1.0Mb       xz
* 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 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

aCGH.Rcheck/00install.out:

* installing *source* package 'aCGH' ...
** libs
x86_64-w64-mingw32-g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include" -g3         -O2 -Wall  -mtune=core2 -c hmm.cpp -o hmm.o
x86_64-w64-mingw32-g++ -shared -s -static-libgcc -o aCGH.dll tmp.def hmm.o -lm -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/aCGH.Rcheck/aCGH/libs/x64
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'aCGH.Rnw' 
** testing if installed package can be loaded

* DONE (aCGH)

aCGH.Rcheck/aCGH-Ex.timings:

nameusersystemelapsed
aCGH3.630.134.20
aCGH.process0.090.000.10
aCGH.read.Sprocs0.50.00.5
clusterGenome2.360.092.81
colorectal0.70.00.7
fga.func0.720.010.74
find.hmm.states0.830.000.83
gainLoss1.860.021.87
heatmap0.780.050.83
impute.HMM0.910.000.91
impute.lowess0.140.000.14
mergeLevels0.110.000.11
plotFreqStat7.110.007.12
plotGenome2.150.032.34
plotHmmStates0.550.010.63
plotSummaryProfile1.620.051.69
summarize.clones0.750.000.75
threshold.func0.470.000.47