Back to the "Multiple platform build/check report"[A] B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

Package 7/436HostnameOS / ArchBUILDCHECKBUILD BIN
affy 1.29.2
Rafael A. Irizarry
Snapshot Date: 2011-02-24 11:26:35 -0800 (Thu, 24 Feb 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affy
Last Changed Rev: 51673 / Revision: 53255
Last Changed Date: 2010-12-26 04:46:49 -0800 (Sun, 26 Dec 2010)
lamb2 Linux (openSUSE 11.2) / 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 (10.6.4) / i386  OK  OK  OK 

Summary

Package: affy
Version: 1.29.2
Command: E:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings affy_1.29.2.tar.gz
StartedAt: 2011-02-24 16:34:02 -0800 (Thu, 24 Feb 2011)
EndedAt: 2011-02-24 16:38:03 -0800 (Thu, 24 Feb 2011)
EllapsedTime: 241.2 seconds
RetCode: 0
Status:  OK  
CheckDir: affy.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.8-bioc/meat/affy.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'affy/DESCRIPTION' ... OK
* this is package 'affy' version '1.29.2'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'affy' can be installed ... OK
* 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 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
cleancdfname: no visible binding for global variable 'mapCdfName'
* 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 ... NOTE
'library' or 'require' call not declared from: widgetTools
* checking data for non-ASCII characters ... 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 ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

affy.Rcheck/00install.out:

* installing *source* package 'affy' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/BBS-2˜1.8-B/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c chipbackground.c -o chipbackground.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/BBS-2˜1.8-B/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c getall_locations.c -o getall_locations.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/BBS-2˜1.8-B/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c mas5calls.c -o mas5calls.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/BBS-2˜1.8-B/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c rma2.c -o rma2.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/BBS-2˜1.8-B/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c rma_common.c -o rma_common.o
gcc -shared -s -static-libgcc -o affy.dll tmp.def chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -lRzlib -LE:/biocbld/BBS-2˜1.8-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.8-bioc/meat/affy.Rcheck/affy/libs/i386
** R
** data
** demo
** inst
** preparing package for lazy loading

Welcome to Bioconductor

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

Creating a new generic function for "open" in "affy"
Creating a new generic function for "close" in "affy"
Creating a new generic function for "colnames" in "affy"
Creating a new generic function for "barplot" in "affy"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (affy)

affy.Rcheck/affy-Ex.timings:

nameusersystemelapsed
AffyBatch-class2.940.133.24
AffyRNAdeg5.720.015.73
MAplot27.70 0.4128.30
ProbeSet-class1.120.061.20
ProgressBarText-class 0.75 0.0016.47
affy-options000
barplot.ProbeSet1.140.021.15
bgc7.360.067.64
cleancdfname0.020.000.02
expresso26.45 0.2527.05
expressoWidget000
fit.li.wong0.020.000.02
generateExprSet-methods1.150.001.17
generateExprVal-methods1.170.021.18
generateExprVal.method.avgdiff0.610.000.61
list.celfiles000
maffy.normalise3.610.023.63
maffy.subset0.020.010.03
mas554.87 0.1355.47
mas5calls2.890.032.94
mva.pairs0.150.000.16
normalize-methods0.780.000.79
normalize.loess0.040.000.04
plot.ProbeSet000
plot.density1.490.041.53
plotLocation4.860.185.14
pmcorrect1.030.071.11
ppsetApply000
read.affybatch4.610.105.50
rma4.700.034.77
setAffyOptions000
xy2indices4.840.165.67