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Package 13/609HostnameOS / ArchBUILDCHECKBUILD BIN
affy 1.36.1
Rafael A. Irizarry
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/affy
Last Changed Rev: 72927 / Revision: 74773
Last Changed Date: 2013-01-25 09:54:50 -0800 (Fri, 25 Jan 2013)
lamb1 Linux (openSUSE 12.1) / x86_64  OK [ WARNINGS ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: affy
Version: 1.36.1
Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings affy_1.36.1.tar.gz
StartedAt: 2013-03-24 22:56:50 -0700 (Sun, 24 Mar 2013)
EndedAt: 2013-03-24 23:00:29 -0700 (Sun, 24 Mar 2013)
EllapsedTime: 219.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: affy.Rcheck
Warnings: 1

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/affy.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘affy/DESCRIPTION’ ... OK
* this is package ‘affy’ version ‘1.36.1’
* 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 ‘affy’ 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 ... WARNING
Foreign function calls with ‘PACKAGE’ argument in a base package:
  .C("loess_raw", ..., PACKAGE = "stats")
  .Fortran("lowesp", ..., PACKAGE = "stats")
  .Fortran("lowesw", ..., PACKAGE = "stats")
Foreign function calls with ‘PACKAGE’ argument in a different package:
  .Call("read_abatch", ..., PACKAGE = "affyio")
  .Call("read_abatch_stddev", ..., PACKAGE = "affyio")
Packages should not make .C/.Call/.Fortran calls to base packages. They
are not part of the API, for use only by R itself and subject to change
without notice.
* checking R code for possible problems ... NOTE
featureNames,AffyBatch: warning in ls(env = cdf.envir): partial
  argument match of 'env' to 'envir'
geneNames,AffyBatch: warning in ls(env = cdf.envir): partial argument
  match of 'env' to 'envir'
show,AffyBatch: warning in ls(env = cdf.env): partial argument match of
  'env' to 'envir'
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 ... 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 compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
mas5                  41.623  0.120  45.338
MAplot                26.090  0.300  27.152
expresso              20.449  0.548  23.134
bgc                    7.129  0.340   8.036
AffyBatch-class        6.940  0.140   7.328
AffyRNAdeg             5.696  0.060   5.942
ProgressBarText-class  1.148  0.024  16.826
* 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

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/affy.Rcheck/00check.log’
for details.

affy.Rcheck/00install.out:

* installing *source* package ‘affy’ ...
loading site script /usr/share/site/x86_64-unknown-linux-gnu
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c chipbackground.c -o chipbackground.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c getall_locations.c -o getall_locations.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c mas5calls.c -o mas5calls.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c rma2.c -o rma2.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c rma_common.c -o rma_common.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o affy.so chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -lz -L/home/biocbuild/bbs-2.11-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.11-bioc/meat/affy.Rcheck/affy/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
Creating a generic function for ‘open’ from package ‘base’ in package ‘affy’
Creating a generic function for ‘close’ from package ‘base’ in package ‘affy’
Creating a generic function for ‘barplot’ from package ‘graphics’ in package ‘affy’
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘affy.Rnw’ 
   ‘builtinMethods.Rnw’ 
   ‘customMethods.Rnw’ 
   ‘vim.Rnw’ 
** testing if installed package can be loaded

* DONE (affy)

affy.Rcheck/affy-Ex.timings:

nameusersystemelapsed
AffyBatch-class6.9400.1407.328
AffyRNAdeg5.6960.0605.942
MAplot26.090 0.30027.152
ProbeSet-class0.4200.0120.497
ProgressBarText-class 1.148 0.02416.826
affy-options000
barplot.ProbeSet0.4320.0200.469
bgc7.1290.3408.036
cleancdfname0.0080.0000.008
expresso20.449 0.54823.134
expressoWidget000
fit.li.wong0.2760.0160.303
generateExprSet-methods0.3800.0080.480
generateExprVal-methods0.4480.0200.473
generateExprVal.method.avgdiff0.5520.0000.553
list.celfiles0.0000.0000.001
maffy.normalise2.5360.0122.631
maffy.subset0.0280.0000.029
mas541.623 0.12045.338
mas5calls1.8120.0201.834
mva.pairs0.1000.0040.102
normalize-methods0.2600.0000.259
normalize.loess0.0240.0000.025
plot.ProbeSet0.0160.0000.015
plot.density0.8200.0080.829
plotLocation2.4560.0442.505
pmcorrect0.3880.0080.572
ppsetApply0.0000.0000.001
read.affybatch3.2160.0164.465
rma2.8520.0844.417
setAffyOptions000
xy2indices3.1610.0643.672