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Package 586/658HostnameOS / ArchBUILDCHECKBUILD BIN
simpleaffy 2.35.1
Crispin Miller
Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/simpleaffy
Last Changed Rev: 72298 / Revision: 74774
Last Changed Date: 2013-01-04 13:18:09 -0800 (Fri, 04 Jan 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / 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 

Summary

Package: simpleaffy
Version: 2.35.1
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings simpleaffy_2.35.1.tar.gz
StartedAt: 2013-03-25 04:40:13 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 04:44:47 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 273.7 seconds
RetCode: 0
Status:  OK 
CheckDir: simpleaffy.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/simpleaffy.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘simpleaffy/DESCRIPTION’ ... OK
* this is package ‘simpleaffy’ version ‘2.35.1’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘simpleaffy’ can be installed ... [25s/26s] OK
* checking installed package size ... OK
* checking package directory ... 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 ... OK
* checking R code for possible problems ... NOTE
File ‘simpleaffy/R/zzz.R’:
  .onLoad calls:
    require("methods", quietly = TRUE)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.
* 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 ... NOTE
  No methods found in "Biobase" for requests: geneNames
* 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 ... NOTE
File ‘/home/biocbuild/bbs-2.12-bioc/meat/simpleaffy.Rcheck/simpleaffy/libs/simpleaffy.so’:
  Found ‘stderr’, possibly from ‘stderr’ (C)
    Object: ‘simpleaffy.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [15s/15s] 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 3 notes.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/simpleaffy.Rcheck/00check.log’
for details.

simpleaffy.Rcheck/00install.out:

* installing *source* package ‘simpleaffy’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c simpleaffy.c -o simpleaffy.o
gcc -std=gnu99 -shared -L/usr/local/lib -o simpleaffy.so simpleaffy.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-bioc/meat/simpleaffy.Rcheck/simpleaffy/libs
** R
** data
** inst
** preparing package for lazy loading
No methods found in "Biobase" for requests: geneNames
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘simpleAffy.Rnw’ 
** testing if installed package can be loaded
No methods found in "Biobase" for requests: geneNames
* DONE (simpleaffy)

simpleaffy.Rcheck/simpleaffy-Ex.timings:

nameusersystemelapsed
all.present0.5720.0040.586
all.present.in.group0.0120.0160.025
bg.correct.sa0.0160.0120.025
call.exprs0.0160.0080.023
detection.p.val0.0160.0080.024
get.annotation0.0120.0120.026
get.array.indices0.0160.0080.024
get.array.subset0.0160.0080.024
get.array.subset.affy0.0160.0080.028
get.fold.change.and.t.test0.0160.0080.026
hmap.colors0.0080.0080.013
hmap.eset0.0200.0080.029
hmap.pc0.0120.0120.031
journalpng0.0200.0040.024
justMAS0.0120.0080.023
pairwise.comparison0.0200.0040.022
pairwise.filter0.0120.0160.029
plot.pairwise.comparison0.0080.0080.015
plot.qc.stats0.1080.0080.117
qc0.1320.0160.149
qc.affy0.1160.0120.126
qc.get.alpha10.0280.0040.033
qc.get.array0.0280.0000.027
qc.get.probes0.0280.0000.032
qc.get.ratios0.0200.0000.021
qc.get.spikes0.020.000.02
qc.have.params0.0320.0080.039
qc.ok0.0160.0000.014
qc.read.file0.0240.0000.024
qc.stats0.0680.0000.070
read.affy0.0200.0000.018
read.affy.mixed0.0280.0000.026
setQCEnvironment0.0240.0040.028
simpleaffy-deprecated0.0600.0040.064
standard.pearson0.0160.0000.017
trad.scatter.plot0.0160.0000.014