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BioC 2.12: CHECK report for affy on george2

This page was generated on 2013-10-09 09:37:10 -0700 (Wed, 09 Oct 2013).

Package 13/671HostnameOS / ArchBUILDCHECKBUILD BIN
affy 1.38.1
Rafael A. Irizarry
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/affy
Last Changed Rev: 75788 / Revision: 81334
Last Changed Date: 2013-04-18 14:30:32 -0700 (Thu, 18 Apr 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 Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: affy
Version: 1.38.1
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings affy_1.38.1.tar.gz
StartedAt: 2013-10-08 23:52:20 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 23:57:33 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 312.3 seconds
RetCode: 0
Status:  OK 
CheckDir: affy.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/affy.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘1.38.1’
* 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 ‘affy’ can be installed ... [9s/10s] 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 ... NOTE
Foreign function calls with ‘PACKAGE’ argument in a different package:
  .Call("read_abatch", ..., PACKAGE = "affyio")
  .Call("read_abatch_stddev", ..., PACKAGE = "affyio")
See the chapter ‘System and foreign language interfaces’ of the
‘Writing R Extensions’ manual.
* 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 ... [199s/226s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
mas5                  61.023  0.176  65.773
MAplot                39.482  0.484  40.851
expresso              32.622  0.292  34.269
bgc                   11.569  0.220  12.500
AffyBatch-class       10.908  0.296  11.622
AffyRNAdeg             8.313  0.112   9.204
xy2indices             4.453  0.160   5.412
ProgressBarText-class  1.860  0.004  17.585
* 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 2 notes.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/affy.Rcheck/00check.log’
for details.

affy.Rcheck/00install.out:

* installing *source* package ‘affy’ ...
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-2.12-bioc/R/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c chipbackground.c -o chipbackground.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c getall_locations.c -o getall_locations.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c mas5calls.c -o mas5calls.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c rma2.c -o rma2.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c rma_common.c -o rma_common.o
gcc -std=gnu99 -shared -L/usr/local/lib -o affy.so chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -lz -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-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
** testing if installed package can be loaded
* DONE (affy)

affy.Rcheck/affy-Ex.timings:

nameusersystemelapsed
AffyBatch-class10.908 0.29611.622
AffyRNAdeg8.3130.1129.204
MAplot39.482 0.48440.851
ProbeSet-class0.5840.0240.671
ProgressBarText-class 1.860 0.00417.585
affy-options0.0080.0040.015
barplot.ProbeSet0.6640.0440.837
bgc11.569 0.22012.500
cleancdfname0.0120.0040.017
expresso32.622 0.29234.269
expressoWidget0.0080.0000.006
fit.li.wong0.3440.0280.371
generateExprSet-methods0.5000.0240.525
generateExprVal-methods0.6840.0120.695
generateExprVal.method.avgdiff0.8720.0001.030
list.celfiles0.0040.0000.007
maffy.normalise3.1290.0203.657
maffy.subset0.0560.0000.057
mas561.023 0.17665.773
mas5calls2.6890.0282.817
mva.pairs0.1480.0000.148
normalize-methods0.3240.0000.338
normalize.loess0.0440.0040.046
plot.ProbeSet0.0240.0000.025
plot.density1.1960.0081.233
plotLocation3.9640.0964.193
pmcorrect0.4840.0200.511
ppsetApply0.0760.0000.073
read.affybatch3.4040.0723.643
rma3.920.124.51
setAffyOptions0.0040.0000.007
xy2indices4.4530.1605.412