BioC 2.12: CHECK report for affy on george2

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

* 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.

* 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)

name	user	system	elapsed
AffyBatch-class	10.908	0.296	11.622
AffyRNAdeg	8.313	0.112	9.204
MAplot	39.482	0.484	40.851
ProbeSet-class	0.584	0.024	0.671
ProgressBarText-class	1.860	0.004	17.585
affy-options	0.008	0.004	0.015
barplot.ProbeSet	0.664	0.044	0.837
bgc	11.569	0.220	12.500
cleancdfname	0.012	0.004	0.017
expresso	32.622	0.292	34.269
expressoWidget	0.008	0.000	0.006
fit.li.wong	0.344	0.028	0.371
generateExprSet-methods	0.500	0.024	0.525
generateExprVal-methods	0.684	0.012	0.695
generateExprVal.method.avgdiff	0.872	0.000	1.030
list.celfiles	0.004	0.000	0.007
maffy.normalise	3.129	0.020	3.657
maffy.subset	0.056	0.000	0.057
mas5	61.023	0.176	65.773
mas5calls	2.689	0.028	2.817
mva.pairs	0.148	0.000	0.148
normalize-methods	0.324	0.000	0.338
normalize.loess	0.044	0.004	0.046
plot.ProbeSet	0.024	0.000	0.025
plot.density	1.196	0.008	1.233
plotLocation	3.964	0.096	4.193
pmcorrect	0.484	0.020	0.511
ppsetApply	0.076	0.000	0.073
read.affybatch	3.404	0.072	3.643
rma	3.92	0.12	4.51
setAffyOptions	0.004	0.000	0.007
xy2indices	4.453	0.160	5.412