BioC 2.13: CHECK report for affy on zin1

Package: affy

Version: 1.40.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings affy_1.40.0.tar.gz

StartedAt: 2014-04-04 23:17:27 -0700 (Fri, 04 Apr 2014)

EndedAt: 2014-04-04 23:20:10 -0700 (Fri, 04 Apr 2014)

EllapsedTime: 162.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: affy.Rcheck

Warnings: 1

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/affy.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.40.0’
* 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 ... [4s/5s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
Unexported objects imported by ‘:::’ calls:
  ‘stats:::C_loess_raw’ ‘stats:::C_lowesp’ ‘stats:::C_lowesw’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘bg.correct’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... WARNING
Foreign function calls to a base package:
  .C(stats:::C_loess_raw, ...)
  .Fortran(stats:::C_lowesp, ...)
  .Fortran(stats:::C_lowesw, ...)
Packages should not make .C/.Call/.External/.Fortran calls to a base
package. 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 ... OK
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... [100s/119s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
mas5                  34.074  0.040  34.213
MAplot                17.889  0.216  18.200
expresso              16.357  0.112  18.710
ProgressBarText-class  0.692  0.004  16.623
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.13-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-2.13-bioc/R/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c chipbackground.c -o chipbackground.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c getall_locations.c -o getall_locations.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c mas5calls.c -o mas5calls.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c rma2.c -o rma2.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-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-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-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	4.100	0.108	4.212
AffyRNAdeg	3.560	0.044	3.611
MAplot	17.889	0.216	18.200
ProbeSet-class	0.372	0.008	0.381
ProgressBarText-class	0.692	0.004	16.623
affy-options	0.004	0.000	0.001
barplot.ProbeSet	0.364	0.012	0.374
bgc	4.269	0.072	4.857
cleancdfname	0.008	0.000	0.022
expresso	16.357	0.112	18.710
expressoWidget	0.000	0.000	0.001
fit.li.wong	0.224	0.004	0.227
generateExprSet-methods	0.320	0.008	0.329
generateExprVal-methods	0.368	0.004	0.375
generateExprVal.method.avgdiff	0.404	0.000	0.403
list.celfiles	0.000	0.000	0.001
maffy.normalise	1.820	0.012	1.835
maffy.subset	0.04	0.00	0.04
mas5	34.074	0.040	34.213
mas5calls	1.512	0.000	1.514
mva.pairs	0.116	0.000	0.116
normalize-methods	0.280	0.004	0.286
normalize.loess	0.020	0.000	0.022
plot.ProbeSet	0.012	0.000	0.014
plot.density	0.676	0.004	0.683
plotLocation	2.000	0.024	2.028
pmcorrect	0.340	0.008	0.350
ppsetApply	0.000	0.000	0.002
read.affybatch	2.316	0.028	2.360
rma	2.460	0.060	2.528
setAffyOptions	0.000	0.000	0.001
xy2indices	2.557	0.028	2.619