BioC 2.12: CHECK report for oligo on george2

Package: oligo

Version: 1.23.1

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings oligo_1.23.1.tar.gz

StartedAt: 2013-03-25 03:28:17 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:41:32 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 794.7 seconds

RetCode: 0

Status: OK

CheckDir: oligo.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/oligo.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 ‘oligo/DESCRIPTION’ ... OK
* this is package ‘oligo’ version ‘1.23.1’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking: ‘doMC’ ‘doMPI’
* 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 ‘oligo’ can be installed ... [27s/28s] OK
* checking installed package size ... NOTE
  installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       2.6Mb
    scripts   2.7Mb
* 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("ReadHeader", ..., PACKAGE = "affyio")
  .Call("read_abatch", ..., PACKAGE = "affyio")
See the chapter ‘System and foreign language interfaces’ of the
‘Writing R Extensions’ manual.
* 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 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 ... [139s/148s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
getProbeInfo            41.199  1.248  46.449
preprocessTools         35.002  0.172  37.024
fitProbeLevelModel      12.789  0.256  13.138
read.celfiles           10.197  1.244  12.074
MAplot-methods           6.832  0.072   7.035
IntensityMatrix-methods  5.053  0.120   5.625
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘doRUnit.R’ [358s/373s]
 [358s/374s] 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/oligo.Rcheck/00check.log’
for details.

* installing *source* package ‘oligo’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c DABG.c -o DABG.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c ParserGzXYS.c -o ParserGzXYS.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c ParserXYS.c -o ParserXYS.o
ParserXYS.c: In function ‘R_read_xys_header’:
ParserXYS.c:320:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
ParserXYS.c: In function ‘xys_header_field’:
ParserXYS.c:145:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c baseProfile.c -o baseProfile.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c basecontent.c -o basecontent.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -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  -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  -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  -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 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c trimmed.c -o trimmed.o
gcc -std=gnu99 -shared -L/usr/local/lib -o oligo.so DABG.o ParserGzXYS.o ParserXYS.o baseProfile.o basecontent.o chipbackground.o mas5calls.o rma2.o rma_common.o trimmed.o -lz -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-2.12-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-2.12-bioc/R/lib -lRblas -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-bioc/meat/oligo.Rcheck/oligo/libs
** R
** inst
** preparing package for lazy loading
Note: in method for ‘pm<-’ with signature
‘object="TilingFeatureSet",subset="ANY",target="ANY",value="array"’:
expanding the signature to include omitted arguments in definition: =
"missing"
Note: in method for ‘mm<-’ with signature
‘object="TilingFeatureSet",subset="ANY",target="ANY",value="array"’:
expanding the signature to include omitted arguments in definition: =
"missing"
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘primer.Rnw’ 
** testing if installed package can be loaded
* DONE (oligo)

name	user	system	elapsed
Index-methods	0.008	0.008	0.019
IntensityMatrix-methods	5.053	0.120	5.625
MAplot-methods	6.832	0.072	7.035
basecontent	0.008	0.000	0.007
basicPLM	2.620	0.140	2.895
basicRMA	2.628	0.132	2.841
colors	0.084	0.004	0.109
coordinates	0.004	0.000	0.007
fitProbeLevelModel	12.789	0.256	13.138
getProbeInfo	41.199	1.248	46.449
image	1.512	0.056	1.893
justSNPRMA	0.004	0.000	0.006
list.xysfiles	0.004	0.000	0.008
oligoPLM-class	0.004	0.004	0.010
paCalls	0.000	0.012	0.010
preprocessTools	35.002	0.172	37.024
read.celfiles	10.197	1.244	12.074
read.xysfiles	1.592	0.072	1.951
rma-methods	3.228	0.016	3.320
sequenceDesignMatrix	0.028	0.000	0.028

Summary

Command output