BioC 2.11: CHECK report for oligo on lamb1

Package: oligo

Version: 1.22.0

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings oligo_1.22.0.tar.gz

StartedAt: 2013-03-25 03:24:55 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:34:14 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 559.2 seconds

RetCode: 0

Status: WARNINGS

CheckDir: oligo.Rcheck

Warnings: 1

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/oligo.Rcheck’
* using R version 2.15.3 (2013-03-01)
* 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 ‘1.22.0’
* 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 whether package ‘oligo’ can be installed ... WARNING
Found the following significant warnings:
  /home/biocbuild/bbs-2.11-bioc/R/include/R_ext/RConverters.h:32:2: warning: #warning "R_ext/RConverters.h was deprecated in R 2.15.1 and will be removed in R 3.0.0" [-Wcpp]
See ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/oligo.Rcheck/00install.out’ for details.
* 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 for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
getProbeInfo       25.650  2.620  29.813
preprocessTools    24.089  0.092  25.766
read.celfiles       8.001  2.636  10.932
fitProbeLevelModel  9.260  0.144  10.418
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘doRUnit.R’
 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

WARNING: There was 1 warning.
NOTE: There were 3 notes.
See
  ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/oligo.Rcheck/00check.log’
for details.

* installing *source* package ‘oligo’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c DABG.c -o DABG.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c ParserGzXYS.c -o ParserGzXYS.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c ParserXYS.c -o ParserXYS.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c baseProfile.c -o baseProfile.o
In file included from baseProfile.c:4:0:
/home/biocbuild/bbs-2.11-bioc/R/include/R_ext/RConverters.h:32:2: warning: #warning "R_ext/RConverters.h was deprecated in R 2.15.1 and will be removed in R 3.0.0" [-Wcpp]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c basecontent.c -o basecontent.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c chipbackground.c -o chipbackground.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c mas5calls.c -o mas5calls.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c rma2.c -o rma2.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c rma_common.c -o rma_common.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c trimmed.c -o trimmed.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -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-2.11-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-2.11-bioc/R/lib -lRblas -L/home/biocbuild/bbs-2.11-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.11-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	0	0
IntensityMatrix-methods	2.956	0.080	4.606
MAplot-methods	3.692	0.024	4.570
basecontent	0.000	0.000	0.001
basicPLM	1.884	0.040	2.630
basicRMA	1.889	0.036	2.246
colors	0.028	0.004	0.033
coordinates	0	0	0
fitProbeLevelModel	9.260	0.144	10.418
getProbeInfo	25.650	2.620	29.813
image	1.228	0.016	1.358
justSNPRMA	0	0	0
list.xysfiles	0.000	0.000	0.001
oligoPLM-class	0.000	0.000	0.001
paCalls	0	0	0
preprocessTools	24.089	0.092	25.766
read.celfiles	8.001	2.636	10.932
read.xysfiles	0.920	0.012	1.020
rma-methods	2.464	0.016	2.585
sequenceDesignMatrix	0.012	0.000	0.013

Summary

Command output