BioC 2.12: CHECK report for RWebServices on george2

Package: RWebServices

Version: 1.24.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings RWebServices_1.24.0.tar.gz

StartedAt: 2013-10-09 04:50:47 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 04:52:07 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 79.6 seconds

RetCode: 0

Status:  OK

CheckDir: RWebServices.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/RWebServices.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 ‘RWebServices/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RWebServices’ version ‘1.24.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... NOTE
Found the following non-portable file paths:
  RWebServices/inst/unitTests/java/src/org/bioconductor/packages/rservices/Rinput/ClassUnionConverter.R
  RWebServices/inst/unitTests/java/src/org/bioconductor/packages/rservices/testdata/MyUnionFactory.java
  RWebServices/inst/unitTests/java/src/org/bioconductor/packages/rservices/testdata/MyUnionRCharFactory.java
  RWebServices/inst/unitTests/java/src/org/bioconductor/packages/rservices/testdata/MyUnionRLogicalFactory.java

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RWebServices’ can be installed ... [7s/8s] 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 ... OK
* 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 ... [3s/3s] 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 2 notes.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/RWebServices.Rcheck/00check.log’
for details.

* installing *source* package ‘RWebServices’ ...

Guessing SJava home: /home/biocbuild/bbs-2.12-bioc/meat/RWebServices.Rcheck/SJava

checking Java support in R... configure: creating ./config.status
config.status: creating inst/scripts/RWebServicesEnv.properties
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/lib/jvm/java-6-openjdk-amd64/jre/../include -I/usr/local/include    -fpic  -g -O2  -Wall -c RWebServicesConverters.c -o RWebServicesConverters.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/lib/jvm/java-6-openjdk-amd64/jre/../include -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -std=gnu99 -shared -L/usr/local/lib -o RWebServices.so RWebServicesConverters.o init.o -L/usr/lib/jvm/java-6-openjdk-amd64/jre/lib/amd64/server -ljvm -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-bioc/meat/RWebServices.Rcheck/RWebServices/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RWebServices)

name	user	system	elapsed
ArrayAndMatrix-class	0.080	0.000	0.079
FileReferences-class	0.016	0.000	0.014
FileReferences	0.020	0.000	0.023
RJavaPkgFunctions-class	0.068	0.000	0.069
RJavaSignature-class	0.076	0.000	0.075
SinkOutput-class	0.020	0.000	0.017
createMap	0.016	0.000	0.015
generateDataMap	0.008	0.000	0.007
generateDataTest	0.000	0.004	0.007
generateFunctionMap	0.008	0.000	0.007
getRSessionInfo	0.008	0.004	0.015
printLookup	0.004	0.000	0.006
retrieve	0.044	0.000	0.092
sinkSetup	0.024	0.000	0.025
typeInfo2Java	0.168	0.004	0.171
unpackAntScript	0.012	0.000	0.012