Back to the "Multiple platform build/check report"

NOTES: (1) a maintainance reboot of lemming prevented these builds to complete on this machine (2) these are the last builds with R 2.6.0 (2007-06-03 r41797) on lamb1 and lemming, next builds will be with R 2.6.0 (2007-06-10 r41908) configured with --enable-strict-barrier
Package 67/238HostnameOSArchBUILDCHECKBUILD BIN

externalVector

1.5.2

Biocore Team
Last Changed Date: 2007-06-03 08:44:51 -0700
Last Changed Rev: 25133
lamb1 Linux (SUSE 10.1) x86_64  OK [ ERROR ]
wellington Linux (SUSE 9.2) i686  OK  ERROR 
churchill Solaris 2.9 sparc  OK  ERROR 
lemming Windows Server 2003 (32-bit) x64  OK  ERROR skipped
Package: externalVector
Version: 1.5.2
Command: /home/biocbuild/bbs-2.1-bioc/R/bin/R CMD check externalVector_1.5.2.tar.gz
RetCode: 1
Time: 33.5 seconds
Status: ERROR
CheckDir: externalVector.Rcheck
Warnings: NA

Command output

* checking for working latex ... OK
* using log directory '/home/biocbuild/bbs-2.1-bioc/meat/externalVector.Rcheck'
* using R version 2.6.0 Under development (unstable) (2007-06-03 r41797)
* checking for file 'externalVector/DESCRIPTION' ... OK
* this is package 'externalVector' version '1.5.2'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'externalVector' can be installed ... OK
* 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 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 name space can be loaded with stated dependencies ... 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 cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  all any max min prod range sum
Undocumented S4 methods:
  generic '[<-' and siglist
    'indirectExternalVector,missing,missing,ANY'
  generic '[<-' and siglist 'indirectExternalVector,ANY,missing,ANY'
  generic '[<-' and siglist
    'indirectExternalMatrix,missing,missing,ANY'
  generic '[<-' and siglist 'indirectExternalMatrix,ANY,ANY,ANY'
  generic 'dimnames<-' and siglist 'indirectExternalVector,ANY'
  generic 'dimnames<-' and siglist 'indirectExternalMatrix,ANY'
  generic 'initializeResource' and siglist 'nativeStorageMethods,ANY'
  generic 'initializeResource' and siglist 'externalStorage,ANY'
  generic 'names<-' and siglist 'indirectExternalMatrix,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking for CRLF line endings in C/C++/Fortran sources/headers ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating externalVector-Ex.R ... OK
* checking examples ... ERROR
Running examples in 'externalVector-Ex.R' failed.
The error most likely occurred in:

> ### * asEach
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: asEach
> ### Title: Coerce each element of an external vector to a particular type
> ### Aliases: asEach asEach,ANY,character-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> x <- externalCharacter(4)
Error in initializeResource(resource, ptr, size, type, ...) : 
  Trying to call virtual method for "initializeResource" with signature resource = "nativeStorageMethods"
Execution halted

externalVector.Rcheck/00install.out:

* Installing *source* package 'externalVector' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c allocator.c -o allocator.o
allocator.c: In function 'gcExternalPtr_new':
allocator.c:32: warning: passing argument 1 of 'R_MakeExternalPtr' discards qualifiers from pointer target type
allocator.c:44: warning: passing argument 1 of 'R_MakeExternalPtr' discards qualifiers from pointer target type
allocator.c: In function 'gcExternalPtr_restore':
allocator.c:76: warning: passing argument 2 of 'R_SetExternalPtrAddr' discards qualifiers from pointer target type
allocator.c: In function 'gcExternalPtr_resizeInternal':
allocator.c:100: warning: passing argument 2 of 'R_SetExternalPtrAddr' discards qualifiers from pointer target type
allocator.c:136: warning: passing argument 1 of 'memcpy' discards qualifiers from pointer target type
allocator.c:141: warning: passing argument 2 of 'R_SetExternalPtrAddr' discards qualifiers from pointer target type
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c arraySummary.c -o arraySummary.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c coerce.c -o coerce.o
coerce.c: In function 'IntegerFromString':
coerce.c:111: warning: passing argument 1 of 'Rf_isBlankString' discards qualifiers from pointer target type
coerce.c: In function 'RealFromString':
coerce.c:157: warning: passing argument 1 of 'Rf_isBlankString' discards qualifiers from pointer target type
coerce.c: In function 'ComplexFromString':
coerce.c:213: warning: initialization discards qualifiers from pointer target type
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c externalVector.c -o externalVector.o
externalVector.c:7: warning: 'ScalarVector' defined but not used
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c groups.c -o groups.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c math.c -o math.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c slice.c -o slice.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c storage.c -o storage.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c subscript.c -o subscript.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o externalVector.so allocator.o arraySummary.o coerce.o externalVector.o groups.o math.o slice.o storage.o subscript.o   -L/home/biocbuild/bbs-2.1-bioc/R/lib -lR
** R
** preparing package for lazy loading
Creating a new generic function for "match" in "externalVector"
Creating a new generic function for "as.vector" in "externalVector"
Creating a new generic function for "as.single" in "externalVector"
Creating a new generic function for "as.list" in "externalVector"
Creating a new generic function for "as.matrix" in "externalVector"
Creating a new generic function for "as.data.frame" in "externalVector"
Creating a new generic function for "log" in "externalVector"
Creating a new generic function for "apply" in "externalVector"
Creating a new generic function for "lapply" in "externalVector"
Creating a new generic function for "sapply" in "externalVector"
Creating a new generic function for "mean" in "externalVector"
Creating a new generic function for "median" in "externalVector"
Creating a new generic function for "cov2cor" in "externalVector"
** help
 >>> Building/Updating help pages for package 'externalVector'
     Formats: text html latex example 
  NAIndex-class                     text    html    latex
  SubscriptList                     text    html    latex   example
  Subset                            text    html    latex
  allIndex-class                    text    html    latex
  allNA                             text    html    latex   example
  allocators                        text    html    latex
  as.Rvector                        text    html    latex   example
  asEach                            text    html    latex   example
  defaultElement                    text    html    latex   example
  exprMatrix-class                  text    html    latex
  externalAllocator-class           text    html    latex
  externalMatrix                    text    html    latex   example
  externalResource-class            text    html    latex
  externalStorage-class             text    html    latex
  externalVector-class              text    html    latex
  externalVector                    text    html    latex   example
  externalVectorWithStorage-class   text    html    latex
  gcAllocator-class                 text    html    latex   example
  getExternalStorage                text    html    latex
  getNativeStorageMethods           text    html    latex
  indirectExternalMatrix-class      text    html    latex
  indirectExternalVector-class      text    html    latex
  internalType                      text    html    latex
  makeSlice                         text    html    latex   example
  matrixIndex-class                 text    html    latex
  nativeStorageMethods-class        text    html    latex
  nativeStorageMethodsList-class    text    html    latex
  nonSlotAttributes                 text    html    latex
  noneIndex-class                   text    html    latex
  positiveIndex-class               text    html    latex
  rebind                            text    html    latex
  setDimNames                       text    html    latex
  setExternalStorageClass           text    html    latex   example
  setVirtualMethod                  text    html    latex   example
  simpleStorage-class               text    html    latex
  sliceIndex-class                  text    html    latex
  union-class                       text    html    latex
  var                               text    html    latex   example
  vectorIndex-class                 text    html    latex
** building package indices ...
* DONE (externalVector)