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BioC 2.12: CHECK report for externalVector on george2

This page was generated on 2013-10-09 09:37:12 -0700 (Wed, 09 Oct 2013).

Package 212/671HostnameOS / ArchBUILDCHECKBUILD BIN
externalVector 1.26.0
Bioconductor Package Maintainer
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/externalVector
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: externalVector
Version: 1.26.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings externalVector_1.26.0.tar.gz
StartedAt: 2013-10-09 01:38:49 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 01:40:18 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 88.7 seconds
RetCode: 0
Status:  OK 
CheckDir: externalVector.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/externalVector.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 ‘externalVector/DESCRIPTION’ ... OK
* this is package ‘externalVector’ version ‘1.26.0’
* 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 ‘externalVector’ can be installed ... [18s/18s] 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 ... NOTE
File ‘externalVector/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage(paste(msg, collapse = "\n"))
  .onAttach calls:
    library.dynam("externalVector", pkg, lib)

See section ‘Good practice’ in '?.onAttach'.

Arith,externalVectorWithStorage-missing: no visible binding for global
  variable ‘.generic’
Complex,externalVectorWithStorage: no visible binding for global
  variable ‘x’
Subset2,ANY-ANY-noneIndex: possible error in Subset(x, i, NULL): unused
  argument (NULL)
Subset2,ANY-noneIndex-ANY: possible error in Subset(x, NULL, j): unused
  argument (j)
external.size,externalResource-gcAllocator: no visible binding for
  global variable ‘x’
* 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 use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘/home/biocbuild/bbs-2.12-bioc/meat/externalVector.Rcheck/externalVector/libs/externalVector.so’:
  Found non-API calls to R: ‘Rf_EncodeComplex’, ‘Rf_EncodeInteger’,
    ‘Rf_EncodeLogical’, ‘Rf_EncodeReal’, ‘Rf_formatComplex’,
    ‘Rf_formatInteger’, ‘Rf_formatLogical’, ‘Rf_formatReal’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking examples ... [3s/3s] OK
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/externalVector.Rcheck/00check.log’
for details.

externalVector.Rcheck/00install.out:

* installing *source* package ‘externalVector’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c allocator.c -o allocator.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c arraySummary.c -o arraySummary.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c coerce.c -o coerce.o
coerce.c: In function ‘ComplexFromString’:
coerce.c:213:18: warning: initialization from incompatible pointer type [enabled by default]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c externalVector.c -o externalVector.o
externalVector.c:6:1: warning: ‘ScalarVector’ defined but not used [-Wunused-function]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c groups.c -o groups.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c math.c -o math.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c slice.c -o slice.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c storage.c -o storage.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c subscript.c -o subscript.o
subscript.c: In function ‘SubscriptList’:
subscript.c:422:20: warning: assignment from incompatible pointer type [enabled by default]
subscript.c:464:16: warning: assignment from incompatible pointer type [enabled by default]
subscript.c:478:28: warning: assignment from incompatible pointer type [enabled by default]
subscript.c:402:9: warning: variable ‘n’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -shared -L/usr/local/lib -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-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-bioc/meat/externalVector.Rcheck/externalVector/libs
** R
** preparing package for lazy loading
Creating a new generic function for ‘setNames’ in package ‘externalVector’
Creating a generic function for ‘match’ from package ‘base’ in package ‘externalVector’
Creating a generic function for ‘as.vector’ from package ‘base’ in package ‘externalVector’
Creating a generic function for ‘as.single’ from package ‘base’ in package ‘externalVector’
Creating a generic function for ‘as.list’ from package ‘base’ in package ‘externalVector’
Creating a generic function for ‘as.matrix’ from package ‘base’ in package ‘externalVector’
Creating a generic function for ‘as.data.frame’ from package ‘base’ in package ‘externalVector’
Creating a generic function for ‘colSums’ from package ‘base’ in package ‘externalVector’
Creating a generic function for ‘colMeans’ from package ‘base’ in package ‘externalVector’
Creating a generic function for ‘rowSums’ from package ‘base’ in package ‘externalVector’
Creating a generic function for ‘rowMeans’ from package ‘base’ in package ‘externalVector’
Creating a generic function for ‘apply’ from package ‘base’ in package ‘externalVector’
Creating a generic function for ‘lapply’ from package ‘base’ in package ‘externalVector’
Creating a generic function for ‘sapply’ from package ‘base’ in package ‘externalVector’
Creating a generic function for ‘mean’ from package ‘base’ in package ‘externalVector’
Creating a generic function for ‘median’ from package ‘stats’ in package ‘externalVector’
Creating a new generic function for ‘var’ in package ‘externalVector’
Creating a new generic function for ‘cov’ in package ‘externalVector’
Creating a new generic function for ‘cor’ in package ‘externalVector’
Creating a generic function for ‘cov2cor’ from package ‘stats’ in package ‘externalVector’
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (externalVector)

externalVector.Rcheck/externalVector-Ex.timings:

nameusersystemelapsed
SubscriptList0.0240.0000.027
allNA0.0360.0000.034
as.Rvector0.0240.0040.030
asEach0.0800.0000.079
defaultElement0.0160.0000.016
externalMatrix0.1640.0000.163
externalVector0.0320.0040.037
gcAllocator-class0.1120.0040.114
makeSlice0.0200.0000.018
setExternalStorageClass0.0200.0040.020
setVirtualMethod0.0760.0000.075
var0.1880.0000.187