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BioC 2.12: CHECK report for BufferedMatrix on moscato2

This page was generated on 2013-10-09 09:38:20 -0700 (Wed, 09 Oct 2013).

Package 91/671HostnameOS / ArchBUILDCHECKBUILD BIN
BufferedMatrix 1.24.0
Benjamin Milo Bolstad
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/BufferedMatrix
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: BufferedMatrix
Version: 1.24.0
Command: rm -rf BufferedMatrix.buildbin-libdir && mkdir BufferedMatrix.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BufferedMatrix.buildbin-libdir BufferedMatrix_1.24.0.tar.gz >BufferedMatrix-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=BufferedMatrix.buildbin-libdir --install="check:BufferedMatrix-install.out" --force-multiarch --no-vignettes --timings BufferedMatrix_1.24.0.tar.gz && mv BufferedMatrix.buildbin-libdir/* BufferedMatrix.Rcheck/ && rmdir BufferedMatrix.buildbin-libdir
StartedAt: 2013-10-09 01:19:24 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 01:20:51 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 87.1 seconds
RetCode: 0
Status:  OK  
CheckDir: BufferedMatrix.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/BufferedMatrix.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BufferedMatrix/DESCRIPTION' ... OK
* this is package 'BufferedMatrix' 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 ... OK
* checking for portable file names ... OK
* checking whether package 'BufferedMatrix' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

as.BufferedMatrix: warning in createBufferedMatrix(rows = dim(x)[1],
  cols = dim(x)[2], bufferrows = bufferrows, buffercols = buffercols,
  director = directory): partial argument match of 'director' to
  'directory'
* checking Rd files ... NOTE
prepare_Rd: createBufferedMatrix.Rd:26: Dropping empty section \keyword
prepare_Rd: createBufferedMatrix.Rd:17-18: Dropping empty section \details
prepare_Rd: createBufferedMatrix.Rd:15-16: Dropping empty section \value
prepare_Rd: createBufferedMatrix.Rd:19-20: Dropping empty section \references
prepare_Rd: createBufferedMatrix.Rd:21-22: Dropping empty section \seealso
prepare_Rd: createBufferedMatrix.Rd:23-24: Dropping empty section \examples
* 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
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'E:/biocbld/bbs-2.12-bioc/meat/BufferedMatrix.buildbin-libdir/BufferedMatrix/libs/i386/BufferedMatrix.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'E:/biocbld/bbs-2.12-bioc/meat/BufferedMatrix.buildbin-libdir/BufferedMatrix/libs/x64/BufferedMatrix.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.  The detected symbols
are linked into the code but might come from libraries and not actually
be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking examples ... NONE
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'Rcodetesting.R' [1s]
  Running 'c_code_level_tests.R' [1s]
  Running 'objectTesting.R' [16s]
  Running 'rawCalltesting.R' [1s]
 [18s] OK
** running tests for arch 'x64'
  Running 'Rcodetesting.R' [1s]
  Running 'c_code_level_tests.R' [1s]
  Running 'objectTesting.R' [17s]
  Running 'rawCalltesting.R' [1s]
 [20s] 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
  'E:/biocbld/bbs-2.12-bioc/meat/BufferedMatrix.Rcheck/00check.log'
for details.

BufferedMatrix.Rcheck/00install.out:


install for i386

* installing *source* package 'BufferedMatrix' ...
** libs
gcc -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c RBufferedMatrix.c -o RBufferedMatrix.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c doubleBufferedMatrix.c -o doubleBufferedMatrix.o
doubleBufferedMatrix.c: In function 'dbm_ReadOnlyMode':
doubleBufferedMatrix.c:1580:3: warning: suggest parentheses around operand of '!' or change '&' to '&&' or '!' to '˜' [-Wparentheses]
doubleBufferedMatrix.c: At top level:
doubleBufferedMatrix.c:3327:12: warning: 'sort_double' defined but not used [-Wunused-function]
gcc -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c doubleBufferedMatrix_C_tests.c -o doubleBufferedMatrix_C_tests.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c init_package.c -o init_package.o
gcc -m32 -shared -s -static-libgcc -o BufferedMatrix.dll tmp.def RBufferedMatrix.o doubleBufferedMatrix.o doubleBufferedMatrix_C_tests.o init_package.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.12-/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.12-bioc/meat/BufferedMatrix.buildbin-libdir/BufferedMatrix/libs/i386
** R
** inst
** preparing package for lazy loading
Creating a new generic function for 'rowMeans' in package 'BufferedMatrix'
Creating a new generic function for 'rowSums' in package 'BufferedMatrix'
Creating a new generic function for 'colMeans' in package 'BufferedMatrix'
Creating a new generic function for 'colSums' in package 'BufferedMatrix'
Creating a generic function for 'ncol' from package 'base' in package 'BufferedMatrix'
Creating a generic function for 'nrow' from package 'base' in package 'BufferedMatrix'
Creating a generic function for 'mean' from package 'base' in package 'BufferedMatrix'
Creating a generic function for 'as.matrix' from package 'base' in package 'BufferedMatrix'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: ignoring .First.lib() for package 'BufferedMatrix'

install for x64

* installing *source* package 'BufferedMatrix' ...
** libs
gcc -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c RBufferedMatrix.c -o RBufferedMatrix.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c doubleBufferedMatrix.c -o doubleBufferedMatrix.o
doubleBufferedMatrix.c: In function 'dbm_ReadOnlyMode':
doubleBufferedMatrix.c:1580:3: warning: suggest parentheses around operand of '!' or change '&' to '&&' or '!' to '˜' [-Wparentheses]
doubleBufferedMatrix.c: At top level:
doubleBufferedMatrix.c:3327:12: warning: 'sort_double' defined but not used [-Wunused-function]
gcc -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c doubleBufferedMatrix_C_tests.c -o doubleBufferedMatrix_C_tests.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c init_package.c -o init_package.o
gcc -m64 -shared -s -static-libgcc -o BufferedMatrix.dll tmp.def RBufferedMatrix.o doubleBufferedMatrix.o doubleBufferedMatrix_C_tests.o init_package.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.12-/R/bin/x64 -lR
installing to E:/biocbld/bbs-2.12-bioc/meat/BufferedMatrix.buildbin-libdir/BufferedMatrix/libs/x64
** testing if installed package can be loaded
Warning: ignoring .First.lib() for package 'BufferedMatrix'
* MD5 sums
packaged installation of 'BufferedMatrix' as BufferedMatrix_1.24.0.zip
* DONE (BufferedMatrix)