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BioC 3.2: CHECK report for rhdf5 on windows1.bioconductor.org

This page was generated on 2015-10-27 17:29:49 -0400 (Tue, 27 Oct 2015).

Package 880/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rhdf5 2.14.0
Bernd Fischer
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/rhdf5
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: rhdf5
Version: 2.14.0
Command: rm -rf rhdf5.buildbin-libdir rhdf5.Rcheck && mkdir rhdf5.buildbin-libdir rhdf5.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=rhdf5.buildbin-libdir rhdf5_2.14.0.tar.gz >rhdf5.Rcheck\00install.out 2>&1 && cp rhdf5.Rcheck\00install.out rhdf5-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=rhdf5.buildbin-libdir --install="check:rhdf5-install.out" --force-multiarch --no-vignettes --timings rhdf5_2.14.0.tar.gz
StartedAt: 2015-10-27 05:02:59 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 05:04:26 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 86.6 seconds
RetCode: 0
Status:  OK  
CheckDir: rhdf5.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf rhdf5.buildbin-libdir rhdf5.Rcheck && mkdir rhdf5.buildbin-libdir rhdf5.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=rhdf5.buildbin-libdir rhdf5_2.14.0.tar.gz >rhdf5.Rcheck\00install.out 2>&1 && cp rhdf5.Rcheck\00install.out rhdf5-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=rhdf5.buildbin-libdir --install="check:rhdf5-install.out" --force-multiarch --no-vignettes --timings rhdf5_2.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/rhdf5.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rhdf5/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rhdf5' version '2.14.0'
* 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 'rhdf5' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
* checking package directory ... OK
* checking 'build' 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 dependencies in R code ... NOTE
'library' or 'require' call to 'bit64' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'h5constants' 'h5validObjects'
* 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 ... NOTE
prepare_Rd: h5set_extent.Rd:14-16: Dropping empty section \details
* 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 compilation flags in Makevars ... OK
* checking for GNU extensions 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 'C:/biocbld/bbs-3.2-bioc/meat/rhdf5.buildbin-libdir/rhdf5/libs/i386/libhdf5ForBioC-7.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/biocbld/bbs-3.2-bioc/meat/rhdf5.buildbin-libdir/rhdf5/libs/x64/libhdf5ForBioC-7.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/biocbld/bbs-3.2-bioc/meat/rhdf5.buildbin-libdir/rhdf5/libs/i386/libsz-2.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/biocbld/bbs-3.2-bioc/meat/rhdf5.buildbin-libdir/rhdf5/libs/x64/libsz-2.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/biocbld/bbs-3.2-bioc/meat/rhdf5.buildbin-libdir/rhdf5/libs/i386/rhdf5.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
File 'C:/biocbld/bbs-3.2-bioc/meat/rhdf5.buildbin-libdir/rhdf5/libs/x64/rhdf5.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'puts', possibly from 'printf' (C), 'puts' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [1s] OK
** running examples for arch 'x64' ... [1s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  'C:/biocbld/bbs-3.2-bioc/meat/rhdf5.Rcheck/00check.log'
for details.

rhdf5.Rcheck/00install.out:


install for i386

* installing *source* package 'rhdf5' ...
** libs
cp includeWin/i386/* includeWin/
cp libwin/i386/*.dll .
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I"C:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c H5.c -o H5.o
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I"C:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c H5A.c -o H5A.o
H5A.c: In function 'H5Aread_helper_INTEGER':
H5A.c:153:10: warning: unused variable 'herr' [-Wunused-variable]
H5A.c: In function 'H5Aread_helper_FLOAT':
H5A.c:186:10: warning: unused variable 'herr' [-Wunused-variable]
H5A.c: In function 'H5Aread_helper_STRING':
H5A.c:213:12: warning: unused variable 'herr' [-Wunused-variable]
H5A.c:220:12: warning: unused variable 'herr' [-Wunused-variable]
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I"C:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c H5D.c -o H5D.o
H5D.c: In function 'H5Dread_helper_INTEGER':
H5D.c:220:9: warning: unused variable 'status' [-Wunused-variable]
H5D.c:217:14: warning: unused variable 'status' [-Wunused-variable]
H5D.c:232:12: warning: unused variable 'herr' [-Wunused-variable]
H5D.c:268:9: warning: unused variable 'status' [-Wunused-variable]
H5D.c:265:14: warning: unused variable 'status' [-Wunused-variable]
H5D.c:273:12: warning: unused variable 'herr' [-Wunused-variable]
H5D.c: In function 'H5Dread_helper_FLOAT':
H5D.c:438:14: warning: unused variable 'status' [-Wunused-variable]
H5D.c:435:12: warning: unused variable 'status' [-Wunused-variable]
H5D.c:450:10: warning: unused variable 'herr' [-Wunused-variable]
H5D.c: In function 'H5Dread_helper_STRING':
H5D.c:471:14: warning: unused variable 'status' [-Wunused-variable]
H5D.c:468:12: warning: unused variable 'status' [-Wunused-variable]
H5D.c:479:12: warning: unused variable 'herr' [-Wunused-variable]
H5D.c:490:12: warning: unused variable 'herr' [-Wunused-variable]
H5D.c: In function 'H5Dread_helper_ENUM':
H5D.c:525:14: warning: unused variable 'status' [-Wunused-variable]
H5D.c:536:9: warning: unused variable 'status' [-Wunused-variable]
H5D.c:533:14: warning: unused variable 'status' [-Wunused-variable]
H5D.c:550:12: warning: unused variable 'herr' [-Wunused-variable]
H5D.c: In function 'H5Dread_helper_ARRAY':
H5D.c:601:13: warning: unused variable 'status' [-Wunused-variable]
H5D.c:598:14: warning: unused variable 'status' [-Wunused-variable]
H5D.c:623:12: warning: unused variable 'herr' [-Wunused-variable]
H5D.c: In function 'H5Dread_helper_COMPOUND':
H5D.c:656:9: warning: unused variable 'mem_type_id' [-Wunused-variable]
H5D.c: In function 'H5Dread_helper_INTEGER':
H5D.c:385:60: warning: 'intbuf' may be used uninitialized in this function [-Wuninitialized]
H5D.c:267:32: warning: 'dtypeNative' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I"C:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c H5E.c -o H5E.o
H5E.c: In function 'custom_print_cb':
H5E.c:76:3: warning: label 'Rf_error' defined but not used [-Wunused-label]
H5E.c: In function 'custom_print_cb_compact':
H5E.c:112:3: warning: label 'Rf_error' defined but not used [-Wunused-label]
H5E.c:87:16: warning: unused variable 'indent' [-Wunused-variable]
H5E.c: In function '_rhdf5PrintErrorR':
H5E.c:121:12: warning: unused variable 'eee' [-Wunused-variable]
H5E.c: In function '_rhdf5PrintErrorRcompact':
H5E.c:153:12: warning: unused variable 'eee' [-Wunused-variable]
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I"C:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c H5F.c -o H5F.o
H5F.c: In function '_H5Fget_name':
H5F.c:110:5: warning: passing argument 2 of 'H5Fget_name' from incompatible pointer type [enabled by default]
includeWin/H5Fpublic.h:174:16: note: expected 'char *' but argument is of type 'char (*)[(unsigned int)((int)size + 1)]'
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I"C:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c H5G.c -o H5G.o
H5G.c: In function '_H5Gget_info':
H5G.c:66:10: warning: unused variable 'herr' [-Wunused-variable]
H5G.c: In function '_H5Gget_info_by_name':
H5G.c:113:10: warning: unused variable 'herr' [-Wunused-variable]
H5G.c: In function '_H5Gget_info_by_idx':
H5G.c:163:10: warning: unused variable 'herr' [-Wunused-variable]
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I"C:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c H5I.c -o H5I.o
H5I.c: In function '_H5Iget_name':
H5I.c:24:3: warning: passing argument 2 of 'H5Iget_name' from incompatible pointer type [enabled by default]
includeWin/H5Ipublic.h:85:16: note: expected 'char *' but argument is of type 'char (*)[(unsigned int)((int)st + 1)]'
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I"C:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c H5L.c -o H5L.o
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I"C:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c H5O.c -o H5O.o
H5O.c: In function 'H5Oget_num_attrs':
H5O.c:13:10: warning: unused variable 'herr' [-Wunused-variable]
H5O.c: In function '_H5Oopen':
H5O.c:56:3: warning: implicit declaration of function 'addHandle' [-Wimplicit-function-declaration]
H5O.c: In function '_H5Oclose':
H5O.c:69:5: warning: implicit declaration of function 'removeHandle' [-Wimplicit-function-declaration]
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I"C:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c H5P.c -o H5P.o
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I"C:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c H5S.c -o H5S.o
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I"C:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c H5T.c -o H5T.o
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I"C:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c H5constants.c -o H5constants.o
g++ -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I"C:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O2 -Wall  -mtune=core2 -c HandleList.cpp -o HandleList.o
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I"C:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c h5dump.c -o h5dump.o
h5dump.c: In function 'opAddToLinfoTree':
h5dump.c:85:3: warning: implicit declaration of function 'H5Oget_num_attrs' [-Wimplicit-function-declaration]
h5dump.c:114:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'hsize_t' [-Wformat]
h5dump.c:116:8: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'hsize_t' [-Wformat]
h5dump.c:124:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'hsize_t' [-Wformat]
h5dump.c:126:4: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'hsize_t' [-Wformat]
h5dump.c: In function '_h5dump':
h5dump.c:314:10: warning: unused variable 'herr' [-Wunused-variable]
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I"C:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c h5ls.c -o h5ls.o
h5ls.c: In function 'opAddToLinfoList':
h5ls.c:99:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'hsize_t' [-Wformat]
h5ls.c:101:4: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'hsize_t' [-Wformat]
h5ls.c:109:4: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'hsize_t' [-Wformat]
h5ls.c:111:6: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'hsize_t' [-Wformat]
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I"C:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c h5writeDataFrame.c -o h5writeDataFrame.o
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I"C:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c printdatatype.c -o printdatatype.o
printdatatype.c: In function 'getDatatypeName':
printdatatype.c:21:16: warning: variable 'sign_s' set but not used [-Wunused-but-set-variable]
printdatatype.c:19:16: warning: variable 'order_s' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I"C:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c wrap.c -o wrap.o
C:\Rtools\gcc-4.6.3\bin\nm.exe: 'libhdf5ForBioC': No such file
g++ -m32 -shared -s -static-libgcc -o rhdf5.dll tmp.def H5.o H5A.o H5D.o H5E.o H5F.o H5G.o H5I.o H5L.o H5O.o H5P.o H5S.o H5T.o H5constants.o HandleList.o h5dump.o h5ls.o h5writeDataFrame.o printdatatype.o wrap.o -llibhdf5ForBioC-7 -LC:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -llibsz-2 -lm -L. -Ld:/RCompile/r-compiling/local/local320/lib/i386 -Ld:/RCompile/r-compiling/local/local320/lib -LC:/biocbld/BBS-3˜1.2-B/R/bin/i386 -lR
installing to C:/biocbld/bbs-3.2-bioc/meat/rhdf5.buildbin-libdir/rhdf5/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'rhdf5' ...
** libs
cp includeWin/x64/* includeWin/
cp libwin/x64/*.dll .
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I"C:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c H5.c -o H5.o
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I"C:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c H5A.c -o H5A.o
H5A.c: In function 'H5Aread_helper_INTEGER':
H5A.c:153:10: warning: unused variable 'herr' [-Wunused-variable]
H5A.c: In function 'H5Aread_helper_FLOAT':
H5A.c:186:10: warning: unused variable 'herr' [-Wunused-variable]
H5A.c: In function 'H5Aread_helper_STRING':
H5A.c:213:12: warning: unused variable 'herr' [-Wunused-variable]
H5A.c:220:12: warning: unused variable 'herr' [-Wunused-variable]
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I"C:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c H5D.c -o H5D.o
H5D.c: In function 'H5Dread_helper_INTEGER':
H5D.c:220:9: warning: unused variable 'status' [-Wunused-variable]
H5D.c:217:14: warning: unused variable 'status' [-Wunused-variable]
H5D.c:232:12: warning: unused variable 'herr' [-Wunused-variable]
H5D.c:268:9: warning: unused variable 'status' [-Wunused-variable]
H5D.c:265:14: warning: unused variable 'status' [-Wunused-variable]
H5D.c:273:12: warning: unused variable 'herr' [-Wunused-variable]
H5D.c: In function 'H5Dread_helper_FLOAT':
H5D.c:438:14: warning: unused variable 'status' [-Wunused-variable]
H5D.c:435:12: warning: unused variable 'status' [-Wunused-variable]
H5D.c:450:10: warning: unused variable 'herr' [-Wunused-variable]
H5D.c: In function 'H5Dread_helper_STRING':
H5D.c:471:14: warning: unused variable 'status' [-Wunused-variable]
H5D.c:468:12: warning: unused variable 'status' [-Wunused-variable]
H5D.c:479:12: warning: unused variable 'herr' [-Wunused-variable]
H5D.c:490:12: warning: unused variable 'herr' [-Wunused-variable]
H5D.c: In function 'H5Dread_helper_ENUM':
H5D.c:525:14: warning: unused variable 'status' [-Wunused-variable]
H5D.c:536:9: warning: unused variable 'status' [-Wunused-variable]
H5D.c:533:14: warning: unused variable 'status' [-Wunused-variable]
H5D.c:550:12: warning: unused variable 'herr' [-Wunused-variable]
H5D.c: In function 'H5Dread_helper_ARRAY':
H5D.c:601:13: warning: unused variable 'status' [-Wunused-variable]
H5D.c:598:14: warning: unused variable 'status' [-Wunused-variable]
H5D.c:623:12: warning: unused variable 'herr' [-Wunused-variable]
H5D.c: In function 'H5Dread_helper_COMPOUND':
H5D.c:656:9: warning: unused variable 'mem_type_id' [-Wunused-variable]
H5D.c: In function 'H5Dread_helper_INTEGER':
H5D.c:385:60: warning: 'intbuf' may be used uninitialized in this function [-Wuninitialized]
H5D.c:267:32: warning: 'dtypeNative' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I"C:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c H5E.c -o H5E.o
H5E.c: In function 'custom_print_cb':
H5E.c:76:3: warning: label 'Rf_error' defined but not used [-Wunused-label]
H5E.c: In function 'custom_print_cb_compact':
H5E.c:112:3: warning: label 'Rf_error' defined but not used [-Wunused-label]
H5E.c:87:16: warning: unused variable 'indent' [-Wunused-variable]
H5E.c: In function '_rhdf5PrintErrorR':
H5E.c:121:12: warning: unused variable 'eee' [-Wunused-variable]
H5E.c: In function '_rhdf5PrintErrorRcompact':
H5E.c:153:12: warning: unused variable 'eee' [-Wunused-variable]
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I"C:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c H5F.c -o H5F.o
H5F.c: In function '_H5Fget_name':
H5F.c:110:5: warning: passing argument 2 of 'H5Fget_name' from incompatible pointer type [enabled by default]
includeWin/H5Fpublic.h:174:16: note: expected 'char *' but argument is of type 'char (*)[(long long unsigned int)(size + 1)]'
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I"C:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c H5G.c -o H5G.o
H5G.c: In function '_H5Gget_info':
H5G.c:66:10: warning: unused variable 'herr' [-Wunused-variable]
H5G.c: In function '_H5Gget_info_by_name':
H5G.c:113:10: warning: unused variable 'herr' [-Wunused-variable]
H5G.c: In function '_H5Gget_info_by_idx':
H5G.c:163:10: warning: unused variable 'herr' [-Wunused-variable]
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I"C:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c H5I.c -o H5I.o
H5I.c: In function '_H5Iget_name':
H5I.c:24:3: warning: passing argument 2 of 'H5Iget_name' from incompatible pointer type [enabled by default]
includeWin/H5Ipublic.h:85:16: note: expected 'char *' but argument is of type 'char (*)[(long long unsigned int)(st + 1)]'
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I"C:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c H5L.c -o H5L.o
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I"C:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c H5O.c -o H5O.o
H5O.c: In function 'H5Oget_num_attrs':
H5O.c:13:10: warning: unused variable 'herr' [-Wunused-variable]
H5O.c: In function '_H5Oopen':
H5O.c:56:3: warning: implicit declaration of function 'addHandle' [-Wimplicit-function-declaration]
H5O.c: In function '_H5Oclose':
H5O.c:69:5: warning: implicit declaration of function 'removeHandle' [-Wimplicit-function-declaration]
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I"C:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c H5P.c -o H5P.o
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I"C:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c H5S.c -o H5S.o
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I"C:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c H5T.c -o H5T.o
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I"C:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c H5constants.c -o H5constants.o
g++ -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I"C:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O2 -Wall  -mtune=core2 -c HandleList.cpp -o HandleList.o
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I"C:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c h5dump.c -o h5dump.o
h5dump.c: In function 'opAddToLinfoTree':
h5dump.c:85:3: warning: implicit declaration of function 'H5Oget_num_attrs' [-Wimplicit-function-declaration]
h5dump.c:114:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'hsize_t' [-Wformat]
h5dump.c:116:8: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'hsize_t' [-Wformat]
h5dump.c:124:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'hsize_t' [-Wformat]
h5dump.c:126:4: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'hsize_t' [-Wformat]
h5dump.c: In function '_h5dump':
h5dump.c:314:10: warning: unused variable 'herr' [-Wunused-variable]
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I"C:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c h5ls.c -o h5ls.o
h5ls.c: In function 'opAddToLinfoList':
h5ls.c:99:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'hsize_t' [-Wformat]
h5ls.c:101:4: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'hsize_t' [-Wformat]
h5ls.c:109:4: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'hsize_t' [-Wformat]
h5ls.c:111:6: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'hsize_t' [-Wformat]
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I"C:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c h5writeDataFrame.c -o h5writeDataFrame.o
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I"C:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c printdatatype.c -o printdatatype.o
printdatatype.c: In function 'getDatatypeName':
printdatatype.c:21:16: warning: variable 'sign_s' set but not used [-Wunused-but-set-variable]
printdatatype.c:19:16: warning: variable 'order_s' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"C:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"  -I"C:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c wrap.c -o wrap.o
C:\Rtools\gcc-4.6.3\bin\nm.exe: 'libhdf5ForBioC': No such file
g++ -m64 -shared -s -static-libgcc -o rhdf5.dll tmp.def H5.o H5A.o H5D.o H5E.o H5F.o H5G.o H5I.o H5L.o H5O.o H5P.o H5S.o H5T.o H5constants.o HandleList.o h5dump.o h5ls.o h5writeDataFrame.o printdatatype.o wrap.o -llibhdf5ForBioC-7 -LC:/biocbld/bbs-3.2-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -llibsz-2 -lm -L. -Ld:/RCompile/r-compiling/local/local320/lib/x64 -Ld:/RCompile/r-compiling/local/local320/lib -LC:/biocbld/BBS-3˜1.2-B/R/bin/x64 -lR
installing to C:/biocbld/bbs-3.2-bioc/meat/rhdf5.buildbin-libdir/rhdf5/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rhdf5' as rhdf5_2.14.0.zip
* DONE (rhdf5)

rhdf5.Rcheck/examples_i386/rhdf5-Ex.timings:

nameusersystemelapsed
H5000
H5A0.030.000.03
H5D0.020.000.02
H5F0.000.000.01
H5G000
H5I0.010.000.02
H5IdComponent-class000
H5L0.020.000.01
H5O0.010.000.02
H5P000
H5P_DATASET_ACCESS000
H5P_DATASET_CREATE0.020.000.01
H5P_LINK_CREATE000
H5S000
H5T000
h5const000
h5createAttribute0.010.000.02
h5createDataset0.030.020.05
h5createFile0.020.000.01
h5createGroup0.020.000.02
h5errorHandling000
h5listIdentifier000
h5ls0.030.000.03
h5save0.040.000.05
h5set_extent0.020.000.01
h5version0.020.000.02
h5write0.030.000.03
rhdf50.060.000.06

rhdf5.Rcheck/examples_x64/rhdf5-Ex.timings:

nameusersystemelapsed
H5000
H5A0.020.000.03
H5D0.030.000.03
H5F000
H5G000
H5I0.010.000.02
H5IdComponent-class000
H5L000
H5O0.010.000.02
H5P0.020.000.02
H5P_DATASET_ACCESS000
H5P_DATASET_CREATE000
H5P_LINK_CREATE0.000.010.01
H5S000
H5T000
h5const000
h5createAttribute0.020.000.02
h5createDataset0.060.020.08
h5createFile0.000.010.02
h5createGroup0.020.000.02
h5errorHandling000
h5listIdentifier000
h5ls0.050.000.05
h5save0.110.000.11
h5set_extent0.010.000.02
h5version000
h5write0.030.020.05
rhdf50.060.000.06