Mike Smith
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/Rhdf5lib |
| Branch: master |
| Last Commit: aa2b5e6 |
| Last Changed Date: 2019-03-25 13:27:13 -0400 (Mon, 25 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 12:31:35 -0400 (Tue, 09 Apr 2019).
| Package 1346/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Rhdf5lib 1.5.4 Mike Smith
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: Rhdf5lib |
| Version: 1.5.4 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Rhdf5lib.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings Rhdf5lib_1.5.4.tar.gz |
| StartedAt: 2019-04-09 05:23:16 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 05:24:50 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 93.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Rhdf5lib.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Rhdf5lib.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings Rhdf5lib_1.5.4.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhdf5lib.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Rhdf5lib/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Rhdf5lib' version '1.5.4'
* package encoding: UTF-8
* 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 'Rhdf5lib' can be installed ... OK
* checking installed package size ... NOTE
installed size is 25.5Mb
sub-directories of 1Mb or more:
include 2.4Mb
lib 15.5Mb
libs 7.6Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
pkgconfig: no visible global function definition for 'shortPathName'
Undefined global functions or variables:
shortPathName
Consider adding
importFrom("utils", "shortPathName")
to your NAMESPACE file.
* 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 shell scripts ... 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:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/libs/i386/Rhdf5lib.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'puts', possibly from 'printf' (C), 'puts' (C)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/libs/x64/Rhdf5lib.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
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 use Fortran I/O
nor system RNGs. 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhdf5lib.Rcheck/00check.log'
for details.
Rhdf5lib.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/Rhdf5lib_1.5.4.tar.gz && rm -rf Rhdf5lib.buildbin-libdir && mkdir Rhdf5lib.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rhdf5lib.buildbin-libdir Rhdf5lib_1.5.4.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL Rhdf5lib_1.5.4.zip && rm Rhdf5lib_1.5.4.tar.gz Rhdf5lib_1.5.4.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 8758k 100 8758k 0 0 56.3M 0 --:--:-- --:--:-- --:--:-- 58.9M
install for i386
* installing *source* package 'Rhdf5lib' ...
untarring hdf5_headers_1.10.3.tar.gz ...
** libs
mkdir -p "C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhdf5lib.buildbin-libdir/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/i386/" "C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhdf5lib.buildbin-libdir/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "winlib/i386/libhdf5.a" "C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhdf5lib.buildbin-libdir/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/i386/libhdf5.a"
cp "winlib/i386/libhdf5_cpp.a" "C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhdf5lib.buildbin-libdir/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/i386/libhdf5_cpp.a"
cp "winlib/i386/libszip.a" "C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhdf5lib.buildbin-libdir/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/i386/libszip.a"
cp ./hdf5/*.h "C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhdf5lib.buildbin-libdir/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp ./hdf5/c++/*.h "C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhdf5lib.buildbin-libdir/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -I./hdf5 -O3 -Wall -std=gnu99 -mtune=generic -c Rhdf5lib.c -o Rhdf5lib.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o Rhdf5lib.dll tmp.def Rhdf5lib.o winlib/i386/libhdf5.a winlib/i386/libszip.a -lpsapi -lz -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhdf5lib.buildbin-libdir/00LOCK-Rhdf5lib/00new/Rhdf5lib/libs/i386
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'Rhdf5lib'
finding HTML links ... done
Rhdf5lib html
getHdf5Version html
pkgconfig html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'Rhdf5lib' ...
untarring hdf5_headers_1.10.3.tar.gz ...
** libs
mkdir -p "C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/lib/x64/" "C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/include"
cp "winlib/x64/libhdf5.a" "C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/lib/x64/libhdf5.a"
cp "winlib/x64/libhdf5_cpp.a" "C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/lib/x64/libhdf5_cpp.a"
cp "winlib/x64/libszip.a" "C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/lib/x64/libszip.a"
cp ./hdf5/*.h "C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/include"
cp ./hdf5/c++/*.h "C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/include"
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -I./hdf5 -O2 -Wall -std=gnu99 -mtune=generic -c Rhdf5lib.c -o Rhdf5lib.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o Rhdf5lib.dll tmp.def Rhdf5lib.o winlib/x64/libhdf5.a winlib/x64/libszip.a -lpsapi -lz -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rhdf5lib' as Rhdf5lib_1.5.4.zip
* DONE (Rhdf5lib)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'Rhdf5lib' successfully unpacked and MD5 sums checked
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Rhdf5lib.Rcheck/examples_i386/Rhdf5lib-Ex.timings
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Rhdf5lib.Rcheck/examples_x64/Rhdf5lib-Ex.timings
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