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This page was generated on 2024-06-18 17:58 -0400 (Tue, 18 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4464
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 947/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HDF5Array 1.32.0  (landing page)
Hervé Pagès
Snapshot Date: 2024-06-16 14:00 -0400 (Sun, 16 Jun 2024)
git_url: https://git.bioconductor.org/packages/HDF5Array
git_branch: RELEASE_3_19
git_last_commit: eea6c75
git_last_commit_date: 2024-04-30 14:09:32 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


BUILD BIN results for HDF5Array on palomino3

To the developers/maintainers of the HDF5Array package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HDF5Array.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: HDF5Array
Version: 1.32.0
Command: rm -rf HDF5Array.buildbin-libdir && mkdir HDF5Array.buildbin-libdir && F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL --build --library=HDF5Array.buildbin-libdir HDF5Array_1.32.0.tar.gz
StartedAt: 2024-06-17 16:27:50 -0400 (Mon, 17 Jun 2024)
EndedAt: 2024-06-17 16:29:58 -0400 (Mon, 17 Jun 2024)
EllapsedTime: 127.6 seconds
RetCode: 0
Status:   OK  
PackageFile: HDF5Array_1.32.0.zip
PackageFileSize: 11.15 MiB

Command output

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###
### Running command:
###
###   rm -rf HDF5Array.buildbin-libdir && mkdir HDF5Array.buildbin-libdir && F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL --build --library=HDF5Array.buildbin-libdir HDF5Array_1.32.0.tar.gz
###
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* installing *source* package 'HDF5Array' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c H5File.c -o H5File.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c global_errmsg_buf.c -o global_errmsg_buf.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c H5DSetDescriptor.c -o H5DSetDescriptor.o
H5DSetDescriptor.c: In function 'print_H5TypeDescriptor':
H5DSetDescriptor.c:720:38: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'hid_t' {aka 'long long int'} [-Wformat=]
  720 |         Rprintf("%s  * h5type_id = %ld\n", margin, h5type->h5type_id);
      |                                    ~~^             ~~~~~~~~~~~~~~~~~
      |                                      |                   |
      |                                      long int            hid_t {aka long long int}
      |                                    %lld
H5DSetDescriptor.c:722:40: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  722 |         Rprintf("%s  * h5type_size = %lu\n", margin, h5type->h5type_size);
      |                                      ~~^             ~~~~~~~~~~~~~~~~~~~
      |                                        |                   |
      |                                        long unsigned int   size_t {aka long long unsigned int}
      |                                      %llu
H5DSetDescriptor.c:762:47: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  762 |                 Rprintf("%s  * Rtype_size = %lu\n", margin, h5type->Rtype_size);
      |                                             ~~^             ~~~~~~~~~~~~~~~~~~
      |                                               |                   |
      |                                               long unsigned int   size_t {aka long long unsigned int}
      |                                             %llu
H5DSetDescriptor.c:777:45: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  777 |         Rprintf("%s  * native_type_size = %lu\n", margin,
      |                                           ~~^
      |                                             |
      |                                             long unsigned int
      |                                           %llu
  778 |                 h5type->native_type_size);
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~     
      |                       |
      |                       size_t {aka long long unsigned int}
H5DSetDescriptor.c: In function 'C_show_H5DSetDescriptor_xp':
H5DSetDescriptor.c:1204:32: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'hid_t' {aka 'long long int'} [-Wformat=]
 1204 |         Rprintf("- dset_id = %ld\n", h5dset->dset_id);
      |                              ~~^     ~~~~~~~~~~~~~~~
      |                                |           |
      |                                long int    hid_t {aka long long int}
      |                              %lld
H5DSetDescriptor.c:1222:35: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'hid_t' {aka 'long long int'} [-Wformat=]
 1222 |         Rprintf("- h5space_id = %ld\n", h5dset->h5space_id);
      |                                 ~~^     ~~~~~~~~~~~~~~~~~~
      |                                   |           |
      |                                   long int    hid_t {aka long long int}
      |                                 %lld
H5DSetDescriptor.c:1226:35: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'hid_t' {aka 'long long int'} [-Wformat=]
 1226 |         Rprintf("- h5plist_id = %ld\n", h5dset->h5plist_id);
      |                                 ~~^     ~~~~~~~~~~~~~~~~~~
      |                                   |           |
      |                                   long int    hid_t {aka long long int}
      |                                 %lld
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c h5dimscales.c -o h5dimscales.o
In file included from h5dimscales.c:7:
H5File.h:11: warning: "__USE_MINGW_ANSI_STDIO" redefined
   11 | #define __USE_MINGW_ANSI_STDIO 1
      | 
In file included from C:/rtools44/x86_64-w64-mingw32.static.posix/include/corecrt.h:10,
                 from C:/rtools44/x86_64-w64-mingw32.static.posix/include/crtdefs.h:10,
                 from C:/rtools44/x86_64-w64-mingw32.static.posix/include/stddef.h:7,
                 from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/stddef.h:1,
                 from F:/biocbuild/bbs-3.19-bioc/R/include/R_ext/Memory.h:36,
                 from F:/biocbuild/bbs-3.19-bioc/R/include/Rdefines.h:37,
                 from h5dimscales.h:4,
                 from h5dimscales.c:5:
C:/rtools44/x86_64-w64-mingw32.static.posix/include/_mingw.h:434: note: this is the location of the previous definition
  434 | #define __USE_MINGW_ANSI_STDIO 0      /* was not defined so it should be 0 */
      | 
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c uaselection.c -o uaselection.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c h5mread_helpers.c -o h5mread_helpers.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c h5mread_startscounts.c -o h5mread_startscounts.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ChunkIterator.c -o ChunkIterator.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c h5mread_index.c -o h5mread_index.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c h5mread_sparse.c -o h5mread_sparse.o
h5mread_sparse.c:206:13: warning: 'NOT_USED_make_nzindex_from_bufs' defined but not used [-Wunused-function]
  206 | static SEXP NOT_USED_make_nzindex_from_bufs(const IntAEAE *nzindex_bufs,
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
h5mread_sparse.c:179:13: warning: 'NOT_USED_make_nzdata_from_IntAE_bufs' defined but not used [-Wunused-function]
  179 | static SEXP NOT_USED_make_nzdata_from_IntAE_bufs(const IntAEAE *nzdata_bufs,
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
h5mread_sparse.c:123:13: warning: 'NOT_USED_make_nzindex_from_buf' defined but not used [-Wunused-function]
  123 | static SEXP NOT_USED_make_nzindex_from_buf(const IntAE *nzindex_buf,
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c h5mread.c -o h5mread.o
In file included from h5mread.c:7:
H5File.h:11: warning: "__USE_MINGW_ANSI_STDIO" redefined
   11 | #define __USE_MINGW_ANSI_STDIO 1
      | 
In file included from C:/rtools44/x86_64-w64-mingw32.static.posix/include/corecrt.h:10,
                 from C:/rtools44/x86_64-w64-mingw32.static.posix/include/crtdefs.h:10,
                 from C:/rtools44/x86_64-w64-mingw32.static.posix/include/stddef.h:7,
                 from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/stddef.h:1,
                 from F:/biocbuild/bbs-3.19-bioc/R/include/R_ext/Memory.h:36,
                 from F:/biocbuild/bbs-3.19-bioc/R/include/Rdefines.h:37,
                 from h5mread.h:4,
                 from h5mread.c:5:
C:/rtools44/x86_64-w64-mingw32.static.posix/include/_mingw.h:434: note: this is the location of the previous definition
  434 | #define __USE_MINGW_ANSI_STDIO 0      /* was not defined so it should be 0 */
      | 
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c h5summarize.c -o h5summarize.o
In file included from h5summarize.c:7:
H5File.h:11: warning: "__USE_MINGW_ANSI_STDIO" redefined
   11 | #define __USE_MINGW_ANSI_STDIO 1
      | 
In file included from C:/rtools44/x86_64-w64-mingw32.static.posix/include/corecrt.h:10,
                 from C:/rtools44/x86_64-w64-mingw32.static.posix/include/crtdefs.h:10,
                 from C:/rtools44/x86_64-w64-mingw32.static.posix/include/stddef.h:7,
                 from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/stddef.h:1,
                 from F:/biocbuild/bbs-3.19-bioc/R/include/R_ext/Memory.h:36,
                 from F:/biocbuild/bbs-3.19-bioc/R/include/Rdefines.h:37,
                 from h5summarize.h:4,
                 from h5summarize.c:5:
C:/rtools44/x86_64-w64-mingw32.static.posix/include/_mingw.h:434: note: this is the location of the previous definition
  434 | #define __USE_MINGW_ANSI_STDIO 0      /* was not defined so it should be 0 */
      | 
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_init_HDF5Array.c -o R_init_HDF5Array.o
gcc -shared -s -static-libgcc -o HDF5Array.dll tmp.def S4Vectors_stubs.o H5File.o global_errmsg_buf.o H5DSetDescriptor.o h5dimscales.o uaselection.o h5mread_helpers.o h5mread_startscounts.o ChunkIterator.o h5mread_index.o h5mread_sparse.o h5mread.o h5summarize.o R_init_HDF5Array.o -LF:/biocbuild/bbs-3.19-bioc/R/library/Rhdf5lib/lib/x64-ucrt -lhdf5_hl -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lsz -laec -lz -lpsapi -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-bioc/meat/HDF5Array.buildbin-libdir/00LOCK-HDF5Array/00new/HDF5Array/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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
* MD5 sums
packaged installation of 'HDF5Array' as HDF5Array_1.32.0.zip
* DONE (HDF5Array)