Hervé Pagès
| Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024) |
| git_url: https://git.bioconductor.org/packages/HDF5Array |
| git_branch: devel |
| git_last_commit: 1f630b0 |
| git_last_commit_date: 2024-06-20 13:18:50 -0400 (Thu, 20 Jun 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4677 |
| palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4416 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4393 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4373 |
| 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 922/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| HDF5Array 1.33.3 (landing page) Hervé Pagès
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
|
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. |
| Package: HDF5Array |
| Version: 1.33.3 |
| Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:HDF5Array.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings HDF5Array_1.33.3.tar.gz |
| StartedAt: 2024-07-16 00:43:20 -0400 (Tue, 16 Jul 2024) |
| EndedAt: 2024-07-16 00:52:18 -0400 (Tue, 16 Jul 2024) |
| EllapsedTime: 537.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: HDF5Array.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:HDF5Array.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings HDF5Array_1.33.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/HDF5Array.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'HDF5Array/DESCRIPTION' ... OK
* this is package 'HDF5Array' version '1.33.3'
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'HDF5Array' can be installed ... WARNING
Found the following significant warnings:
H5DSetDescriptor.c:698:38: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'hid_t' {aka 'long long int'} [-Wformat=]
H5DSetDescriptor.c:700:40: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
H5DSetDescriptor.c:740:47: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
H5DSetDescriptor.c:755:45: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
H5DSetDescriptor.c:1166:32: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'hid_t' {aka 'long long int'} [-Wformat=]
H5DSetDescriptor.c:1184:35: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'hid_t' {aka 'long long int'} [-Wformat=]
H5DSetDescriptor.c:1188:35: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'hid_t' {aka 'long long int'} [-Wformat=]
H5DSetDescriptor.c:1210:37: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
uaselection.c:53:45: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
uaselection.c:55:45: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
uaselection.c:64:45: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
uaselection.c:68:45: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
uaselection.c:75:45: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
uaselection.c:78:45: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
uaselection.c:199:25: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
uaselection.c:204:25: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
uaselection.c:204:25: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
uaselection.c:217:37: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
uaselection.c:217:37: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
uaselection.c:220:37: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
uaselection.c:220:37: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
uaselection.c:220:37: warning: format '%ld' expects argument of type 'long int', but argument 10 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
uaselection.c:233:37: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
uaselection.c:288:45: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
uaselection.c:428:53: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
ChunkIterator.c:457:28: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
ChunkIterator.c:457:32: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
See 'C:/Users/biocbuild/bbs-3.20-bioc/meat/HDF5Array.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* checking installed package size ... NOTE
installed size is 15.3Mb
sub-directories of 1Mb or more:
extdata 7.7Mb
libs 6.6Mb
* 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 code 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: 'rhdf5:::h5checktypeOrOpenLocS3'
See the note in ?`:::` about the use of this operator.
* 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 ... 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 compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.20-bioc/R/library/HDF5Array/libs/x64/HDF5Array.dll':
Found '_assert', possibly from 'assert' (C)
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
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 nor [v]sprintf. 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 examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
h5mread 48.00 8.08 56.87
TENxMatrix-class 37.79 11.76 178.15
writeTENxMatrix 19.38 1.31 21.47
HDF5Array-class 2.34 0.25 6.93
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'run_unitTests.R'
OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 5 NOTEs
See
'C:/Users/biocbuild/bbs-3.20-bioc/meat/HDF5Array.Rcheck/00check.log'
for details.
HDF5Array.Rcheck/00install.out
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL HDF5Array
###
##############################################################################
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* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'HDF5Array' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-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:698:38: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'hid_t' {aka 'long long int'} [-Wformat=]
698 | Rprintf("%s * h5type_id = %ld\n", margin, h5type->h5type_id);
| ~~^ ~~~~~~~~~~~~~~~~~
| | |
| long int hid_t {aka long long int}
| %lld
H5DSetDescriptor.c:700:40: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
700 | Rprintf("%s * h5type_size = %lu\n", margin, h5type->h5type_size);
| ~~^ ~~~~~~~~~~~~~~~~~~~
| | |
| long unsigned int size_t {aka long long unsigned int}
| %llu
H5DSetDescriptor.c:740:47: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
740 | Rprintf("%s * Rtype_size = %lu\n", margin, h5type->Rtype_size);
| ~~^ ~~~~~~~~~~~~~~~~~~
| | |
| long unsigned int size_t {aka long long unsigned int}
| %llu
H5DSetDescriptor.c:755:45: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
755 | Rprintf("%s * native_type_size = %lu\n", margin,
| ~~^
| |
| long unsigned int
| %llu
756 | h5type->native_type_size);
| ~~~~~~~~~~~~~~~~~~~~~~~~
| |
| size_t {aka long long unsigned int}
H5DSetDescriptor.c: In function 'C_show_H5DSetDescriptor_xp':
H5DSetDescriptor.c:1166:32: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'hid_t' {aka 'long long int'} [-Wformat=]
1166 | Rprintf("- dset_id = %ld\n", h5dset->dset_id);
| ~~^ ~~~~~~~~~~~~~~~
| | |
| long int hid_t {aka long long int}
| %lld
H5DSetDescriptor.c:1184:35: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'hid_t' {aka 'long long int'} [-Wformat=]
1184 | Rprintf("- h5space_id = %ld\n", h5dset->h5space_id);
| ~~^ ~~~~~~~~~~~~~~~~~~
| | |
| long int hid_t {aka long long int}
| %lld
H5DSetDescriptor.c:1188:35: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'hid_t' {aka 'long long int'} [-Wformat=]
1188 | Rprintf("- h5plist_id = %ld\n", h5dset->h5plist_id);
| ~~^ ~~~~~~~~~~~~~~~~~~
| | |
| long int hid_t {aka long long int}
| %lld
H5DSetDescriptor.c:1210:37: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
1210 | Rprintf(" %lu", h5dset->h5nchunk[h5along]);
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long unsigned int size_t {aka long long unsigned int}
| %llu
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-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 C:/Users/biocbuild/bbs-3.20-bioc/R/include/R_ext/Memory.h:36,
from C:/Users/biocbuild/bbs-3.20-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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-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
In file included from uaselection.c:7:
uaselection.c: In function 'get_untrusted_elt':
uaselection.c:53:45: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
53 | PRINT_TO_ERRMSG_BUF("%s[%ld] is NA", what, i + 1);
| ^~~~~~~~~~~~~~~ ~~~~~
| |
| R_xlen_t {aka long long int}
global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
| ^~~~~~~~~~~
uaselection.c:53:51: note: format string is defined here
53 | PRINT_TO_ERRMSG_BUF("%s[%ld] is NA", what, i + 1);
| ~~^
| |
| long int
| %lld
uaselection.c:53:45: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
53 | PRINT_TO_ERRMSG_BUF("%s[%ld] is NA", what, i + 1);
| ^~~~~~~~~~~~~~~ ~~~~~
| |
| R_xlen_t {aka long long int}
global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
| ^~~~~~~~~~~
uaselection.c:53:51: note: format string is defined here
53 | PRINT_TO_ERRMSG_BUF("%s[%ld] is NA", what, i + 1);
| ~~^
| |
| long int
| %lld
uaselection.c:55:45: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
55 | PRINT_TO_ERRMSG_BUF("%s[[%d]][%ld] is NA",
| ^~~~~~~~~~~~~~~~~~~~~
56 | what, along + 1, i + 1);
| ~~~~~
| |
| R_xlen_t {aka long long int}
global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
| ^~~~~~~~~~~
uaselection.c:55:57: note: format string is defined here
55 | PRINT_TO_ERRMSG_BUF("%s[[%d]][%ld] is NA",
| ~~^
| |
| long int
| %lld
uaselection.c:55:45: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
55 | PRINT_TO_ERRMSG_BUF("%s[[%d]][%ld] is NA",
| ^~~~~~~~~~~~~~~~~~~~~
56 | what, along + 1, i + 1);
| ~~~~~
| |
| R_xlen_t {aka long long int}
global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
| ^~~~~~~~~~~
uaselection.c:55:57: note: format string is defined here
55 | PRINT_TO_ERRMSG_BUF("%s[[%d]][%ld] is NA",
| ~~^
| |
| long int
| %lld
uaselection.c:64:45: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
64 | PRINT_TO_ERRMSG_BUF("%s[%ld] is NA or NaN "
| ^~~~~~~~~~~~~~~~~~~~~~~
65 | "or not a finite number",
66 | what, i + 1);
| ~~~~~
| |
| R_xlen_t {aka long long int}
global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
| ^~~~~~~~~~~
uaselection.c:64:51: note: format string is defined here
64 | PRINT_TO_ERRMSG_BUF("%s[%ld] is NA or NaN "
| ~~^
| |
| long int
| %lld
uaselection.c:64:45: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
64 | PRINT_TO_ERRMSG_BUF("%s[%ld] is NA or NaN "
| ^~~~~~~~~~~~~~~~~~~~~~~
65 | "or not a finite number",
66 | what, i + 1);
| ~~~~~
| |
| R_xlen_t {aka long long int}
global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
| ^~~~~~~~~~~
uaselection.c:64:51: note: format string is defined here
64 | PRINT_TO_ERRMSG_BUF("%s[%ld] is NA or NaN "
| ~~^
| |
| long int
| %lld
uaselection.c:68:45: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
68 | PRINT_TO_ERRMSG_BUF("%s[[%d]][%ld] is NA or NaN "
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
69 | "or not a finite number",
70 | what, along + 1, i + 1);
| ~~~~~
| |
| R_xlen_t {aka long long int}
global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
| ^~~~~~~~~~~
uaselection.c:68:57: note: format string is defined here
68 | PRINT_TO_ERRMSG_BUF("%s[[%d]][%ld] is NA or NaN "
| ~~^
| |
| long int
| %lld
uaselection.c:68:45: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
68 | PRINT_TO_ERRMSG_BUF("%s[[%d]][%ld] is NA or NaN "
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
69 | "or not a finite number",
70 | what, along + 1, i + 1);
| ~~~~~
| |
| R_xlen_t {aka long long int}
global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
| ^~~~~~~~~~~
uaselection.c:68:57: note: format string is defined here
68 | PRINT_TO_ERRMSG_BUF("%s[[%d]][%ld] is NA or NaN "
| ~~^
| |
| long int
| %lld
uaselection.c:75:45: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
75 | PRINT_TO_ERRMSG_BUF("%s[%ld] is too large (= %e)",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
76 | what, i + 1, tmp2);
| ~~~~~
| |
| R_xlen_t {aka long long int}
global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
| ^~~~~~~~~~~
uaselection.c:75:51: note: format string is defined here
75 | PRINT_TO_ERRMSG_BUF("%s[%ld] is too large (= %e)",
| ~~^
| |
| long int
| %lld
uaselection.c:75:45: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
75 | PRINT_TO_ERRMSG_BUF("%s[%ld] is too large (= %e)",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
76 | what, i + 1, tmp2);
| ~~~~~
| |
| R_xlen_t {aka long long int}
global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
| ^~~~~~~~~~~
uaselection.c:75:51: note: format string is defined here
75 | PRINT_TO_ERRMSG_BUF("%s[%ld] is too large (= %e)",
| ~~^
| |
| long int
| %lld
uaselection.c:78:45: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
78 | PRINT_TO_ERRMSG_BUF("%s[[%d]][%ld] is too large (= %e)",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
79 | what, along + 1, i + 1, tmp2);
| ~~~~~
| |
| R_xlen_t {aka long long int}
global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
| ^~~~~~~~~~~
uaselection.c:78:57: note: format string is defined here
78 | PRINT_TO_ERRMSG_BUF("%s[[%d]][%ld] is too large (= %e)",
| ~~^
| |
| long int
| %lld
uaselection.c:78:45: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
78 | PRINT_TO_ERRMSG_BUF("%s[[%d]][%ld] is too large (= %e)",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
79 | what, along + 1, i + 1, tmp2);
| ~~~~~
| |
| R_xlen_t {aka long long int}
global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
| ^~~~~~~~~~~
uaselection.c:78:57: note: format string is defined here
78 | PRINT_TO_ERRMSG_BUF("%s[[%d]][%ld] is too large (= %e)",
| ~~^
| |
| long int
| %lld
uaselection.c: In function 'set_errmsg_for_uaselection_beyond_dim':
uaselection.c:199:25: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
199 | "%s starts[[%d]][%ld] "
| ^~~~~~~~~~~~~~~~~~~~~~~
200 | "> dimension %d in array",
201 | msg, along1, i + 1, along1);
| ~~~~~
| |
| R_xlen_t {aka long long int}
global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
| ^~~~~~~~~~~
uaselection.c:199:44: note: format string is defined here
199 | "%s starts[[%d]][%ld] "
| ~~^
| |
| long int
| %lld
uaselection.c:199:25: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
199 | "%s starts[[%d]][%ld] "
| ^~~~~~~~~~~~~~~~~~~~~~~
200 | "> dimension %d in array",
201 | msg, along1, i + 1, along1);
| ~~~~~
| |
| R_xlen_t {aka long long int}
global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
| ^~~~~~~~~~~
uaselection.c:199:44: note: format string is defined here
199 | "%s starts[[%d]][%ld] "
| ~~^
| |
| long int
| %lld
uaselection.c:204:25: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
204 | "%s starts[[%d]][%ld] + counts[[%d]][%ld] - 1 "
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
205 | "> dimension %d in array",
206 | msg, along1, i + 1, along1, i + 1, along1);
| ~~~~~
| |
| R_xlen_t {aka long long int}
global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
| ^~~~~~~~~~~
uaselection.c:204:44: note: format string is defined here
204 | "%s starts[[%d]][%ld] + counts[[%d]][%ld] - 1 "
| ~~^
| |
| long int
| %lld
uaselection.c:204:25: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
204 | "%s starts[[%d]][%ld] + counts[[%d]][%ld] - 1 "
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
205 | "> dimension %d in array",
206 | msg, along1, i + 1, along1, i + 1, along1);
| ~~~~~
| |
| R_xlen_t {aka long long int}
global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
| ^~~~~~~~~~~
uaselection.c:204:64: note: format string is defined here
204 | "%s starts[[%d]][%ld] + counts[[%d]][%ld] - 1 "
| ~~^
| |
| long int
| %lld
uaselection.c:204:25: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
204 | "%s starts[[%d]][%ld] + counts[[%d]][%ld] - 1 "
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
205 | "> dimension %d in array",
206 | msg, along1, i + 1, along1, i + 1, along1);
| ~~~~~
| |
| R_xlen_t {aka long long int}
global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
| ^~~~~~~~~~~
uaselection.c:204:44: note: format string is defined here
204 | "%s starts[[%d]][%ld] + counts[[%d]][%ld] - 1 "
| ~~^
| |
| long int
| %lld
uaselection.c:204:25: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
204 | "%s starts[[%d]][%ld] + counts[[%d]][%ld] - 1 "
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
205 | "> dimension %d in array",
206 | msg, along1, i + 1, along1, i + 1, along1);
| ~~~~~
| |
| R_xlen_t {aka long long int}
global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
| ^~~~~~~~~~~
uaselection.c:204:64: note: format string is defined here
204 | "%s starts[[%d]][%ld] + counts[[%d]][%ld] - 1 "
| ~~^
| |
| long int
| %lld
uaselection.c: In function 'set_errmsg_for_non_strictly_ascending_uaselection':
uaselection.c:217:37: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
217 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] <= starts[[%d]][%ld]",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
218 | msg, along1, i + 1, along1, i);
| ~~~~~
| |
| R_xlen_t {aka long long int}
global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
| ^~~~~~~~~~~
uaselection.c:217:56: note: format string is defined here
217 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] <= starts[[%d]][%ld]",
| ~~^
| |
| long int
| %lld
uaselection.c:217:37: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
217 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] <= starts[[%d]][%ld]",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
218 | msg, along1, i + 1, along1, i);
| ~
| |
| R_xlen_t {aka long long int}
global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
| ^~~~~~~~~~~
uaselection.c:217:77: note: format string is defined here
217 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] <= starts[[%d]][%ld]",
| ~~^
| |
| long int
| %lld
uaselection.c:217:37: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
217 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] <= starts[[%d]][%ld]",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
218 | msg, along1, i + 1, along1, i);
| ~~~~~
| |
| R_xlen_t {aka long long int}
global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
| ^~~~~~~~~~~
uaselection.c:217:56: note: format string is defined here
217 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] <= starts[[%d]][%ld]",
| ~~^
| |
| long int
| %lld
uaselection.c:217:37: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
217 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] <= starts[[%d]][%ld]",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
218 | msg, along1, i + 1, along1, i);
| ~
| |
| R_xlen_t {aka long long int}
global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
| ^~~~~~~~~~~
uaselection.c:217:77: note: format string is defined here
217 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] <= starts[[%d]][%ld]",
| ~~^
| |
| long int
| %lld
uaselection.c:220:37: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
220 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] < starts[[%d]][%ld] "
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
221 | " + counts[[%d]][%ld]",
222 | msg, along1, i + 1, along1, i, along1, i);
| ~~~~~
| |
| R_xlen_t {aka long long int}
global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
| ^~~~~~~~~~~
uaselection.c:220:56: note: format string is defined here
220 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] < starts[[%d]][%ld] "
| ~~^
| |
| long int
| %lld
uaselection.c:220:37: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
220 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] < starts[[%d]][%ld] "
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
221 | " + counts[[%d]][%ld]",
222 | msg, along1, i + 1, along1, i, along1, i);
| ~
| |
| R_xlen_t {aka long long int}
global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
| ^~~~~~~~~~~
uaselection.c:220:76: note: format string is defined here
220 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] < starts[[%d]][%ld] "
| ~~^
| |
| long int
| %lld
uaselection.c:220:37: warning: format '%ld' expects argument of type 'long int', but argument 10 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
220 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] < starts[[%d]][%ld] "
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
221 | " + counts[[%d]][%ld]",
222 | msg, along1, i + 1, along1, i, along1, i);
| ~
| |
| R_xlen_t {aka long long int}
global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
| ^~~~~~~~~~~
uaselection.c:220:37: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
220 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] < starts[[%d]][%ld] "
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
221 | " + counts[[%d]][%ld]",
222 | msg, along1, i + 1, along1, i, along1, i);
| ~~~~~
| |
| R_xlen_t {aka long long int}
global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
| ^~~~~~~~~~~
uaselection.c:220:56: note: format string is defined here
220 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] < starts[[%d]][%ld] "
| ~~^
| |
| long int
| %lld
uaselection.c:220:37: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
220 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] < starts[[%d]][%ld] "
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
221 | " + counts[[%d]][%ld]",
222 | msg, along1, i + 1, along1, i, along1, i);
| ~
| |
| R_xlen_t {aka long long int}
global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
| ^~~~~~~~~~~
uaselection.c:220:76: note: format string is defined here
220 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] < starts[[%d]][%ld] "
| ~~^
| |
| long int
| %lld
uaselection.c:220:37: warning: format '%ld' expects argument of type 'long int', but argument 10 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
220 | PRINT_TO_ERRMSG_BUF("%s starts[[%d]][%ld] < starts[[%d]][%ld] "
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
221 | " + counts[[%d]][%ld]",
222 | msg, along1, i + 1, along1, i, along1, i);
| ~
| |
| R_xlen_t {aka long long int}
global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
| ^~~~~~~~~~~
uaselection.c: In function 'get_untrusted_start':
uaselection.c:233:37: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
233 | PRINT_TO_ERRMSG_BUF("starts[[%d]][%ld] is < 1",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
234 | along + 1, i + 1);
| ~~~~~
| |
| R_xlen_t {aka long long int}
global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
| ^~~~~~~~~~~
uaselection.c:233:53: note: format string is defined here
233 | PRINT_TO_ERRMSG_BUF("starts[[%d]][%ld] is < 1",
| ~~^
| |
| long int
| %lld
uaselection.c:233:37: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
233 | PRINT_TO_ERRMSG_BUF("starts[[%d]][%ld] is < 1",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
234 | along + 1, i + 1);
| ~~~~~
| |
| R_xlen_t {aka long long int}
global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
| ^~~~~~~~~~~
uaselection.c:233:53: note: format string is defined here
233 | PRINT_TO_ERRMSG_BUF("starts[[%d]][%ld] is < 1",
| ~~^
| |
| long int
| %lld
uaselection.c: In function 'check_uaselection_along':
uaselection.c:288:45: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
288 | PRINT_TO_ERRMSG_BUF("counts[[%d]][%ld] is < 0",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
289 | along + 1, i + 1);
| ~~~~~
| |
| R_xlen_t {aka long long int}
global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
| ^~~~~~~~~~~
uaselection.c:288:61: note: format string is defined here
288 | PRINT_TO_ERRMSG_BUF("counts[[%d]][%ld] is < 0",
| ~~^
| |
| long int
| %lld
uaselection.c:288:45: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
288 | PRINT_TO_ERRMSG_BUF("counts[[%d]][%ld] is < 0",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
289 | along + 1, i + 1);
| ~~~~~
| |
| R_xlen_t {aka long long int}
global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
| ^~~~~~~~~~~
uaselection.c:288:61: note: format string is defined here
288 | PRINT_TO_ERRMSG_BUF("counts[[%d]][%ld] is < 0",
| ~~^
| |
| long int
| %lld
uaselection.c: In function 'check_ordered_uaselection_along':
uaselection.c:428:53: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
428 | PRINT_TO_ERRMSG_BUF("counts[[%d]][%ld] is < 0",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
429 | along + 1, i + 1);
| ~~~~~
| |
| R_xlen_t {aka long long int}
global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
| ^~~~~~~~~~~
uaselection.c:428:69: note: format string is defined here
428 | PRINT_TO_ERRMSG_BUF("counts[[%d]][%ld] is < 0",
| ~~^
| |
| long int
| %lld
uaselection.c:428:53: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
428 | PRINT_TO_ERRMSG_BUF("counts[[%d]][%ld] is < 0",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
429 | along + 1, i + 1);
| ~~~~~
| |
| R_xlen_t {aka long long int}
global_errmsg_buf.h:9:69: note: in definition of macro 'PRINT_TO_ERRMSG_BUF'
9 | snprintf(_HDF5Array_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
| ^~~~~~~~~~~
uaselection.c:428:69: note: format string is defined here
428 | PRINT_TO_ERRMSG_BUF("counts[[%d]][%ld] is < 0",
| ~~^
| |
| long int
| %lld
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-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
ChunkIterator.c: In function '_print_tchunk_info':
ChunkIterator.c:457:28: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
457 | Rprintf("%lu/%lu", i, chunk_iter->num_tchunks[along]);
| ~~^ ~
| | |
| | size_t {aka long long unsigned int}
| long unsigned int
| %llu
ChunkIterator.c:457:32: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
457 | Rprintf("%lu/%lu", i, chunk_iter->num_tchunks[along]);
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long unsigned int size_t {aka long long unsigned int}
| %llu
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-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
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-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 C:/Users/biocbuild/bbs-3.20-bioc/R/include/R_ext/Memory.h:36,
from C:/Users/biocbuild/bbs-3.20-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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-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 C:/Users/biocbuild/bbs-3.20-bioc/R/include/R_ext/Memory.h:36,
from C:/Users/biocbuild/bbs-3.20-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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-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 -LC:/Users/BIOCBU~1/BBS-3~1.20-/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 -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.20-bioc/R/library/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
* DONE (HDF5Array)
HDF5Array.Rcheck/tests/run_unitTests.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> require("HDF5Array") || stop("unable to load HDF5Array package")
Loading required package: HDF5Array
Loading required package: SparseArray
Loading required package: Matrix
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
union, unique, unsplit, which.max, which.min
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:Matrix':
expand, unname
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: S4Arrays
Loading required package: abind
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Attaching package: 'S4Arrays'
The following object is masked from 'package:abind':
abind
The following object is masked from 'package:base':
rowsum
Loading required package: DelayedArray
Attaching package: 'DelayedArray'
The following objects are masked from 'package:base':
apply, scale, sweep
Loading required package: rhdf5
Attaching package: 'HDF5Array'
The following object is masked from 'package:rhdf5':
h5ls
[1] TRUE
> HDF5Array:::.test()
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:SparseArray':
rowMedians
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\117~1.0\ZELLKO~1\115~1.1\ZELLKO~1.6\Lib\site-packages\anndata\_core\anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
warnings.warn(
C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\117~1.0\ZELLKO~1\115~1.1\ZELLKO~1.6\Lib\site-packages\anndata\_core\anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
warnings.warn(
automatic block size set to 77 bytes (was 1e+08)
automatic block size set to 1e+08 bytes (was 77)
automatic block size set to 77 bytes (was 1e+08)
automatic block size set to 1e+08 bytes (was 77)
RUNIT TEST PROTOCOL -- Tue Jul 16 00:52:05 2024
***********************************************
Number of test functions: 19
Number of errors: 0
Number of failures: 0
1 Test Suite :
HDF5Array RUnit Tests - 19 test functions, 0 errors, 0 failures
Number of test functions: 19
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
46.82 17.84 92.25
HDF5Array.Rcheck/HDF5Array-Ex.timings
| name | user | system | elapsed | |
| H5ADMatrix-class | 4.27 | 0.18 | 4.46 | |
| H5ADMatrixSeed-class | 0.07 | 0.05 | 0.11 | |
| H5File-class | 0.13 | 0.02 | 3.73 | |
| H5SparseMatrix-class | 0.47 | 0.21 | 0.69 | |
| H5SparseMatrixSeed-class | 0 | 0 | 0 | |
| HDF5Array-class | 2.34 | 0.25 | 6.93 | |
| HDF5ArraySeed-class | 0.09 | 0.04 | 0.15 | |
| ReshapedHDF5Array-class | 0.14 | 0.00 | 0.14 | |
| ReshapedHDF5ArraySeed-class | 0.07 | 0.00 | 0.06 | |
| TENxMatrix-class | 37.79 | 11.76 | 178.15 | |
| TENxMatrixSeed-class | 2.22 | 0.52 | 3.30 | |
| dump-management | 0.56 | 0.06 | 0.79 | |
| h5ls | 0.02 | 0.00 | 0.02 | |
| h5mread | 48.00 | 8.08 | 56.87 | |
| h5mread_from_reshaped | 0.20 | 0.01 | 0.38 | |
| h5writeDimnames | 0.61 | 0.19 | 1.29 | |
| saveHDF5SummarizedExperiment | 0.58 | 0.18 | 0.81 | |
| writeHDF5Array | 1.43 | 0.08 | 1.77 | |
| writeTENxMatrix | 19.38 | 1.31 | 21.47 | |