Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

This page was generated on 2024-06-18 17:59 -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 1763/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rhdf5lib 1.26.0  (landing page)
Mike Smith
Snapshot Date: 2024-06-16 14:00 -0400 (Sun, 16 Jun 2024)
git_url: https://git.bioconductor.org/packages/Rhdf5lib
git_branch: RELEASE_3_19
git_last_commit: 9755392
git_last_commit_date: 2024-04-30 10:58:46 -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    OK    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


CHECK results for Rhdf5lib on palomino3

To the developers/maintainers of the Rhdf5lib package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rhdf5lib.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: Rhdf5lib
Version: 1.26.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Rhdf5lib.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings Rhdf5lib_1.26.0.tar.gz
StartedAt: 2024-06-17 10:12:34 -0400 (Mon, 17 Jun 2024)
EndedAt: 2024-06-17 10:15:47 -0400 (Mon, 17 Jun 2024)
EllapsedTime: 193.5 seconds
RetCode: 0
Status:   OK  
CheckDir: Rhdf5lib.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Rhdf5lib.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings Rhdf5lib_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib.Rcheck'
* using R version 4.4.0 (2024-04-24 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 'Rhdf5lib/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Rhdf5lib' version '1.26.0'
* 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
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* checking installed package size ... NOTE
  installed size is 18.9Mb
  sub-directories of 1Mb or more:
    include   2.5Mb
    lib      13.4Mb
    libs      2.8Mb
* 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 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 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 ... 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 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.19-bioc/R/library/Rhdf5lib/libs/x64/Rhdf5lib.dll':
  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 files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'tinytest.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'F:/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib.Rcheck/00check.log'
for details.


Installation output

Rhdf5lib.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL Rhdf5lib
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'Rhdf5lib' ...
** using staged installation
untarring hdf5_headers_1.10.7.tar.gz ...
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
mkdir -p "F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/x64-ucrt" "F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
"F:/biocbuild/bbs-3.19-bioc/R/bin/x64/Rscript.exe" "../tools/copy_hdf5_files.R" "F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/x64-ucrt" "F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
Copying libraries
Copying headers
Done
"F:/biocbuild/bbs-3.19-bioc/R/bin/x64/Rscript.exe" "../tools/winlibs.R" "F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/x64-ucrt"
Copying libcurl etc
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I"F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Rhdf5lib.c -o Rhdf5lib.o
gcc -shared -s -static-libgcc -o Rhdf5lib.dll tmp.def Rhdf5lib.o F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/x64-ucrt/libhdf5.a F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/x64-ucrt/libsz.a F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/x64-ucrt/libaec.a -lpsapi -lz -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/R/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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
* DONE (Rhdf5lib)

Tests output

Rhdf5lib.Rcheck/tests/tinytest.Rout


R version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
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.

> if ( requireNamespace("tinytest", quietly=TRUE) ) {
+   tinytest::test_package("Rhdf5lib")
+ }

test_library_version.R........    1 tests OK 
test_library_version.R........    2 tests OK 59ms

test_link_flags.R.............    0 tests    
test_link_flags.R.............    0 tests    
test_link_flags.R.............    0 tests    
test_link_flags.R.............    0 tests    
test_link_flags.R.............    0 tests    
test_link_flags.R.............    1 tests OK 
test_link_flags.R.............    2 tests OK 
test_link_flags.R.............    3 tests OK 
test_link_flags.R.............    4 tests OK 
test_link_flags.R.............    5 tests OK 
test_link_flags.R.............    6 tests OK 
test_link_flags.R.............    7 tests OK 
test_link_flags.R.............    8 tests OK 1.5s
All ok, 10 results (1.5s)
> 
> proc.time()
   user  system elapsed 
   0.56    4.18    4.79 

Example timings

Rhdf5lib.Rcheck/Rhdf5lib-Ex.timings

nameusersystemelapsed
getHdf5Version000
pkgconfig0.010.020.03