| Back to Multiple platform build/check report for BioC 3.17 |
|
This page was generated on 2023-04-12 10:55:41 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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 | ||||
|
To the developers/maintainers of the rhdf5 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rhdf5.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1691/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| rhdf5 2.43.4 (landing page) Mike Smith
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS | ||||||||||
| Package: rhdf5 |
| Version: 2.43.4 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:rhdf5.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings rhdf5_2.43.4.tar.gz |
| StartedAt: 2023-04-12 08:49:56 -0400 (Wed, 12 Apr 2023) |
| EndedAt: 2023-04-12 09:04:42 -0400 (Wed, 12 Apr 2023) |
| EllapsedTime: 885.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: rhdf5.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:rhdf5.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings rhdf5_2.43.4.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/rhdf5.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘rhdf5/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rhdf5’ version ‘2.43.4’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘rhdf5’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0’
* used C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0’
* checking installed package size ... NOTE
installed size is 18.2Mb
sub-directories of 1Mb or more:
libs 17.3Mb
* 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
* 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 loading without being on the library search path ... 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 ... 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 ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.17-bioc/R/site-library/rhdf5/libs/rhdf5.so’:
Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
Found ‘abort’, possibly from ‘abort’ (C)
Found ‘rand_r’, possibly from ‘rand_r’ (C)
Found ‘stderr’, possibly from ‘stderr’ (C)
Found ‘stdout’, possibly from ‘stdout’ (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 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 ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘practical_tips.Rmd’ using ‘UTF-8’... OK
‘rhdf5.Rmd’ using ‘UTF-8’... OK
‘rhdf5_cloud_reading.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/rhdf5.Rcheck/00check.log’
for details.
rhdf5.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL rhdf5 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘rhdf5’ ... ** using staged installation configure: creating ./config.status config.status: creating src/external_filters.h ** libs using C compiler: ‘gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0’ using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5.c -o H5.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5A.c -o H5A.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5D.c -o H5D.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5E.c -o H5E.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5F.c -o H5F.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5G.c -o H5G.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5I.c -o H5I.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5L.c -o H5L.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5O.c -o H5O.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5P.c -o H5P.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5R.c -o H5R.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5S.c -o H5S.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5S_extras.c -o H5S_extras.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5T.c -o H5T.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5Z.c -o H5Z.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5constants.c -o H5constants.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c HandleList.cpp -o HandleList.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c HandleListWrap.c -o HandleListWrap.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c bit64conversion.c -o bit64conversion.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c external_filters.c -o external_filters.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c h5dump.c -o h5dump.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c h5ls.c -o h5ls.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c h5testLock.c -o h5testLock.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c h5writeDataFrame.c -o h5writeDataFrame.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c printdatatype.c -o printdatatype.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c utils.c -o utils.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c wrap.c -o wrap.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o rhdf5.so H5.o H5A.o H5D.o H5E.o H5F.o H5G.o H5I.o H5L.o H5O.o H5P.o H5R.o H5S.o H5S_extras.o H5T.o H5Z.o H5constants.o HandleList.o HandleListWrap.o bit64conversion.o external_filters.o h5dump.o h5ls.o h5testLock.o h5writeDataFrame.o printdatatype.o utils.o wrap.o /home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/lib/libhdf5.a -lcrypto -lcurl -lsz -laec -lz -ldl -lm -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-rhdf5/00new/rhdf5/libs ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rhdf5)
rhdf5.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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.
> library(testthat)
> library(rhdf5)
>
> test_check("rhdf5")
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 1060 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On CRAN (2)
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 1060 ]
>
> proc.time()
user system elapsed
7.016 4.358 11.359
rhdf5.Rcheck/rhdf5-Ex.timings
| name | user | system | elapsed | |
| H5Dopen | 0.017 | 0.001 | 0.017 | |
| H5Fget_name | 0.012 | 0.002 | 0.014 | |
| H5Gget_info | 0.011 | 0.000 | 0.011 | |
| H5Iget_type | 0.003 | 0.000 | 0.003 | |
| H5Iis_valid | 0.002 | 0.000 | 0.002 | |
| H5Lcreate_external | 0.007 | 0.000 | 0.007 | |
| H5Ldelete | 0.005 | 0.000 | 0.005 | |
| H5Lmove | 0.033 | 0.000 | 0.033 | |
| H5Ocopy | 0.016 | 0.000 | 0.016 | |
| H5Olink | 0.006 | 0.000 | 0.006 | |
| H5Oopen | 0.016 | 0.000 | 0.016 | |
| H5P_create_intermediate_group | 0.002 | 0.000 | 0.002 | |
| H5Pset_fapl_ros3 | 0 | 0 | 0 | |
| H5R | 0.019 | 0.004 | 0.023 | |
| H5Scombine_hyperslab | 0.003 | 0.000 | 0.003 | |
| H5Scombine_select | 0.003 | 0.000 | 0.003 | |
| H5Sselect_hyperslab | 0.001 | 0.000 | 0.001 | |
| H5Sselect_index | 0.002 | 0.000 | 0.002 | |
| H5T_enum | 0.001 | 0.000 | 0.001 | |
| H5functions | 0 | 0 | 0 | |
| h5_FileLocking | 0 | 0 | 0 | |
| h5_createAttribute | 0.014 | 0.000 | 0.014 | |
| h5_createDataset | 0.147 | 0.000 | 0.149 | |
| h5_createFile | 0.017 | 0.000 | 0.017 | |
| h5_createGroup | 0.008 | 0.000 | 0.008 | |
| h5_dump | 0.021 | 0.000 | 0.021 | |
| h5_errorHandling | 0 | 0 | 0 | |
| h5_read | 0.037 | 0.003 | 0.041 | |
| h5_save | 0.038 | 0.000 | 0.038 | |
| h5_set_extent | 0.016 | 0.000 | 0.016 | |
| h5_write | 0.027 | 0.000 | 0.028 | |
| h5closeAll | 0.012 | 0.000 | 0.012 | |
| h5constants | 0 | 0 | 0 | |
| h5listObjects | 0.004 | 0.000 | 0.004 | |
| h5ls | 0.018 | 0.000 | 0.018 | |
| h5version | 0.004 | 0.000 | 0.003 | |