| Back to Using R 4.1.3 to BUILD/CHECK a small subset of 3.18 packages |
This page was generated on 2024-03-08 16:41:48 -0500 (Fri, 08 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 655 |
| 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 90/118 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||||
| rhdf5 2.46.1 (landing page) Mike Smith
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ||||||||
|
To the developers/maintainers of the rhdf5 package: - 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: rhdf5 |
| Version: 2.46.1 |
| Command: /home/hpages/bbs-3.18-bioc-R41/R/bin/R CMD check --install=check:rhdf5.install-out.txt --library=/home/hpages/bbs-3.18-bioc-R41/R/site-library --timings rhdf5_2.46.1.tar.gz |
| StartedAt: 2024-03-08 16:14:15 -0500 (Fri, 08 Mar 2024) |
| EndedAt: 2024-03-08 16:27:59 -0500 (Fri, 08 Mar 2024) |
| EllapsedTime: 824.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: rhdf5.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/hpages/bbs-3.18-bioc-R41/R/bin/R CMD check --install=check:rhdf5.install-out.txt --library=/home/hpages/bbs-3.18-bioc-R41/R/site-library --timings rhdf5_2.46.1.tar.gz
###
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##############################################################################
* using log directory ‘/home/hpages/bbs-3.18-bioc-R41/meat/rhdf5.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘rhdf5/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rhdf5’ version ‘2.46.1’
* 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
* checking installed package size ... NOTE
installed size is 13.2Mb
sub-directories of 1Mb or more:
libs 12.3Mb
* 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 ... NOTE
Namespace in Imports field not imported from: ‘S4Vectors’
All declared Imports should be used.
* 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 ... NOTE
Note: information on .o files is not available
File ‘/home/hpages/bbs-3.18-bioc-R41/R/site-library/rhdf5/libs/rhdf5.so’:
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. 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: 4 NOTEs
See
‘/home/hpages/bbs-3.18-bioc-R41/meat/rhdf5.Rcheck/00check.log’
for details.
rhdf5.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/hpages/bbs-3.18-bioc-R41/R/bin/R CMD INSTALL rhdf5 ### ############################################################################## ############################################################################## * installing to library ‘/home/hpages/bbs-3.18-bioc-R41/R/site-library’ * installing *source* package ‘rhdf5’ ... ** using staged installation configure: creating ./config.status config.status: creating src/external_filters.h ** libs gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5.c -o H5.o gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5A.c -o H5A.o gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5D.c -o H5D.o gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5E.c -o H5E.o gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5F.c -o H5F.o gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5G.c -o H5G.o gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5I.c -o H5I.o gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5L.c -o H5L.o gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5O.c -o H5O.o gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5P.c -o H5P.o gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5R.c -o H5R.o gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5S.c -o H5S.o gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5S_extras.c -o H5S_extras.o gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5T.c -o H5T.o gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5T_extras.c -o H5T_extras.o gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5Z.c -o H5Z.o gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5constants.c -o H5constants.o g++ -std=gnu++14 -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c HandleList.cpp -o HandleList.o gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c HandleListWrap.c -o HandleListWrap.o gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c bit64conversion.c -o bit64conversion.o gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c external_filters.c -o external_filters.o gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c h5dump.c -o h5dump.o gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c h5ls.c -o h5ls.o gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c h5testLock.c -o h5testLock.o gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c h5writeDataFrame.c -o h5writeDataFrame.o gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c printdatatype.c -o printdatatype.o gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c utils.c -o utils.o gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c wrap.c -o wrap.o g++ -std=gnu++14 -shared -L/home/hpages/bbs-3.18-bioc-R41/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 H5T_extras.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/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/lib/libhdf5.a -L/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -L/home/hpages/bbs-3.18-bioc-R41/R/lib -lR installing to /home/hpages/bbs-3.18-bioc-R41/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 version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 1075 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• On CRAN (2): 'test_S3.R:19:9', 'test_S3.R:28:9'
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 1075 ]
>
> proc.time()
user system elapsed
7.563 2.317 9.869
rhdf5.Rcheck/rhdf5-Ex.timings
| name | user | system | elapsed | |
| H5Dopen | 0.015 | 0.000 | 0.015 | |
| H5Fget_name | 0.000 | 0.002 | 0.003 | |
| H5Gget_info | 0.005 | 0.004 | 0.010 | |
| H5Iget_type | 0.002 | 0.000 | 0.002 | |
| H5Iis_valid | 0.002 | 0.000 | 0.002 | |
| H5Lcreate_external | 0.006 | 0.000 | 0.006 | |
| H5Ldelete | 0.004 | 0.000 | 0.004 | |
| H5Lmove | 0.023 | 0.000 | 0.024 | |
| H5Ocopy | 0.013 | 0.000 | 0.014 | |
| H5Olink | 0.01 | 0.00 | 0.01 | |
| H5Oopen | 0.013 | 0.000 | 0.013 | |
| H5P_create_intermediate_group | 0.001 | 0.000 | 0.001 | |
| H5Pset_fapl_ros3 | 0 | 0 | 0 | |
| H5R | 0.016 | 0.000 | 0.015 | |
| H5Scombine_hyperslab | 0.003 | 0.000 | 0.002 | |
| H5Scombine_select | 0.003 | 0.000 | 0.002 | |
| H5Sselect_hyperslab | 0.001 | 0.000 | 0.001 | |
| H5Sselect_index | 0.001 | 0.000 | 0.002 | |
| H5T_enum | 0.001 | 0.000 | 0.000 | |
| H5functions | 0 | 0 | 0 | |
| h5_FileLocking | 0.000 | 0.000 | 0.001 | |
| h5_createAttribute | 0.012 | 0.000 | 0.011 | |
| h5_createDataset | 0.109 | 0.003 | 0.113 | |
| h5_createFile | 0.003 | 0.004 | 0.007 | |
| h5_createGroup | 0.006 | 0.004 | 0.011 | |
| h5_dump | 0.014 | 0.000 | 0.015 | |
| h5_errorHandling | 0 | 0 | 0 | |
| h5_read | 0.022 | 0.004 | 0.026 | |
| h5_save | 0.025 | 0.000 | 0.025 | |
| h5_set_extent | 0.011 | 0.000 | 0.012 | |
| h5_write | 0.02 | 0.00 | 0.02 | |
| h5closeAll | 0.004 | 0.000 | 0.005 | |
| h5constants | 0.001 | 0.000 | 0.000 | |
| h5listObjects | 0.000 | 0.003 | 0.003 | |
| h5ls | 0.014 | 0.001 | 0.013 | |
| h5version | 0.003 | 0.000 | 0.003 | |