| Back to Long Tests report for BioC 3.15 |
This page was generated on 2022-10-15 21:00:02 -0400 (Sat, 15 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4383 |
| 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: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 24/26 | Hostname | OS / Arch | CHECK | |||||||
| rhdf5 2.40.0 (landing page) Mike Smith
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | |||||||
| Package: rhdf5 |
| Version: 2.40.0 |
| Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no rhdf5_2.40.0.tar.gz |
| StartedAt: 2022-10-15 08:29:17 -0400 (Sat, 15 Oct 2022) |
| EndedAt: 2022-10-15 08:30:23 -0400 (Sat, 15 Oct 2022) |
| EllapsedTime: 65.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: rhdf5.Rcheck |
| Warnings: 0 |
rhdf5.Rcheck/tests/testthat.Rout
R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
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 0 | PASS 5 ]
>
> proc.time()
user system elapsed
17.450 23.716 42.194
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no rhdf5_2.40.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.15-bioc-longtests/meat/rhdf5.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘rhdf5/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rhdf5’ version ‘2.40.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘rhdf5’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 9.6Mb
sub-directories of 1Mb or more:
libs 9.1Mb
* 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 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 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 ... NOTE
H5Lexists: no visible global function definition for ‘head’
Undefined global functions or variables:
head
Consider adding
importFrom("utils", "head")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* 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 ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
Running ‘testthat.R’
OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.15-bioc-longtests/meat/rhdf5.Rcheck/00check.log’
for details.
rhdf5.Rcheck/00install.out
* installing *source* package ‘rhdf5’ ... ** using staged installation configure: creating ./config.status config.status: creating src/external_filters.h ** libs gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5.c -o H5.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5A.c -o H5A.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5D.c -o H5D.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5E.c -o H5E.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5F.c -o H5F.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5G.c -o H5G.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5I.c -o H5I.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5L.c -o H5L.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5O.c -o H5O.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5P.c -o H5P.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5R.c -o H5R.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5S.c -o H5S.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5S_extras.c -o H5S_extras.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5T.c -o H5T.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5Z.c -o H5Z.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5constants.c -o H5constants.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c HandleList.cpp -o HandleList.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c HandleListWrap.c -o HandleListWrap.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c bit64conversion.c -o bit64conversion.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c external_filters.c -o external_filters.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c h5dump.c -o h5dump.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c h5ls.c -o h5ls.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c h5testLock.c -o h5testLock.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c h5writeDataFrame.c -o h5writeDataFrame.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c printdatatype.c -o printdatatype.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c utils.c -o utils.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c wrap.c -o wrap.o g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.15-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-3.15-bioc/R/library/Rhdf5lib/lib/libhdf5.a -lcrypto -lcurl -lsz -laec -lz -ldl -lm -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.15-bioc-longtests/meat/rhdf5.Rcheck/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)