Aaron Lun
| Snapshot Date: 2024-05-30 18:28:32 -0400 (Thu, 30 May 2024) |
| git_url: https://git.bioconductor.org/packages/alabaster.base |
| git_branch: RELEASE_3_19 |
| git_last_commit: be210ea |
| git_last_commit_date: 2024-05-03 03:04:31 -0400 (Fri, 03 May 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-31 17:02:48 -0400 (Fri, 31 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (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 40/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| alabaster.base 1.4.1 (landing page) Aaron Lun
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
|
To the developers/maintainers of the alabaster.base package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/alabaster.base.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: alabaster.base |
| Version: 1.4.1 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:alabaster.base.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings alabaster.base_1.4.1.tar.gz |
| StartedAt: 2024-05-31 01:07:56 -0400 (Fri, 31 May 2024) |
| EndedAt: 2024-05-31 01:09:29 -0400 (Fri, 31 May 2024) |
| EllapsedTime: 93.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: alabaster.base.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:alabaster.base.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings alabaster.base_1.4.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/alabaster.base.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘alabaster.base/DESCRIPTION’ ... OK
* this is package ‘alabaster.base’ version ‘1.4.1’
* 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 ‘alabaster.base’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking C++ specification ... OK
Not all R platforms support C++17
* checking installed package size ... NOTE
installed size is 18.8Mb
sub-directories of 1Mb or more:
libs 17.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 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-3.19-bioc/R/site-library/alabaster.base/libs/alabaster.base.so’:
Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
Found ‘abort’, possibly from ‘abort’ (C)
Found ‘exit’, possibly from ‘exit’ (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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 3 NOTEs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/alabaster.base.Rcheck/00check.log’
for details.
alabaster.base.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL alabaster.base
###
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘alabaster.base’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++17
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c check_csv.cpp -o check_csv.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c check_list.cpp -o check_list.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c choose_numeric_missing_placeholder.cpp -o choose_numeric_missing_placeholder.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c is_rfc3339.cpp -o is_rfc3339.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c load_csv.cpp -o load_csv.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c load_list.cpp -o load_list.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c validate.cpp -o validate.o
In file included from ../inst/include/chihaya/validate.hpp:13,
from ../inst/include/chihaya/chihaya.hpp:10,
from ../inst/include/takane/utils_public.hpp:13,
from ../inst/include/takane/_validate.hpp:9,
from ../inst/include/takane/takane.hpp:4,
from validate.cpp:2:
../inst/include/chihaya/sparse_matrix.hpp: In function ‘void chihaya::sparse_matrix::internal::validate_indices(const H5::DataSet&, const std::vector<long unsigned int>&, size_t, size_t, bool) [with Index_ = long unsigned int]’:
../inst/include/chihaya/sparse_matrix.hpp:51:32: warning: ‘previous’ may be used uninitialized in this function [-Wmaybe-uninitialized]
51 | if (x > start && i <= previous) {
| ~~^~~~~~~~~~~
../inst/include/chihaya/sparse_matrix.hpp: In function ‘void chihaya::sparse_matrix::internal::validate_indices(const H5::DataSet&, const std::vector<long unsigned int>&, size_t, size_t, bool) [with Index_ = int]’:
../inst/include/chihaya/sparse_matrix.hpp:51:32: warning: ‘previous’ may be used uninitialized in this function [-Wmaybe-uninitialized]
51 | if (x > start && i <= previous) {
| ~~^~~~~~~~~~~
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o alabaster.base.so RcppExports.o check_csv.o check_list.o choose_numeric_missing_placeholder.o is_rfc3339.o load_csv.o load_list.o validate.o /home/biocbuild/bbs-3.19-bioc/R/site-library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/bbs-3.19-bioc/R/site-library/Rhdf5lib/lib/libhdf5.a -L/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -lz -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-alabaster.base/00new/alabaster.base/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (alabaster.base)
alabaster.base.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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(alabaster.base)
> test_check("alabaster.base")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 519 ]
>
> proc.time()
user system elapsed
49.052 1.110 40.597
alabaster.base.Rcheck/alabaster.base-Ex.timings
| name | user | system | elapsed | |
| Rfc3339 | 0.000 | 0.003 | 0.003 | |
| acquireFile | 0.552 | 0.020 | 0.548 | |
| altReadObject | 0.063 | 0.012 | 0.076 | |
| altSaveObject | 0.049 | 0.004 | 0.053 | |
| anyMissing | 0.000 | 0.001 | 0.000 | |
| chooseMissingPlaceholderForHdf5 | 0.000 | 0.002 | 0.002 | |
| createRedirection | 0.350 | 0.034 | 0.331 | |
| listObjects | 0.074 | 0.000 | 0.073 | |
| loadDirectory | 0.688 | 0.032 | 0.578 | |
| moveObject | 0.712 | 0.075 | 0.678 | |
| quickLoadObject | 0.592 | 0.033 | 0.520 | |
| quickReadCsv | 0.03 | 0.00 | 0.03 | |
| readAtomicVector | 0.014 | 0.000 | 0.014 | |
| readBaseFactor | 0.014 | 0.000 | 0.014 | |
| readBaseList | 0.059 | 0.008 | 0.067 | |
| readDataFrame | 0.045 | 0.004 | 0.049 | |
| readDataFrameFactor | 0.155 | 0.016 | 0.171 | |
| readObject | 0.051 | 0.000 | 0.051 | |
| readObjectFile | 0.001 | 0.000 | 0.001 | |
| removeObject | 0.565 | 0.008 | 0.484 | |
| saveAtomicVector | 0.019 | 0.000 | 0.019 | |
| saveBaseFactor | 0.004 | 0.004 | 0.008 | |
| saveBaseList | 0.036 | 0.000 | 0.036 | |
| saveDataFrameFactor | 0.078 | 0.004 | 0.082 | |
| saveFormats | 0.000 | 0.001 | 0.000 | |
| saveObject | 0.035 | 0.002 | 0.037 | |
| stageDataFrame | 0.037 | 0.000 | 0.038 | |
| transformVectorForHdf5 | 0.001 | 0.000 | 0.001 | |
| validateDirectory | 0.770 | 0.015 | 0.599 | |
| validateObject | 0.04 | 0.00 | 0.04 | |
| writeMetadata | 0.220 | 0.012 | 0.177 | |