Lambda Moses
| Snapshot Date: 2025-01-24 13:40 -0500 (Fri, 24 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/BUSpaRse |
| git_branch: devel |
| git_last_commit: 0e32057 |
| git_last_commit_date: 2024-10-29 19:12:35 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-25 15:38 -0500 (Sat, 25 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4658 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4455 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4408 |
| 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 255/2286 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BUSpaRse 1.21.0 (landing page) Lambda Moses
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the BUSpaRse package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BUSpaRse.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: BUSpaRse |
| Version: 1.21.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:BUSpaRse.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BUSpaRse_1.21.0.tar.gz |
| StartedAt: 2025-01-25 05:09:39 -0000 (Sat, 25 Jan 2025) |
| EndedAt: 2025-01-25 05:20:05 -0000 (Sat, 25 Jan 2025) |
| EllapsedTime: 626.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BUSpaRse.Rcheck |
| Warnings: 5 |
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### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:BUSpaRse.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BUSpaRse_1.21.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/BUSpaRse.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BUSpaRse/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BUSpaRse’ version ‘1.21.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 ‘BUSpaRse’ can be installed ... WARNING
Found the following significant warnings:
Warning: program compiled against libxml 212 using older 211
See ‘/home/biocbuild/bbs-3.21-bioc/meat/BUSpaRse.Rcheck/00install.out’ for details.
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* 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 ...Warning: program compiled against libxml 212 using older 211
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 ... NOTE
Warning: program compiled against libxml 212 using older 211
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* 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
Warning: program compiled against libxml 212 using older 211
* checking S3 generic/method consistency ... WARNING
Warning: program compiled against libxml 212 using older 211
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Warning: program compiled against libxml 212 using older 211
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Warning: program compiled against libxml 212 using older 211
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
Warning: program compiled against libxml 212 using older 211
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
annot_circular.Rd: BSgenome, XStringSet, genomeStyles, seqlevels
check_genome.Rd: BSgenome, XStringSet, genomeStyles
dl_transcriptome.Rd: listEnsemblArchives
dot-get_velocity_files.Rd: str_length, BSgenome, XStringSet,
genomeStyles
get_velocity_files.Rd: TxDb, EnsDb, str_length, BSgenome, XStringSet,
genomeStyles
match_style.Rd: BSgenome, XStringSet, genomeStyles, seqlevels
subset_annot.Rd: BSgenome, XStringSet, genomeStyles
tr2g_EnsDb.Rd: BSgenome, XStringSet, genomeStyles, columns
tr2g_GRanges.Rd: GRanges, BSgenome, XStringSet, genomeStyles
tr2g_TxDb.Rd: TxDb, BSgenome, XStringSet, genomeStyles
tr2g_ensembl.Rd: listAttributes, listEnsemblArchives, useMart
tr2g_gff3.Rd: BSgenome, XStringSet, genomeStyles
tr2g_gtf.Rd: BSgenome, XStringSet, genomeStyles
transcript2gene.Rd: useMart
validate_velocity_input.Rd: str_length, BSgenome, XStringSet,
genomeStyles
write_velocity_output.Rd: BSgenome, XStringSet, genomeStyles
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... WARNING
Warning: program compiled against libxml 212 using older 211
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
* checking Rd \usage sections ... NOTE
Warning: program compiled against libxml 212 using older 211
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
tr2g_TxDb 39.896 2.451 47.293
knee_plot 24.493 2.221 36.443
dl_transcriptome 9.094 2.363 61.426
transcript2gene 5.855 0.111 16.787
tr2g_ensembl 1.802 0.127 20.214
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 5 WARNINGs, 9 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/BUSpaRse.Rcheck/00check.log’
for details.
BUSpaRse.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD INSTALL BUSpaRse
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘BUSpaRse’ ...
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
using C++11
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppProgress/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppProgress/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c fill_cell_gene.cpp -o fill_cell_gene.o
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/iterator/iterator_adaptor.hpp:14,
from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/token_iterator.hpp:22,
from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/tokenizer.hpp:20,
from fill_cell_gene.cpp:16:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
| -
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
| -
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| -
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
| -
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o BUSpaRse.so RcppExports.o fill_cell_gene.o -lopenblas -lgfortran -lm -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-BUSpaRse/00new/BUSpaRse/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning: program compiled against libxml 212 using older 211
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: program compiled against libxml 212 using older 211
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: program compiled against libxml 212 using older 211
** testing if installed package keeps a record of temporary installation path
* DONE (BUSpaRse)
BUSpaRse.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(BUSpaRse)
Warning: program compiled against libxml 212 using older 211
>
> test_check("BUSpaRse")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 102 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 102 ]
>
> proc.time()
user system elapsed
54.092 1.345 63.714
BUSpaRse.Rcheck/BUSpaRse-Ex.timings
| name | user | system | elapsed | |
| EC2gene | 0.065 | 0.000 | 0.066 | |
| annots_from_fa_df | 0.203 | 0.008 | 0.212 | |
| dl_transcriptome | 9.094 | 2.363 | 61.426 | |
| get_velocity_files | 1.975 | 0.363 | 2.347 | |
| knee_plot | 24.493 | 2.221 | 36.443 | |
| make_sparse_matrix | 0.003 | 0.001 | 0.004 | |
| read_count_output | 0.010 | 0.003 | 0.015 | |
| read_velocity_output | 0.005 | 0.000 | 0.005 | |
| save_tr2g_bustools | 0.536 | 0.004 | 0.546 | |
| sort_tr2g | 0.431 | 0.022 | 0.456 | |
| species2dataset | 0 | 0 | 0 | |
| subset_annot | 1.496 | 0.055 | 1.617 | |
| tr2g_EnsDb | 3.749 | 0.609 | 4.582 | |
| tr2g_TxDb | 39.896 | 2.451 | 47.293 | |
| tr2g_ensembl | 1.802 | 0.127 | 20.214 | |
| tr2g_fasta | 0.026 | 0.000 | 0.026 | |
| tr2g_gff3 | 1.200 | 0.020 | 1.224 | |
| tr2g_gtf | 0.877 | 0.024 | 0.903 | |
| transcript2gene | 5.855 | 0.111 | 16.787 | |