Lambda Moses
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/BUSpaRse |
| git_branch: master |
| git_last_commit: a3b907e |
| git_last_commit_date: 2021-10-26 12:53:45 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:05 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 BUSpaRse package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 229/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BUSpaRse 1.9.0 (landing page) Lambda Moses
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: BUSpaRse |
| Version: 1.9.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BUSpaRse.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings BUSpaRse_1.9.0.tar.gz |
| StartedAt: 2022-03-17 18:37:19 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:44:21 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 422.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BUSpaRse.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BUSpaRse.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings BUSpaRse_1.9.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/BUSpaRse.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BUSpaRse/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BUSpaRse' version '1.9.0'
* 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 whether package 'BUSpaRse' can be installed ... OK
* checking installed package size ... OK
* 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 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 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 for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/BUSpaRse/libs/x64/BUSpaRse.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
knee_plot 32.50 3.58 45.68
tr2g_TxDb 26.77 6.06 32.83
transcript2gene 12.36 0.27 20.96
dl_transcriptome 9.94 0.80 20.27
tr2g_EnsDb 2.78 2.33 5.13
tr2g_ensembl 3.43 0.05 21.75
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
'D:/biocbuild/bbs-3.15-bioc/meat/BUSpaRse.Rcheck/00check.log'
for details.
BUSpaRse.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL BUSpaRse
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'BUSpaRse' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppProgress/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppProgress/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c fill_cell_gene.cpp -o fill_cell_gene.o
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_adaptor.hpp:14,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/token_iterator.hpp:22,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/tokenizer.hpp:20,
from fill_cell_gene.cpp:16:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_<Pred>::************
^
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o BUSpaRse.dll tmp.def RcppExports.o fill_cell_gene.o -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRlapack -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-BUSpaRse/00new/BUSpaRse/libs/x64
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'BUSpaRse'
finding HTML links ... done
EC2gene html
annot_circular html
finding level-2 HTML links ... done
annots_from_fa_df html
cellranger_biotypes html
check_char1 html
check_genome html
check_gff html
check_tag_present html
check_tx html
dl_transcriptome html
dot-get_velocity_files html
ensembl_gene_biotypes html
ensembl_gff_mcols html
ensembl_gtf_mcols html
ensembl_tx_biotypes html
get_intron_flanks html
get_velocity_files html
knee_plot html
make_sparse_matrix html
match_style html
read_count_output html
read_velocity_output html
refseq_gff_mcols html
save_tr2g_bustools html
sort_tr2g html
species2dataset html
standardize_tags html
sub_annot html
subset_annot html
tr2g_EnsDb html
tr2g_GRanges html
tr2g_TxDb html
tr2g_ensembl html
tr2g_fasta html
tr2g_gff3 html
tr2g_gtf html
tr2g_junction html
transcript2gene html
validate_velocity_input html
write_velocity_output html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BUSpaRse)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'VanillaICE' is missing or broken
done
BUSpaRse.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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(BUSpaRse)
>
> test_check("BUSpaRse")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 102 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 102 ]
>
> proc.time()
user system elapsed
43.46 1.75 52.48
BUSpaRse.Rcheck/BUSpaRse-Ex.timings
| name | user | system | elapsed | |
| EC2gene | 0.03 | 0.00 | 0.03 | |
| annots_from_fa_df | 0.22 | 0.00 | 0.22 | |
| dl_transcriptome | 9.94 | 0.80 | 20.27 | |
| get_velocity_files | 0.92 | 0.15 | 1.08 | |
| knee_plot | 32.50 | 3.58 | 45.68 | |
| make_sparse_matrix | 0 | 0 | 0 | |
| read_count_output | 0 | 0 | 0 | |
| read_velocity_output | 0 | 0 | 0 | |
| save_tr2g_bustools | 0.28 | 0.03 | 0.31 | |
| sort_tr2g | 0.22 | 0.01 | 0.24 | |
| species2dataset | 0 | 0 | 0 | |
| subset_annot | 0.83 | 0.22 | 1.04 | |
| tr2g_EnsDb | 2.78 | 2.33 | 5.13 | |
| tr2g_TxDb | 26.77 | 6.06 | 32.83 | |
| tr2g_ensembl | 3.43 | 0.05 | 21.75 | |
| tr2g_fasta | 0.01 | 0.00 | 0.02 | |
| tr2g_gff3 | 0.70 | 0.02 | 0.72 | |
| tr2g_gtf | 0.47 | 0.04 | 0.51 | |
| transcript2gene | 12.36 | 0.27 | 20.96 | |