Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:06:16 -0400 (Wed, 13 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
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 [email protected]:packages/BUSpaRse.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 231/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BUSpaRse 1.8.0 (landing page) Lambda Moses
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: BUSpaRse |
Version: 1.8.0 |
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BUSpaRse.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BUSpaRse_1.8.0.tar.gz |
StartedAt: 2022-04-12 16:43:11 -0400 (Tue, 12 Apr 2022) |
EndedAt: 2022-04-12 16:57:29 -0400 (Tue, 12 Apr 2022) |
EllapsedTime: 858.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BUSpaRse.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BUSpaRse.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BUSpaRse_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/BUSpaRse.Rcheck' * using R version 4.1.3 (2022-03-10) * 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 '1.8.0' * 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BUSpaRse/libs/i386/BUSpaRse.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (C) File 'C:/Users/biocbuild/bbs-3.14-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 ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed knee_plot 49.40 2.86 81.05 tr2g_TxDb 39.41 4.02 44.13 transcript2gene 25.11 0.22 31.51 dl_transcriptome 18.05 0.41 30.19 tr2g_ensembl 11.25 0.15 20.51 tr2g_EnsDb 3.92 1.52 5.43 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed knee_plot 41.72 2.59 55.86 tr2g_TxDb 34.74 3.63 38.39 transcript2gene 16.34 0.08 22.45 dl_transcriptome 14.39 0.45 23.11 tr2g_ensembl 8.01 0.15 12.53 tr2g_EnsDb 4.21 1.45 5.66 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... 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 'C:/Users/biocbuild/bbs-3.14-bioc/meat/BUSpaRse.Rcheck/00check.log' for details.
BUSpaRse.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/BUSpaRse_1.8.0.tar.gz && rm -rf BUSpaRse.buildbin-libdir && mkdir BUSpaRse.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BUSpaRse.buildbin-libdir BUSpaRse_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL BUSpaRse_1.8.0.zip && rm BUSpaRse_1.8.0.tar.gz BUSpaRse_1.8.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 58 88099 58 51090 0 0 312k 0 --:--:-- --:--:-- --:--:-- 311k 100 88099 100 88099 0 0 175k 0 --:--:-- --:--:-- --:--:-- 175k install for i386 * installing *source* package 'BUSpaRse' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppProgress/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppProgress/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fill_cell_gene.cpp -o fill_cell_gene.o In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_adaptor.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/token_iterator.hpp:22, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/tokenizer.hpp:20, from fill_cell_gene.cpp:16: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.14-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/mingw32/bin/g++ -shared -s -static-libgcc -o BUSpaRse.dll tmp.def RcppExports.o fill_cell_gene.o -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/BUSpaRse.buildbin-libdir/00LOCK-BUSpaRse/00new/BUSpaRse/libs/i386 ** 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 install for x64 * installing *source* package 'BUSpaRse' ... ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppProgress/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppProgress/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fill_cell_gene.cpp -o fill_cell_gene.o In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_adaptor.hpp:14, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/token_iterator.hpp:22, from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/tokenizer.hpp:20, from fill_cell_gene.cpp:16: C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.14-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 -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/BUSpaRse.buildbin-libdir/BUSpaRse/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'BUSpaRse' as BUSpaRse_1.8.0.zip * DONE (BUSpaRse) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'BUSpaRse' successfully unpacked and MD5 sums checked
BUSpaRse.Rcheck/tests_i386/testthat.Rout R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-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 60.50 2.65 69.04 |
BUSpaRse.Rcheck/tests_x64/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-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 56.54 1.32 62.78 |
BUSpaRse.Rcheck/examples_i386/BUSpaRse-Ex.timings
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BUSpaRse.Rcheck/examples_x64/BUSpaRse-Ex.timings
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