Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:12 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the mina package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mina.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 1137/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
mina 1.0.0 (landing page) Rui Guan
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: mina |
Version: 1.0.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mina.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings mina_1.0.0.tar.gz |
StartedAt: 2021-10-15 01:57:19 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 02:03:56 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 396.8 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: mina.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mina.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings mina_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/mina.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'mina/DESCRIPTION' ... OK * this is package 'mina' version '1.0.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Package which this enhances but not available for checking: 'doMC' * 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 'mina' can be installed ... OK * checking installed package size ... NOTE installed size is 10.3Mb sub-directories of 1Mb or more: data 7.4Mb libs 2.0Mb * 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 ... NOTE sparcc: no visible binding for global variable 'i' net_dis_indi,character-character: no visible binding for global variable 'out_dir' Undefined global functions or variables: i out_dir * 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 ... WARNING LazyData DB of 7.4 MB without LazyDataCompression set See ยง1.1.6 of 'Writing R Extensions' * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... 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-3.13-bioc/R/library/mina/libs/i386/mina.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-3.13-bioc/R/library/mina/libs/x64/mina.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 net_dis-mina 21.22 6.35 23.80 com_plot-mina 23.75 2.39 3.04 dis_stat_accessor 15.22 3.84 16.48 net_dis 11.70 1.40 9.19 bs_pm-mina 11.14 1.18 8.99 bs_pm 9.38 1.36 7.81 net_cls-mina 9.25 0.94 9.75 net_cls 6.38 0.26 6.34 net_cls-matrix 6.34 0.16 6.15 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed net_dis-mina 22.21 6.01 23.72 com_plot-mina 23.32 0.97 2.88 dis_stat_accessor 17.28 4.19 17.91 net_dis 12.26 1.19 9.04 bs_pm-mina 11.36 1.22 9.63 net_cls-mina 10.78 0.33 10.75 bs_pm 9.11 1.37 7.74 net_cls-matrix 7.65 0.28 7.53 net_cls 7.28 0.36 7.39 * 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 WARNING, 4 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/mina.Rcheck/00check.log' for details.
mina.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/mina_1.0.0.tar.gz && rm -rf mina.buildbin-libdir && mkdir mina.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=mina.buildbin-libdir mina_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL mina_1.0.0.zip && rm mina_1.0.0.tar.gz mina_1.0.0.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 2 4428k 2 101k 0 0 532k 0 0:00:08 --:--:-- 0:00:08 531k 52 4428k 52 2317k 0 0 1955k 0 0:00:02 0:00:01 0:00:01 1955k 100 4428k 100 4428k 0 0 2299k 0 0:00:01 0:00:01 --:--:-- 2299k install for i386 * installing *source* package 'mina' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cp_cor.cpp -o cp_cor.o C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o mina.dll tmp.def RcppExports.o cp_cor.o -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/mina.buildbin-libdir/00LOCK-mina/00new/mina/libs/i386 ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading Creating a new generic function for 'norm' in package 'mina' ** help *** installing help indices converting help for package 'mina' finding HTML links ... done adj-matrix html adj-mina html adj html adj_accessor html adj_method_list html bs_pm-mina html bs_pm html bs_pm_accessor html check_mina html check_mina_de html check_mina_qu html cls html cls_accessor html cls_tab html cls_tab_accessor html com_dis-matrix html com_dis-mina html com_dis html com_dis_list html com_plot-mina html com_plot html com_r2-mina html com_r2 html cp_cor html data-hmp html data-maize html des_accessor html dis_accessor html dis_stat_accessor html dmr-matrix html dmr-mina html dmr html dmr_accessor html filter_mat html fit_tabs-mina html fit_tabs html get_dis_df html get_net_cls_tab-matrix-data.frame-method html get_net_cls_tab html get_r2-mat html get_r2 html get_spectra html get_stat html hmp_des html hmp_otu html maize_asv html maize_asv2 html maize_des html maize_des2 html mat_or_NULL-class html mina-class html net_cls-matrix html net_cls-mina html net_cls html net_cls_tab-mina-method html net_cls_tab html net_dis-mina html net_dis html net_dis_accessor html net_dis_indi html norm_accessor html norm_by_raref html norm_by_total html norm_tab-matrix html norm_tab-mina html norm_tab html norm_tab_method_list html pcoa_plot html rarefaction_subsample html re_format_AP html re_format_MCL html sim_par html sparcc html tab_accessor html tina-matrix-method html tina 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 'mina' ... ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cp_cor.cpp -o cp_cor.o C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o mina.dll tmp.def RcppExports.o cp_cor.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/mina.buildbin-libdir/mina/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'mina' as mina_1.0.0.zip * DONE (mina) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'mina' successfully unpacked and MD5 sums checked
mina.Rcheck/examples_i386/mina-Ex.timings
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mina.Rcheck/examples_x64/mina-Ex.timings
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