Rui Guan
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/mina |
| git_branch: RELEASE_3_13 |
| git_last_commit: 7bf29d4 |
| git_last_commit_date: 2021-05-19 12:58:14 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
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 |
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### 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
###
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* 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
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###
### 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
###
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% 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
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mina.Rcheck/examples_i386/mina-Ex.timings
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mina.Rcheck/examples_x64/mina-Ex.timings
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