Rui Guan
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/mina |
| git_branch: master |
| git_last_commit: 5317203 |
| git_last_commit_date: 2021-10-26 13:05:26 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:02 -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 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 1158/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| mina 1.3.0 (landing page) Rui Guan
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: mina |
| Version: 1.3.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:mina.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings mina_1.3.0.tar.gz |
| StartedAt: 2022-03-17 19:35:40 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:39:48 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 248.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: mina.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:mina.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings mina_1.3.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/mina.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 'mina/DESCRIPTION' ... OK
* this is package 'mina' version '1.3.0'
* 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 9.4Mb
sub-directories of 1Mb or more:
data 7.4Mb
* 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 ... NOTE
sparcc: no visible binding for global variable 'i'
net_dis_pcoa,character: no visible binding for global variable 'y'
net_dis_pcoa,character: no visible binding for global variable 'Group'
net_dis_plot,mina: no visible binding for global variable 'Group1'
net_dis_plot,mina: no visible binding for global variable 'Group2'
net_dis_plot,mina: no visible binding for global variable 'Distance'
net_dis_plot,mina: no visible binding for global variable 'Sig'
Undefined global functions or variables:
Distance Group Group1 Group2 Sig i y
* 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 x64 is not available
File 'D:/biocbuild/bbs-3.15-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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
net_dis_plot 26.47 24.62 46.97
com_plot-mina 31.00 13.36 3.27
net_dis-mina 14.55 12.60 25.09
dis_stat_accessor 10.98 7.00 15.49
net_cls-mina 8.95 1.15 9.86
bs_pm-mina 6.44 1.84 6.72
net_cls 5.99 0.92 6.50
net_cls-matrix 5.62 0.48 5.77
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/mina.Rcheck/00check.log'
for details.
mina.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL mina
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'mina' ...
** 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/RcppParallel/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/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/RcppParallel/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-mina/00new/mina/libs/x64
** 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_contrast html
get_contrast_grp html
get_dis_df html
get_ja html
get_ja0 html
get_ja0_grp html
get_ja_grp html
get_net_cls_tab-matrix-data.frame-method
html
get_net_cls_tab html
get_r2-mat html
get_r2 html
get_rep-matrix html
get_rep-mima 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
net_dis_pcoa html
net_dis_plot html
net_grp_cmp html
net_node_cmp 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
* DONE (mina)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'DelayedArray' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'tweeDEseq' is missing or broken
done
mina.Rcheck/mina-Ex.timings
| name | user | system | elapsed | |
| adj-matrix | 0.34 | 0.05 | 0.30 | |
| adj-mina | 0.52 | 0.08 | 0.40 | |
| adj | 0.85 | 0.06 | 0.53 | |
| adj_method_list | 0.05 | 0.05 | 0.13 | |
| bs_pm-mina | 6.44 | 1.84 | 6.72 | |
| bs_pm | 2.06 | 0.77 | 2.39 | |
| check_mina | 0.06 | 0.05 | 0.11 | |
| check_mina_de | 0.07 | 0.03 | 0.10 | |
| check_mina_qu | 0.06 | 0.03 | 0.10 | |
| cls_tab | 0.05 | 0.08 | 0.13 | |
| com_dis-matrix | 1.00 | 0.01 | 0.27 | |
| com_dis-mina | 0.80 | 0.02 | 0.08 | |
| com_dis | 1.87 | 0.08 | 0.30 | |
| com_dis_list | 0.10 | 0.05 | 0.14 | |
| com_plot-mina | 31.00 | 13.36 | 3.27 | |
| com_plot | 0.11 | 0.01 | 0.13 | |
| com_r2-mina | 1.28 | 0.08 | 0.44 | |
| com_r2 | 1.54 | 0.73 | 0.70 | |
| data-hmp | 0 | 0 | 0 | |
| data-maize | 0 | 0 | 0 | |
| des_accessor | 0 | 0 | 0 | |
| dis_accessor | 0.96 | 0.02 | 0.06 | |
| dis_stat_accessor | 10.98 | 7.00 | 15.49 | |
| dmr-matrix | 1.13 | 0.05 | 0.33 | |
| dmr-mina | 1.39 | 0.08 | 0.49 | |
| dmr | 1.67 | 0.10 | 0.44 | |
| dmr_accessor | 1.98 | 0.02 | 0.47 | |
| fit_tabs-mina | 0.57 | 0.49 | 1.04 | |
| fit_tabs | 0.72 | 0.31 | 1.03 | |
| get_net_cls_tab-matrix-data.frame-method | 1.29 | 0.33 | 1.34 | |
| get_net_cls_tab | 1.35 | 0.71 | 1.68 | |
| get_r2-mat | 1.34 | 0.06 | 0.59 | |
| get_r2 | 2.23 | 0.13 | 0.71 | |
| get_rep-matrix | 0.21 | 0.08 | 0.28 | |
| get_rep-mima | 0.58 | 0.17 | 0.75 | |
| hmp_des | 0 | 0 | 0 | |
| hmp_otu | 0 | 0 | 0 | |
| maize_asv | 0 | 0 | 0 | |
| maize_asv2 | 0 | 0 | 0 | |
| maize_des | 0 | 0 | 0 | |
| maize_des2 | 0 | 0 | 0 | |
| mina-class | 0 | 0 | 0 | |
| net_cls-matrix | 5.62 | 0.48 | 5.77 | |
| net_cls-mina | 8.95 | 1.15 | 9.86 | |
| net_cls | 5.99 | 0.92 | 6.50 | |
| net_cls_tab-mina-method | 1.37 | 0.22 | 1.33 | |
| net_cls_tab | 1.11 | 0.47 | 1.13 | |
| net_dis-mina | 14.55 | 12.60 | 25.09 | |
| net_dis | 1.69 | 1.08 | 2.39 | |
| net_dis_indi | 0 | 0 | 0 | |
| net_dis_pcoa | 0.00 | 0.01 | 0.02 | |
| net_dis_plot | 26.47 | 24.62 | 46.97 | |
| net_grp_cmp | 0 | 0 | 0 | |
| net_node_cmp | 0 | 0 | 0 | |
| norm_accessor | 0.03 | 0.00 | 0.03 | |
| norm_tab-matrix | 0.68 | 0.02 | 0.71 | |
| norm_tab-mina | 0.61 | 0.17 | 0.78 | |
| norm_tab | 0.03 | 0.00 | 0.03 | |
| norm_tab_method_list | 0.07 | 0.02 | 0.10 | |
| pcoa_plot | 1.51 | 0.17 | 0.80 | |
| sim_par | 0.00 | 0.02 | 0.01 | |
| sparcc | 0 | 0 | 0 | |
| tab_accessor | 0.00 | 0.02 | 0.02 | |
| tina-matrix-method | 0 | 0 | 0 | |
| tina | 0.00 | 0.02 | 0.02 | |