| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-01-02 09:00:38 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| 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: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1189/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| mina 1.7.0 (landing page) Rui Guan
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ||||||||
| Package: mina |
| Version: 1.7.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:mina.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings mina_1.7.0.tar.gz |
| StartedAt: 2022-12-29 01:23:40 -0500 (Thu, 29 Dec 2022) |
| EndedAt: 2022-12-29 01:27:14 -0500 (Thu, 29 Dec 2022) |
| EllapsedTime: 213.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: mina.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:mina.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings mina_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/mina.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'mina/DESCRIPTION' ... OK
* this is package 'mina' version '1.7.0'
* 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
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* checking installed package size ... NOTE
installed size is 8.9Mb
sub-directories of 1Mb or more:
data 7.4Mb
libs 1.0Mb
* 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
* 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 'F:/biocbuild/bbs-3.17-bioc/R/library/mina/libs/x64/mina.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
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 nor [v]sprintf. 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 28.55 5.14 28.69
com_plot-mina 21.03 4.86 3.46
net_dis-mina 14.62 2.70 14.97
dis_stat_accessor 11.23 1.82 11.17
net_cls-mina 8.04 0.52 8.33
bs_pm-mina 6.56 0.84 5.77
net_cls 5.99 0.16 5.80
net_cls-matrix 5.65 0.19 5.55
* 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
'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/mina.Rcheck/00check.log'
for details.
mina.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL mina ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'mina' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 12.2.0' g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cp_cor.cpp -o cp_cor.o g++ -std=gnu++11 -shared -s -static-libgcc -o mina.dll tmp.def RcppExports.o cp_cor.o -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.17-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 ** 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)
mina.Rcheck/mina-Ex.timings
| name | user | system | elapsed | |
| adj-matrix | 0.53 | 0.11 | 0.31 | |
| adj-mina | 0.72 | 0.04 | 0.42 | |
| adj | 0.87 | 0.03 | 0.53 | |
| adj_method_list | 0.07 | 0.02 | 0.45 | |
| bs_pm-mina | 6.56 | 0.84 | 5.77 | |
| bs_pm | 1.86 | 0.69 | 2.21 | |
| check_mina | 0.06 | 0.00 | 0.06 | |
| check_mina_de | 0.06 | 0.00 | 0.07 | |
| check_mina_qu | 0.05 | 0.02 | 0.06 | |
| cls_tab | 0.05 | 0.03 | 0.08 | |
| com_dis-matrix | 0.26 | 0.04 | 0.25 | |
| com_dis-mina | 0.36 | 0.03 | 0.08 | |
| com_dis | 0.67 | 0.01 | 0.30 | |
| com_dis_list | 0.13 | 0.03 | 0.15 | |
| com_plot-mina | 21.03 | 4.86 | 3.46 | |
| com_plot | 0.12 | 0.03 | 0.15 | |
| com_r2-mina | 0.83 | 0.02 | 0.41 | |
| com_r2 | 0.91 | 0.30 | 0.66 | |
| data-hmp | 0.00 | 0.01 | 0.01 | |
| data-maize | 0 | 0 | 0 | |
| des_accessor | 0.01 | 0.00 | 0.01 | |
| dis_accessor | 0.46 | 0.00 | 0.07 | |
| dis_stat_accessor | 11.23 | 1.82 | 11.17 | |
| dmr-matrix | 0.71 | 0.01 | 0.33 | |
| dmr-mina | 0.71 | 0.03 | 0.33 | |
| dmr | 0.71 | 0.01 | 0.31 | |
| dmr_accessor | 0.31 | 0.02 | 0.33 | |
| fit_tabs-mina | 0.52 | 0.03 | 0.54 | |
| fit_tabs | 1.20 | 0.20 | 1.41 | |
| get_net_cls_tab-matrix-data.frame-method | 1.17 | 0.16 | 1.09 | |
| get_net_cls_tab | 1.44 | 0.12 | 1.22 | |
| get_r2-mat | 0.94 | 0.00 | 0.59 | |
| get_r2 | 0.37 | 0.08 | 0.46 | |
| get_rep-matrix | 0.27 | 0.08 | 0.34 | |
| get_rep-mima | 0.68 | 0.03 | 0.72 | |
| hmp_des | 0.00 | 0.02 | 0.01 | |
| hmp_otu | 0.02 | 0.00 | 0.02 | |
| maize_asv | 0.01 | 0.00 | 0.01 | |
| maize_asv2 | 0.00 | 0.01 | 0.02 | |
| maize_des | 0 | 0 | 0 | |
| maize_des2 | 0 | 0 | 0 | |
| mina-class | 0 | 0 | 0 | |
| net_cls-matrix | 5.65 | 0.19 | 5.55 | |
| net_cls-mina | 8.04 | 0.52 | 8.33 | |
| net_cls | 5.99 | 0.16 | 5.80 | |
| net_cls_tab-mina-method | 1.62 | 0.09 | 1.34 | |
| net_cls_tab | 1.08 | 0.17 | 1.03 | |
| net_dis-mina | 14.62 | 2.70 | 14.97 | |
| net_dis | 1.83 | 0.79 | 2.35 | |
| net_dis_indi | 0 | 0 | 0 | |
| net_dis_pcoa | 0 | 0 | 0 | |
| net_dis_plot | 28.55 | 5.14 | 28.69 | |
| net_grp_cmp | 0 | 0 | 0 | |
| net_node_cmp | 0.00 | 0.01 | 0.01 | |
| norm_accessor | 0.02 | 0.02 | 0.03 | |
| norm_tab-matrix | 0.68 | 0.01 | 0.71 | |
| norm_tab-mina | 0.67 | 0.07 | 0.73 | |
| norm_tab | 0.02 | 0.02 | 0.03 | |
| norm_tab_method_list | 0.05 | 0.05 | 0.11 | |
| pcoa_plot | 1.47 | 0.09 | 0.80 | |
| sim_par | 0 | 0 | 0 | |
| sparcc | 0.00 | 0.01 | 0.02 | |
| tab_accessor | 0.00 | 0.01 | 0.02 | |
| tina-matrix-method | 0 | 0 | 0 | |
| tina | 0 | 0 | 0 | |