Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2024-06-14 14:38 -0400 (Fri, 14 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
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

Package 1273/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mina 1.12.0  (landing page)
Rui Guan
Snapshot Date: 2024-06-12 14:00 -0400 (Wed, 12 Jun 2024)
git_url: https://git.bioconductor.org/packages/mina
git_branch: RELEASE_3_19
git_last_commit: 82a91b8
git_last_commit_date: 2024-04-30 11:29:43 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for mina on palomino3

To the developers/maintainers of the mina package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: mina
Version: 1.12.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:mina.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings mina_1.12.0.tar.gz
StartedAt: 2024-06-13 06:37:23 -0400 (Thu, 13 Jun 2024)
EndedAt: 2024-06-13 06:44:56 -0400 (Thu, 13 Jun 2024)
EllapsedTime: 453.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: mina.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:mina.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings mina_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/mina.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'mina/DESCRIPTION' ... OK
* this is package 'mina' version '1.12.0'
* 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) 13.2.0'
* checking installed package size ... NOTE
  installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
* 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 code 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 ... NOTE
checkRd: (-1) re_format_AP.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{x}{an {APResult} object from \pkg{apcluster}.}
       |             ^
* 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 7.6 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-3.19-bioc/R/library/mina/libs/x64/mina.dll':
  Found '_exit', possibly from '_exit' (C)
  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      34.54  18.32   47.96
com_plot-mina     43.90   0.30    3.11
net_dis-mina      17.27   8.87   23.59
dis_stat_accessor 13.54   4.66   16.48
net_cls-mina      10.53   1.17   11.30
bs_pm-mina         8.29   1.42    8.15
net_cls            6.23   0.58    6.54
net_cls-matrix     6.27   0.50    6.33
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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, 5 NOTEs
See
  'F:/biocbuild/bbs-3.19-bioc/meat/mina.Rcheck/00check.log'
for details.


Installation output

mina.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL mina
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'mina' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppParallel/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppParallel/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cp_cor.cpp -o cp_cor.o
g++ -std=gnu++17 -shared -s -static-libgcc -o mina.dll tmp.def RcppExports.o cp_cor.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-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)

Tests output


Example timings

mina.Rcheck/mina-Ex.timings

nameusersystemelapsed
adj-matrix0.560.080.44
adj-mina0.860.060.54
adj0.870.160.68
adj_method_list0.040.891.57
bs_pm-mina8.291.428.15
bs_pm2.960.773.21
check_mina0.050.010.08
check_mina_de0.060.030.10
check_mina_qu0.050.030.08
cls_tab0.030.080.11
com_dis-matrix0.560.050.34
com_dis-mina0.040.020.06
com_dis0.720.050.33
com_dis_list0.160.891.13
com_plot-mina43.90 0.30 3.11
com_plot0.160.030.18
com_r2-mina0.900.030.55
com_r21.470.210.81
data-hmp0.000.000.02
data-maize000
des_accessor000
dis_accessor0.040.010.06
dis_stat_accessor13.54 4.6616.48
dmr-matrix0.310.080.39
dmr-mina0.510.070.60
dmr0.770.030.40
dmr_accessor0.890.060.56
fit_tabs-mina0.590.411.00
fit_tabs1.270.411.67
get_net_cls_tab-matrix-data.frame-method1.480.361.65
get_net_cls_tab1.740.381.81
get_r2-mat0.620.080.70
get_r21.020.050.64
get_rep-matrix0.190.170.36
get_rep-mima0.860.060.92
hmp_des0.010.000.02
hmp_otu0.000.020.01
maize_asv000
maize_asv2000
maize_des0.000.020.01
maize_des20.000.020.02
mina-class000
net_cls-matrix6.270.506.33
net_cls-mina10.53 1.1711.30
net_cls6.230.586.54
net_cls_tab-mina-method1.810.191.67
net_cls_tab1.360.221.31
net_dis-mina17.27 8.8723.59
net_dis2.710.843.28
net_dis_indi0.000.020.01
net_dis_pcoa000
net_dis_plot34.5418.3247.96
net_grp_cmp000
net_node_cmp000
norm_accessor0.030.020.05
norm_tab-matrix1.170.111.28
norm_tab-mina0.970.191.16
norm_tab0.030.020.04
norm_tab_method_list0.080.841.04
pcoa_plot1.480.201.25
sim_par0.000.020.02
sparcc000
tab_accessor0.000.010.01
tina-matrix-method0.000.010.01
tina000