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This page was generated on 2021-10-15 15:06:12 -0400 (Fri, 15 Oct 2021).

CHECK results for mina on tokay2

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.
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raw results

Package 1137/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mina 1.0.0  (landing page)
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)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

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

Command output

##############################################################################
##############################################################################
###
### 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.



Installation output

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

Tests output


Example timings

mina.Rcheck/examples_i386/mina-Ex.timings

nameusersystemelapsed
adj-matrix0.700.100.44
adj-mina1.140.020.73
adj1.000.110.84
adj_method_list0.110.050.15
bs_pm-mina11.14 1.18 8.99
bs_pm9.381.367.81
check_mina0.090.070.16
check_mina_de0.090.030.12
check_mina_qu0.080.030.11
cls_tab0.100.010.11
com_dis-matrix1.040.020.41
com_dis-mina0.970.030.09
com_dis1.410.090.63
com_dis_list0.220.040.25
com_plot-mina23.75 2.39 3.04
com_plot0.650.000.19
com_r2-mina1.640.000.63
com_r21.660.201.01
data-hmp000
data-maize0.020.000.01
des_accessor000
dis_accessor0.980.010.10
dis_stat_accessor15.22 3.8416.48
dmr-matrix1.550.000.43
dmr-mina1.620.020.41
dmr1.330.010.42
dmr_accessor1.410.110.56
fit_tabs-mina0.500.250.75
fit_tabs0.950.151.11
get_net_cls_tab-matrix-data.frame-method1.760.131.53
get_net_cls_tab1.860.201.78
get_r2-mat1.410.030.62
get_r21.390.030.55
hmp_des0.010.000.02
hmp_otu000
maize_asv000
maize_asv20.020.000.01
maize_des000
maize_des2000
mina-class000
net_cls-matrix6.340.166.15
net_cls-mina9.250.949.75
net_cls6.380.266.34
net_cls_tab-mina-method1.750.041.53
net_cls_tab1.700.031.38
net_dis-mina21.22 6.3523.80
net_dis11.70 1.40 9.19
net_dis_indi000
norm_accessor0.050.000.05
norm_tab-matrix1.290.031.33
norm_tab-mina101
norm_tab0.040.000.04
norm_tab_method_list0.030.050.08
pcoa_plot2.390.021.01
sim_par000
sparcc000
tab_accessor000
tina-matrix-method0.000.020.02
tina000

mina.Rcheck/examples_x64/mina-Ex.timings

nameusersystemelapsed
adj-matrix0.820.000.42
adj-mina1.250.060.97
adj1.030.020.70
adj_method_list0.160.030.19
bs_pm-mina11.36 1.22 9.63
bs_pm9.111.377.74
check_mina0.170.020.18
check_mina_de0.100.030.13
check_mina_qu0.080.030.11
cls_tab0.060.050.11
com_dis-matrix1.090.060.47
com_dis-mina1.000.000.11
com_dis1.270.030.42
com_dis_list0.190.050.23
com_plot-mina23.32 0.97 2.88
com_plot0.410.010.25
com_r2-mina1.520.000.64
com_r21.400.300.75
data-hmp000
data-maize000
des_accessor000
dis_accessor1.000.000.07
dis_stat_accessor17.28 4.1917.91
dmr-matrix1.010.000.44
dmr-mina1.290.010.42
dmr1.500.050.69
dmr_accessor1.330.000.49
fit_tabs-mina0.890.161.04
fit_tabs0.950.061.02
get_net_cls_tab-matrix-data.frame-method1.630.201.51
get_net_cls_tab1.610.131.43
get_r2-mat1.150.010.56
get_r21.520.000.53
hmp_des000
hmp_otu000
maize_asv000
maize_asv20.020.000.01
maize_des000
maize_des2000
mina-class000
net_cls-matrix7.650.287.53
net_cls-mina10.78 0.3310.75
net_cls7.280.367.39
net_cls_tab-mina-method1.930.101.70
net_cls_tab1.460.061.28
net_dis-mina22.21 6.0123.72
net_dis12.26 1.19 9.04
net_dis_indi0.000.010.02
norm_accessor0.030.020.05
norm_tab-matrix1.130.021.14
norm_tab-mina0.940.071.00
norm_tab0.030.000.04
norm_tab_method_list0.080.010.10
pcoa_plot2.390.020.97
sim_par000
sparcc000
tab_accessor0.000.020.01
tina-matrix-method000
tina000