Multiple platform build/check report for BioC 3.13 - CHECK results for SIAMCAT on tokay2

Package: SIAMCAT

Version: 1.12.0

Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SIAMCAT.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings SIAMCAT_1.12.0.tar.gz

StartedAt: 2021-10-15 05:39:13 -0400 (Fri, 15 Oct 2021)

EndedAt: 2021-10-15 05:45:20 -0400 (Fri, 15 Oct 2021)

EllapsedTime: 366.8 seconds

RetCode: 0

Status: OK

CheckDir: SIAMCAT.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SIAMCAT.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings SIAMCAT_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/SIAMCAT.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 'SIAMCAT/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SIAMCAT' version '1.12.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'SIAMCAT' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    help      2.1Mb
* 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 ... OK
* 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 ... NOTE
  Note: found 10 marked UTF-8 strings
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* 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
train.model 20.56   0.02   20.69
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
train.model 19.58   0.08   19.65
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/SIAMCAT.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/SIAMCAT_1.12.0.tar.gz && rm -rf SIAMCAT.buildbin-libdir && mkdir SIAMCAT.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SIAMCAT.buildbin-libdir SIAMCAT_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL SIAMCAT_1.12.0.zip && rm SIAMCAT_1.12.0.tar.gz SIAMCAT_1.12.0.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 11.8M    2  247k    0     0   759k      0  0:00:15 --:--:--  0:00:15  759k
 14 11.8M   14 1794k    0     0  1350k      0  0:00:08  0:00:01  0:00:07 1350k
 35 11.8M   35 4341k    0     0  1866k      0  0:00:06  0:00:02  0:00:04 1866k
 61 11.8M   61 7459k    0     0  2239k      0  0:00:05  0:00:03  0:00:02 2239k
 95 11.8M   95 11.2M    0     0  2629k      0  0:00:04  0:00:04 --:--:-- 2629k
 95 11.8M   95 11.2M    0     0  2164k      0  0:00:05  0:00:05 --:--:-- 2255k
100 11.8M  100 11.8M    0     0  2190k      0  0:00:05  0:00:05 --:--:-- 2457k

install for i386

* installing *source* package 'SIAMCAT' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SIAMCAT'
    finding HTML links ... done
    SIAMCAT-package                         html  
    accessSlot                              html  
    add.meta.pred                           html  
    assign-associations                     html  
    assign-data_split                       html  
    assign-eval_data                        html  
    assign-filt_feat                        html  
    assign-label                            html  
    assign-meta                             html  
    assign-model_list                       html  
    assign-norm_feat                        html  
    assign-orig_feat                        html  
    assign-physeq                           html  
    assign-pred_matrix                      html  
    assoc_param-methods                     html  
    associations-methods                    html  
    check.associations                      html  
    check.confounders                       html  
    create.data.split                       html  
    create.label                            html  
    data_split-methods                      html  
    eval_data-methods                       html  
    evaluate.predictions                    html  
    feat.crc.zeller                         html  
    feature_type-methods                    html  
    feature_weights-methods                 html  
    filt_feat-methods                       html  
    filt_params-methods                     html  
    filter.features                         html  
    filter.label                            html  
    get.component.classes                   html  
    get.filt_feat.matrix                    html  
    get.norm_feat.matrix                    html  
    get.orig_feat.matrix                    html  
    label-methods                           html  
    make.predictions                        html  
    meta-methods                            html  
    meta.crc.zeller                         html  
    model.evaluation.plot                   html  
    model.interpretation.plot               html  
    model_list-methods                      html  
    model_type-methods                      html  
    models-methods                          html  
    norm_feat-methods                       html  
    norm_params-methods                     html  
    normalize.features                      html  
    orig_feat-methods                       html  
    parse.label.header                      html  
    physeq-methods                          html  
    pred_matrix-methods                     html  
    read.label                              html  
    read.lefse                              html  
    select.samples                          html  
    show-methods                            html  
    siamcat-class                           html  
    siamcat                                 html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/SIAMCAT.buildbin-libdir/00LOCK-SIAMCAT/00new/SIAMCAT/help/siamcat.html
    siamcat.to.lefse                        html  
    siamcat.to.maaslin                      html  
    siamcat_example                         html  
    summarize.features                      html  
    finding level-2 HTML links ... done

    train.model                             html  
    validate.data                           html  
    weight_matrix-methods                   html  
*** copying figures
** 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 'SIAMCAT' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SIAMCAT' as SIAMCAT_1.12.0.zip
* DONE (SIAMCAT)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'SIAMCAT' successfully unpacked and MD5 sums checked

name	user	system	elapsed
accessSlot	0.03	0.00	0.03
add.meta.pred	0.08	0.00	0.08
assign-associations	0.03	0.00	0.03
assign-data_split	0.02	0.00	0.02
assign-eval_data	0.05	0.00	0.05
assign-filt_feat	0.03	0.00	0.03
assign-label	0.01	0.00	0.01
assign-meta	0.03	0.02	0.05
assign-model_list	0.03	0.00	0.03
assign-norm_feat	0.00	0.01	0.02
assign-orig_feat	0.04	0.02	0.04
assign-physeq	0.01	0.00	0.02
assign-pred_matrix	0.02	0.01	0.03
assoc_param-methods	0.01	0.00	0.02
associations-methods	0.02	0.02	0.03
check.associations	0.48	0.02	0.53
check.confounders	0.57	0.03	0.59
create.data.split	0.03	0.03	0.07
create.label	0.00	0.01	0.01
data_split-methods	0.03	0.00	0.03
eval_data-methods	0.03	0.00	0.03
evaluate.predictions	1.98	0.05	2.03
feature_type-methods	0.02	0.00	0.02
feature_weights-methods	0.02	0.00	0.01
filt_feat-methods	0.03	0.00	0.03
filt_params-methods	0.02	0.00	0.02
filter.features	0.03	0.00	0.03
filter.label	0.03	0.00	0.03
get.filt_feat.matrix	0.03	0.00	0.03
get.norm_feat.matrix	0.02	0.00	0.02
get.orig_feat.matrix	0.03	0.00	0.03
label-methods	0.01	0.00	0.01
make.predictions	0.18	0.00	0.18
meta-methods	0.04	0.00	0.04
model.evaluation.plot	0.03	0.00	0.03
model.interpretation.plot	0.1	0.0	0.1
model_list-methods	0.01	0.00	0.01
model_type-methods	0.03	0.00	0.04
models-methods	0.02	0.02	0.03
norm_feat-methods	0.02	0.00	0.01
norm_params-methods	0.01	0.01	0.03
normalize.features	0.03	0.00	0.03
orig_feat-methods	0.02	0.02	0.04
physeq-methods	0.00	0.01	0.01
pred_matrix-methods	0.02	0.00	0.01
read.label	0.01	0.00	0.02
read.lefse	1.21	0.07	1.30
select.samples	0.08	0.00	0.07
siamcat	0.34	0.01	0.36
siamcat.to.lefse	0.06	0.00	0.07
siamcat.to.maaslin	0.08	0.00	0.07
summarize.features	2.25	0.08	2.33
train.model	20.56	0.02	20.69
validate.data	0.03	0.00	0.03
weight_matrix-methods	0.02	0.00	0.02

name	user	system	elapsed
accessSlot	0.05	0.00	0.05
add.meta.pred	0.06	0.00	0.06
assign-associations	0.07	0.01	0.09
assign-data_split	0.04	0.00	0.03
assign-eval_data	0.01	0.00	0.02
assign-filt_feat	0.03	0.00	0.03
assign-label	0.02	0.00	0.02
assign-meta	0.47	0.02	0.48
assign-model_list	0.02	0.00	0.01
assign-norm_feat	0.01	0.00	0.02
assign-orig_feat	0.04	0.00	0.03
assign-physeq	0.01	0.00	0.02
assign-pred_matrix	0.00	0.01	0.01
assoc_param-methods	0.03	0.00	0.03
associations-methods	0.02	0.00	0.02
check.associations	0.48	0.00	1.67
check.confounders	0.53	0.04	0.56
create.data.split	0.05	0.00	0.04
create.label	0.01	0.00	0.02
data_split-methods	0.02	0.00	0.02
eval_data-methods	0.03	0.00	0.03
evaluate.predictions	2.17	0.03	2.20
feature_type-methods	0.02	0.00	0.02
feature_weights-methods	0.03	0.00	0.03
filt_feat-methods	0.01	0.00	0.01
filt_params-methods	0.03	0.00	0.03
filter.features	0.02	0.00	0.02
filter.label	0.02	0.01	0.03
get.filt_feat.matrix	0.03	0.00	0.03
get.norm_feat.matrix	0.01	0.00	0.02
get.orig_feat.matrix	0.02	0.00	0.01
label-methods	0.03	0.00	0.03
make.predictions	0.16	0.00	0.16
meta-methods	0.02	0.02	0.03
model.evaluation.plot	0.04	0.00	0.04
model.interpretation.plot	0.05	0.01	0.07
model_list-methods	0.05	0.00	0.04
model_type-methods	0.01	0.00	0.02
models-methods	0.02	0.00	0.02
norm_feat-methods	0.00	0.02	0.01
norm_params-methods	0.01	0.00	0.02
normalize.features	0.05	0.00	0.04
orig_feat-methods	0.02	0.00	0.02
physeq-methods	0.01	0.00	0.01
pred_matrix-methods	0.02	0.00	0.02
read.label	0.03	0.00	0.03
read.lefse	1.05	0.02	1.06
select.samples	0.06	0.00	0.07
siamcat	0.28	0.00	0.28
siamcat.to.lefse	0.05	0.01	0.06
siamcat.to.maaslin	0.04	0.02	0.06
summarize.features	1.66	0.04	1.71
train.model	19.58	0.08	19.65
validate.data	0.04	0.02	0.06
weight_matrix-methods	0.02	0.01	0.04

CHECK results for SIAMCAT on tokay2

Summary

Command output

Installation output

Tests output

Example timings