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CHECK report for SIAMCAT on tokay1

This page was generated on 2020-04-15 12:30:33 -0400 (Wed, 15 Apr 2020).

Package 1581/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SIAMCAT 1.6.0
Konrad Zych
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/SIAMCAT
Branch: RELEASE_3_10
Last Commit: 68044d5
Last Changed Date: 2019-10-29 13:11:12 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SIAMCAT
Version: 1.6.0
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SIAMCAT.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings SIAMCAT_1.6.0.tar.gz
StartedAt: 2020-04-15 06:36:53 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 06:41:09 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 255.9 seconds
RetCode: 0
Status:  OK  
CheckDir: SIAMCAT.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SIAMCAT.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings SIAMCAT_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/SIAMCAT.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.6.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'SIAMCAT' can be installed ... OK
* checking installed package size ... OK
* 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 data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
train.model          20.49   0.05   20.58
evaluate.predictions  7.41   0.06    7.47
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
train.model          21.69   0.04   21.72
evaluate.predictions  7.60   0.05    7.64
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/SIAMCAT.Rcheck/00check.log'
for details.



Installation output

SIAMCAT.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/SIAMCAT_1.6.0.tar.gz && rm -rf SIAMCAT.buildbin-libdir && mkdir SIAMCAT.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SIAMCAT.buildbin-libdir SIAMCAT_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL SIAMCAT_1.6.0.zip && rm SIAMCAT_1.6.0.tar.gz SIAMCAT_1.6.0.zip
###
##############################################################################
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 3355k  100 3355k    0     0  39.0M      0 --:--:-- --:--:-- --:--:-- 40.9M

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  
    siamcat.to.lefse                        html  
    siamcat.to.maaslin                      html  
    siamcat_example                         html  
    summarize.features                      html  
    train.model                             html  
    validate.data                           html  
    weight_matrix-methods                   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 'SIAMCAT' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SIAMCAT' as SIAMCAT_1.6.0.zip
* DONE (SIAMCAT)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'SIAMCAT' successfully unpacked and MD5 sums checked

Tests output


Example timings

SIAMCAT.Rcheck/examples_i386/SIAMCAT-Ex.timings

nameusersystemelapsed
accessSlot0.040.000.05
add.meta.pred0.050.020.06
assign-associations0.010.000.02
assign-data_split0.020.000.01
assign-eval_data0.030.000.03
assign-filt_feat0.020.000.02
assign-label0.030.000.03
assign-meta0.030.000.03
assign-model_list0.030.000.03
assign-norm_feat0.030.000.03
assign-orig_feat0.020.000.02
assign-physeq0.020.010.03
assign-pred_matrix0.010.000.01
assoc_param-methods0.030.000.04
associations-methods0.020.020.03
check.associations0.290.020.31
check.confounders0.570.030.61
create.data.split0.030.010.05
create.label0.000.020.01
data_split-methods0.010.000.02
eval_data-methods0.020.000.01
evaluate.predictions7.410.067.47
feature_type-methods0.000.020.02
feature_weights-methods0.000.030.03
filt_feat-methods0.030.000.03
filt_params-methods0.010.010.03
filter.features0.020.000.02
filter.label0.010.020.03
get.filt_feat.matrix0.020.000.01
get.norm_feat.matrix0.020.010.03
get.orig_feat.matrix0.010.000.02
label-methods0.030.000.03
make.predictions0.140.020.16
meta-methods0.030.020.04
model.evaluation.plot0.050.010.07
model.interpretation.plot0.060.020.08
model_list-methods0.020.010.03
model_type-methods0.030.020.04
models-methods0.020.000.02
norm_feat-methods0.030.000.03
norm_params-methods0.010.000.02
normalize.features0.030.000.03
orig_feat-methods0.020.000.02
physeq-methods0.030.010.05
pred_matrix-methods0.010.000.01
read.label0.000.000.02
read.lefse0.490.050.68
select.samples0.040.020.07
siamcat0.320.060.37
siamcat.to.lefse0.150.020.17
siamcat.to.maaslin0.050.000.05
summarize.features0.310.030.34
train.model20.49 0.0520.58
validate.data0.030.000.03
weight_matrix-methods0.030.000.03

SIAMCAT.Rcheck/examples_x64/SIAMCAT-Ex.timings

nameusersystemelapsed
accessSlot0.030.000.03
add.meta.pred0.060.000.06
assign-associations0.000.020.01
assign-data_split0.030.000.03
assign-eval_data0.030.000.04
assign-filt_feat0.010.000.01
assign-label0.020.000.02
assign-meta0.030.010.04
assign-model_list0.020.020.04
assign-norm_feat0.010.000.01
assign-orig_feat0.030.000.03
assign-physeq0.020.000.02
assign-pred_matrix0.020.010.03
assoc_param-methods0.010.000.01
associations-methods0.030.000.04
check.associations0.720.000.71
check.confounders0.610.000.61
create.data.split0.030.000.03
create.label000
data_split-methods0.020.000.01
eval_data-methods0.010.000.02
evaluate.predictions7.600.057.64
feature_type-methods0.020.000.02
feature_weights-methods0.010.000.02
filt_feat-methods0.040.000.03
filt_params-methods0.030.000.03
filter.features0.010.000.01
filter.label0.030.000.03
get.filt_feat.matrix0.020.000.02
get.norm_feat.matrix0.020.000.02
get.orig_feat.matrix0.010.020.03
label-methods0.020.000.01
make.predictions0.150.010.17
meta-methods0.030.000.04
model.evaluation.plot0.070.000.06
model.interpretation.plot0.060.020.08
model_list-methods0.010.000.01
model_type-methods0.040.000.03
models-methods0.010.000.02
norm_feat-methods0.030.000.03
norm_params-methods0.020.000.02
normalize.features0.030.000.14
orig_feat-methods0.020.000.01
physeq-methods0.030.000.03
pred_matrix-methods0.030.000.03
read.label000
read.lefse0.670.000.68
select.samples0.060.000.06
siamcat0.850.000.84
siamcat.to.lefse0.040.000.05
siamcat.to.maaslin0.050.000.05
summarize.features0.310.010.32
train.model21.69 0.0421.72
validate.data0.050.010.07
weight_matrix-methods0.030.000.03