Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-17 15:05:58 -0400 (Fri, 17 Sep 2021).

CHECK results for autonomics on tokay2

To the developers/maintainers of the autonomics package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/autonomics.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 102/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
autonomics 1.0.1  (landing page)
Aditya Bhagwat
Snapshot Date: 2021-09-16 04:50:11 -0400 (Thu, 16 Sep 2021)
git_url: https://git.bioconductor.org/packages/autonomics
git_branch: RELEASE_3_13
git_last_commit: 5df16f7
git_last_commit_date: 2021-05-25 07:57:21 -0400 (Tue, 25 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    ERROR    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: autonomics
Version: 1.0.1
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:autonomics.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings autonomics_1.0.1.tar.gz
StartedAt: 2021-09-16 19:45:54 -0400 (Thu, 16 Sep 2021)
EndedAt: 2021-09-16 20:02:55 -0400 (Thu, 16 Sep 2021)
EllapsedTime: 1021.2 seconds
RetCode: 1
Status:   ERROR  
CheckDir: autonomics.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:autonomics.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings autonomics_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/autonomics.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 'autonomics/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'autonomics' version '1.0.1'
* package encoding: UTF-8
* 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:
  .BBSoptions
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 'autonomics' 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 ... WARNING
Undocumented code objects:
  'translate'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'autonomics-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: read_affymetrix
> ### Title: Read affymetrix microarray
> ### Aliases: read_affymetrix
> 
> ### ** Examples
> 
> require(magrittr)
Loading required package: magrittr
> url <- paste0('http://www.bioconductor.org/help/publications/2003/',
+                 'Chiaretti/chiaretti2/T33.tgz')
> localfile <- file.path('~/autonomicscache', basename(url))
> if (!file.exists(localfile)){
+     download.file(url, destfile = localfile)
+     untar(localfile, exdir = path.expand('~/autonomicscache'))
+ }
Error in download.file(url, destfile = localfile) : 
  cannot open destfile '~/autonomicscache/T33.tgz', reason 'No such file or directory'
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'autonomics-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: read_affymetrix
> ### Title: Read affymetrix microarray
> ### Aliases: read_affymetrix
> 
> ### ** Examples
> 
> require(magrittr)
Loading required package: magrittr
> url <- paste0('http://www.bioconductor.org/help/publications/2003/',
+                 'Chiaretti/chiaretti2/T33.tgz')
> localfile <- file.path('~/autonomicscache', basename(url))
> if (!file.exists(localfile)){
+     download.file(url, destfile = localfile)
+     untar(localfile, exdir = path.expand('~/autonomicscache'))
+ }
Error in download.file(url, destfile = localfile) : 
  cannot open destfile '~/autonomicscache/T33.tgz', reason 'No such file or directory'
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* 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: 2 ERRORs, 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/autonomics.Rcheck/00check.log'
for details.


Installation output

autonomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/autonomics_1.0.1.tar.gz && rm -rf autonomics.buildbin-libdir && mkdir autonomics.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=autonomics.buildbin-libdir autonomics_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL autonomics_1.0.1.zip && rm autonomics_1.0.1.tar.gz autonomics_1.0.1.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
  7 9411k    7  701k    0     0   777k      0  0:00:12 --:--:--  0:00:12  777k
 22 9411k   22 2073k    0     0  1083k      0  0:00:08  0:00:01  0:00:07 1083k
 45 9411k   45 4262k    0     0  1469k      0  0:00:06  0:00:02  0:00:04 1469k
 49 9411k   49 4673k    0     0  1192k      0  0:00:07  0:00:03  0:00:04 1192k
 70 9411k   70 6658k    0     0  1354k      0  0:00:06  0:00:04  0:00:02 1354k
 97 9411k   97 9140k    0     0  1545k      0  0:00:06  0:00:05  0:00:01 1683k
100 9411k  100 9411k    0     0  1552k      0  0:00:06  0:00:06 --:--:-- 1769k

install for i386

* installing *source* package 'autonomics' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Note: wrong number of arguments to '/' 
** help
*** installing help indices
  converting help for package 'autonomics'
    finding HTML links ... done
    AUTONOMICS_DATASETS                     html  
    MAXQUANT_PATTERNS_PEPCOUNTS             html  
    MAXQUANT_PATTERNS_QUANTITY              html  
    TESTS                                   html  
    add_smiles                              html  
    analysis                                html  
    analyze                                 html  
    assert_is_valid_sumexp                  html  
    biplot                                  html  
    biplot_corrections                      html  
    biplot_covariates                       html  
    center                                  html  
    contrast_subgroup_cols                  html  
    contrastdefs                            html  
    counts                                  html  
    counts2cpm                              html  
    counts2tpm                              html  
    cpm                                     html  
    create_design                           html  
    create_sfile                            html  
    default_formula                         html  
    default_sfile                           html  
    download_data                           html  
    download_gtf                            html  
    dt2mat                                  html  
    explore_imputations                     html  
    explore_transformations                 html  
    extract_features                        html  
    extract_rectangle                       html  
    fdata                                   html  
    filter_exprs_replicated_in_some_subgroup
                                            html  
    filter_features                         html  
    filter_medoid                           html  
    filter_replicated                       html  
    filter_samples                          html  
    fit_limma                               html  
    flevels                                 html  
    fnames                                  html  
    formula2str                             html  
    fvalues                                 html  
    fvars                                   html  
    guess_maxquant_quantity                 html  
    guess_sep                               html  
    halfnormimpute                          html  
    impute_systematic_nondetects            html  
    invert                                  html  
    is_imputed                              html  
    is_sig                                  html  
    limma                                   html  
    log2counts                              html  
    log2countsratios                        html  
    log2cpm                                 html  
    log2cpmratios                           html  
    log2tpm                                 html  
    log2tpmratios                           html  
    log2transform                           html  
    make_volcano_dt                         html  
    matrix2sumexp                           html  
    merge_sdata                             html  
    merge_sfile                             html  
    message_df                              html  
    occupancies                             html  
    pca                                     html  
    plot_boxplots                           html  
    plot_contrastogram                      html  
    plot_data                               html  
    plot_densities                          html  
    plot_detections                         html  
    plot_features                           html  
    plot_venn                               html  
    plot_violins                            html  
    plot_volcano                            html  
    preprocess_rnaseq_counts                html  
    proteingroups                           html  
    read_affymetrix                         html  
    read_metabolon                          html  
    read_proteingroups                      html  
    read_rectangles                         html  
    read_rnaseq_counts                      html  
    read_somascan                           html  
    rm_singleton_samples                    html  
    scaledlibsizes                          html  
    sdata                                   html  
    slevels                                 html  
    snames                                  html  
    split_by_svar                           html  
    split_extract                           html  
    standardize_maxquant_snames             html  
    subgroup_matrix                         html  
    subtract_baseline                       html  
    sumexp2mae                              html  
    sumexp_to_long_dt                       html  
    summarize_fit                           html  
    svalues                                 html  
    svars                                   html  
    tpm                                     html  
    values                                  html  
    venn_detects                            html  
    weights                                 html  
    zero_to_na                              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 'autonomics' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'autonomics' as autonomics_1.0.1.zip
* DONE (autonomics)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'autonomics' successfully unpacked and MD5 sums checked

Tests output

autonomics.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(autonomics)

Attaching package: 'autonomics'

The following object is masked from 'package:stats':

    biplot

> 
> test_check("autonomics")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 102 ]
> 
> proc.time()
   user  system elapsed 
 113.40    4.76  116.53 

autonomics.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(autonomics)

Attaching package: 'autonomics'

The following object is masked from 'package:stats':

    biplot

> 
> test_check("autonomics")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 102 ]
> 
> proc.time()
   user  system elapsed 
 119.89    2.96  121.26 

Example timings

autonomics.Rcheck/examples_i386/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS000
MAXQUANT_PATTERNS_PEPCOUNTS000
MAXQUANT_PATTERNS_QUANTITY000
TESTS000
add_smiles 2.59 0.3012.25
analysis 1.93 0.1721.25
analyze4.640.415.25
assert_is_valid_sumexp1.920.192.44
biplot2.610.122.73
biplot_corrections3.820.083.89
biplot_covariates8.390.098.49
center 2.60 0.1325.41
contrast_subgroup_cols0.780.060.84
contrastdefs2.590.142.57
counts2.860.073.65
counts2cpm2.120.072.14
counts2tpm1.800.031.77
cpm1.860.081.89
create_design3.020.023.01
create_sfile1.780.091.74
default_formula0.890.100.98
default_sfile0.260.000.27
download_data2.860.174.33
download_gtf000
dt2mat0.020.000.01
explore_imputations11.56 0.3311.69
explore_transformations5.360.155.33
extract_features1.280.021.17
extract_rectangle0.960.111.06
fdata1.370.081.30
filter_exprs_replicated_in_some_subgroup1.580.031.59
filter_features1.200.111.32
filter_medoid12.55 0.1212.71
filter_replicated1.550.051.47
filter_samples0.930.121.07
fit_limma8.820.138.85
flevels1.640.061.49
fnames1.500.021.40
formula2str000
fvalues1.350.011.23
fvars1.530.081.45
guess_maxquant_quantity2.810.092.72
guess_sep000
halfnormimpute1.010.021.03
impute_systematic_nondetects3.320.123.27
invert2.170.022.11
is_imputed1.620.051.56
is_sig12.88 0.0712.75
limma3.060.132.97
log2counts2.280.092.31
log2countsratios2.670.052.67
log2cpm2.080.032.07
log2cpmratios2.270.032.25
log2tpm2.400.032.37
log2tpmratios1.650.081.69
log2transform4.120.084.08
make_volcano_dt2.730.202.72
matrix2sumexp1.940.102.03
merge_sdata0.690.080.76
merge_sfile 2.33 0.1530.30
message_df000
occupancies2.220.062.19
pca12.61 0.1312.75
plot_boxplots3.920.053.97
plot_contrastogram1.580.121.76
plot_data1.890.081.97
plot_densities2.340.122.47
plot_detections9.410.189.23
plot_features4.280.074.36
plot_venn5.310.105.38
plot_violins3.840.083.90
plot_volcano2.490.122.50
preprocess_rnaseq_counts3.250.083.32
proteingroups1.800.051.69

autonomics.Rcheck/examples_x64/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS000
MAXQUANT_PATTERNS_PEPCOUNTS000
MAXQUANT_PATTERNS_QUANTITY000
TESTS000
add_smiles2.790.223.31
analysis2.500.122.49
analyze6.170.166.47
assert_is_valid_sumexp2.310.152.47
biplot4.110.194.29
biplot_corrections4.390.134.52
biplot_covariates8.030.188.22
center3.360.133.28
contrast_subgroup_cols1.030.031.06
contrastdefs3.020.062.92
counts3.170.113.22
counts2cpm2.780.032.77
counts2tpm1.020.001.00
cpm2.070.022.07
create_design3.220.013.18
create_sfile2.220.082.14
default_formula1.080.131.20
default_sfile0.340.010.36
download_data2.550.132.67
download_gtf000
dt2mat000
explore_imputations11.47 0.3011.54
explore_transformations5.690.115.71
extract_features2.340.062.18
extract_rectangle1.060.131.19
fdata1.660.041.51
filter_exprs_replicated_in_some_subgroup1.590.181.77
filter_features1.060.071.14
filter_medoid13.45 0.0813.47
filter_replicated2.080.021.94
filter_samples1.170.171.34
fit_limma10.41 0.0510.41
flevels1.630.111.57
fnames1.430.041.36
formula2str000
fvalues1.580.051.49
fvars1.360.021.29
guess_maxquant_quantity3.190.123.04
guess_sep000
halfnormimpute1.480.031.51
impute_systematic_nondetects3.250.063.16
invert2.080.051.95
is_imputed1.530.051.44
is_sig14.63 0.0614.51
limma3.110.133.07
log2counts3.010.043.00
log2countsratios2.140.052.15
log2cpm2.110.012.11
log2cpmratios1.970.041.99
log2tpm2.110.042.07
log2tpmratios2.690.032.68
log2transform4.780.134.76
make_volcano_dt2.230.062.17
matrix2sumexp1.880.081.96
merge_sdata1.030.051.08
merge_sfile2.310.092.06
message_df000
occupancies1.770.111.72
pca12.01 0.1112.12
plot_boxplots4.940.085.03
plot_contrastogram1.390.061.44
plot_data1.660.091.75
plot_densities2.860.052.91
plot_detections10.06 0.3410.04
plot_features5.170.065.23
plot_venn6.530.036.52
plot_violins4.630.104.73
plot_volcano3.120.012.97
preprocess_rnaseq_counts3.820.053.80
proteingroups3.170.032.95