Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-10-22 12:04:18 -0400 (Fri, 22 Oct 2021).

CHECK results for autonomics on riesling1

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 99/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
autonomics 1.1.7  (landing page)
Aditya Bhagwat
Snapshot Date: 2021-10-21 14:50:08 -0400 (Thu, 21 Oct 2021)
git_url: https://git.bioconductor.org/packages/autonomics
git_branch: master
git_last_commit: 3bb339e
git_last_commit_date: 2021-06-04 06:39:40 -0400 (Fri, 04 Jun 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: autonomics
Version: 1.1.7
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:autonomics.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings autonomics_1.1.7.tar.gz
StartedAt: 2021-10-21 23:59:30 -0400 (Thu, 21 Oct 2021)
EndedAt: 2021-10-22 00:12:04 -0400 (Fri, 22 Oct 2021)
EllapsedTime: 753.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: autonomics.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:autonomics.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings autonomics_1.1.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-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 '1.1.7'
* 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 ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'normimpute'
  'ref' 'pos'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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
read_rnaseq_counts  14.83   0.40   15.00
pca                  9.20   0.08    9.28
explore_imputations  7.76   0.17    7.87
filter_medoid        7.90   0.02    7.94
is_sig               7.74   0.04    7.70
read_somascan        7.04   0.08    7.11
plot_detections      6.50   0.27    6.59
fit_limma            5.66   0.00    5.62
read_rectangles      5.17   0.42    5.79
summarize_fit        4.98   0.12    5.02
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
read_rnaseq_counts  12.25   0.44   13.10
pca                  8.23   0.16    8.39
is_sig               8.22   0.08    8.20
filter_medoid        7.53   0.05    7.56
read_somascan        7.07   0.08    7.14
explore_imputations  6.81   0.19    6.92
fit_limma            5.98   0.03    6.00
plot_detections      5.81   0.19    5.85
read_rectangles      5.68   0.31    6.00
biplot_covariates    4.97   0.15    5.13
* 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: 1 WARNING, 1 NOTE
See
  'D:/biocbuild/bbs-3.14-bioc/meat/autonomics.Rcheck/00check.log'
for details.



Installation output

autonomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/autonomics_1.1.7.tar.gz && rm -rf autonomics.buildbin-libdir && mkdir autonomics.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=autonomics.buildbin-libdir autonomics_1.1.7.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL autonomics_1.1.7.zip && rm autonomics_1.1.7.tar.gz autonomics_1.1.7.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
 20 9413k   20 1922k    0     0  2064k      0  0:00:04 --:--:--  0:00:04 2062k
 52 9413k   52 4960k    0     0  2559k      0  0:00:03  0:00:01  0:00:02 2558k
 84 9413k   84 7952k    0     0  2702k      0  0:00:03  0:00:02  0:00:01 2702k
100 9413k  100 9413k    0     0  2673k      0  0:00:03  0:00:03 --:--:-- 2673k

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_1.1.7.zip
* DONE (autonomics)
* installing to library 'D:/biocbuild/bbs-3.14-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 
  90.84    3.01   92.54 

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 
  73.51    3.40   75.98 

Example timings

autonomics.Rcheck/examples_i386/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS000
MAXQUANT_PATTERNS_PEPCOUNTS000
MAXQUANT_PATTERNS_QUANTITY000
TESTS000
add_smiles1.220.141.66
analysis1.050.081.18
analyze3.750.123.88
assert_is_valid_sumexp1.110.161.28
biplot1.900.031.94
biplot_corrections2.390.192.57
biplot_covariates4.900.094.99
center1.530.081.51
contrast_subgroup_cols0.570.040.63
contrastdefs1.470.081.42
counts1.820.101.86
counts2cpm1.210.031.24
counts2tpm0.990.031.00
cpm1.300.001.28
create_design1.860.061.89
create_sfile0.920.090.92
default_formula0.580.130.71
default_sfile0.170.000.17
download_data1.410.111.97
download_gtf000
dt2mat000
explore_imputations7.760.177.87
explore_transformations3.150.053.13
extract_features0.810.060.76
extract_rectangle0.610.140.75
fdata0.760.060.77
filter_exprs_replicated_in_some_subgroup0.860.130.98
filter_features0.660.090.75
filter_medoid7.900.027.94
filter_replicated0.930.080.91
filter_samples0.570.170.75
fit_limma5.660.005.62
flevels0.750.080.70
fnames0.750.100.75
formula2str000
fvalues0.670.120.72
fvars0.750.080.73
guess_maxquant_quantity1.460.061.38
guess_sep000
halfnormimpute0.450.030.48
impute_systematic_nondetects2.360.062.35
invert1.050.081.09
is_imputed0.680.130.74
is_sig7.740.047.70
limma1.400.051.34
log2counts1.330.021.30
log2countsratios1.700.041.72
log2cpm1.240.021.20
log2cpmratios1.230.011.22
log2tpm1.190.081.25
log2tpmratios1.220.011.22
log2transform2.790.152.80
make_volcano_dt1.250.071.28
matrix2sumexp0.970.131.09
merge_sdata0.580.050.63
merge_sfile1.140.251.17
message_df000
occupancies0.920.090.94
pca9.200.089.28
plot_boxplots2.550.092.64
plot_contrastogram0.950.051.00
plot_data1.080.111.19
plot_densities1.800.121.92
plot_detections6.500.276.59
plot_features2.830.082.91
plot_venn3.140.003.11
plot_violins2.860.093.06
plot_volcano1.620.091.64
preprocess_rnaseq_counts1.970.102.05
proteingroups1.000.121.04
read_affymetrix0.610.020.63
read_metabolon4.630.094.72
read_proteingroups2.890.132.94
read_rectangles5.170.425.79
read_rnaseq_counts14.83 0.4015.00
read_somascan7.040.087.11
rm_singleton_samples0.530.000.53
scaledlibsizes1.270.031.27
sdata0.770.070.76
slevels0.750.110.77
snames0.790.060.77
split_by_svar0.740.050.70
split_extract0.510.090.61
standardize_maxquant_snames000
subgroup_matrix0.530.090.62
subtract_baseline2.910.223.14
sumexp2mae1.370.171.56
sumexp_to_long_dt2.940.323.06
summarize_fit4.980.125.02
svalues0.750.060.73
svars0.750.100.75
tpm1.880.041.91
values0.730.110.75
venn_detects0.660.110.70
weights1.260.131.19
zero_to_na0.020.000.02

autonomics.Rcheck/examples_x64/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS000
MAXQUANT_PATTERNS_PEPCOUNTS000
MAXQUANT_PATTERNS_QUANTITY000
TESTS000
add_smiles1.470.111.85
analysis1.200.091.21
analyze3.390.193.58
assert_is_valid_sumexp1.030.331.36
biplot1.910.172.08
biplot_corrections2.590.192.78
biplot_covariates4.970.155.13
center1.580.071.56
contrast_subgroup_cols0.620.060.69
contrastdefs1.450.091.45
counts1.820.101.88
counts2cpm1.540.041.58
counts2tpm0.570.020.58
cpm1.200.001.18
create_design1.780.061.80
create_sfile0.920.110.92
default_formula0.610.160.77
default_sfile0.170.010.19
download_data1.960.172.12
download_gtf000
dt2mat000
explore_imputations6.810.196.92
explore_transformations3.690.103.69
extract_features0.760.070.78
extract_rectangle0.690.110.80
fdata0.750.110.76
filter_exprs_replicated_in_some_subgroup0.860.211.07
filter_features0.690.070.76
filter_medoid7.530.057.56
filter_replicated1.030.020.95
filter_samples0.740.060.80
fit_limma5.980.036.00
flevels0.720.120.75
fnames0.780.050.75
formula2str000
fvalues0.740.060.73
fvars0.730.100.77
guess_maxquant_quantity1.420.091.42
guess_sep000
halfnormimpute0.460.060.52
impute_systematic_nondetects2.390.072.39
invert1.140.071.12
is_imputed0.760.050.74
is_sig8.220.088.20
limma1.340.091.36
log2counts1.160.081.20
log2countsratios1.620.061.67
log2cpm1.090.021.09
log2cpmratios1.100.061.12
log2tpm1.090.051.13
log2tpmratios1.140.001.12
log2transform2.890.082.90
make_volcano_dt1.330.111.32
matrix2sumexp1.030.181.22
merge_sdata0.610.070.67
merge_sfile1.140.181.11
message_df000
occupancies1.000.080.97
pca8.230.168.39
plot_boxplots2.690.082.76
plot_contrastogram0.910.050.96
plot_data1.170.061.23
plot_densities1.780.141.92
plot_detections5.810.195.85
plot_features3.660.053.70
plot_venn3.080.013.09
plot_violins2.760.132.89
plot_volcano1.630.081.63
preprocess_rnaseq_counts1.890.041.92
proteingroups0.950.110.97
read_affymetrix0.720.030.75
read_metabolon4.690.194.88
read_proteingroups2.910.032.85
read_rectangles5.680.316.00
read_rnaseq_counts12.25 0.4413.10
read_somascan7.070.087.14
rm_singleton_samples0.570.000.58
scaledlibsizes1.130.031.14
sdata0.830.050.81
slevels0.840.040.78
snames0.780.110.78
split_by_svar0.670.130.74
split_extract0.580.090.67
standardize_maxquant_snames000
subgroup_matrix0.600.100.68
subtract_baseline3.120.143.52
sumexp2mae2.140.122.27
sumexp_to_long_dt2.950.363.15
summarize_fit4.080.134.05
svalues0.830.070.81
svars0.830.070.80
tpm1.250.001.23
values0.830.040.82
venn_detects0.860.100.85
weights1.460.151.40
zero_to_na0.020.000.01