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This page was generated on 2024-02-22 11:37:30 -0500 (Thu, 22 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4691
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4444
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4465
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 111/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
autonomics 1.10.2  (landing page)
Aditya Bhagwat
Snapshot Date: 2024-02-21 14:05:05 -0500 (Wed, 21 Feb 2024)
git_url: https://git.bioconductor.org/packages/autonomics
git_branch: RELEASE_3_18
git_last_commit: 230045c
git_last_commit_date: 2023-11-08 04:08:57 -0500 (Wed, 08 Nov 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    ERROR  skipped
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for autonomics on lconway


To the developers/maintainers of the autonomics package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: autonomics
Version: 1.10.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:autonomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings autonomics_1.10.2.tar.gz
StartedAt: 2024-02-21 18:48:34 -0500 (Wed, 21 Feb 2024)
EndedAt: 2024-02-21 18:59:05 -0500 (Wed, 21 Feb 2024)
EllapsedTime: 631.4 seconds
RetCode: 0
Status:   OK  
CheckDir: autonomics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:autonomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings autonomics_1.10.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/autonomics.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘autonomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘autonomics’ version ‘1.10.2’
* 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 for sufficient/correct file permissions ... 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
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
read_rnaseq_counts      15.555  1.052  16.715
pca                     12.207  0.407  12.689
filter_medoid           11.186  0.913  12.179
is_sig                  11.174  0.202  11.431
read_somascan           10.769  0.328  11.177
explore_imputations      9.687  0.339  10.084
read_rectangles          9.055  0.520   9.704
plot_detections          8.269  0.475   8.806
fit_limma                8.393  0.247   8.678
summarize_fit            7.471  0.419   7.948
biplot_covariates        7.503  0.342   7.886
read_metabolon           7.195  0.481   7.724
plot_boxplots            5.783  0.307   6.151
plot_features            5.637  0.259   5.940
explore_transformations  5.513  0.305   5.866
analyze                  5.175  0.390   5.602
subtract_baseline        5.132  0.395   5.574
plot_venn                5.138  0.163   5.341
plot_violins             4.989  0.305   5.346
sumexp_to_long_dt        4.632  0.458   5.141
biplot_corrections       4.712  0.363   5.104
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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 NOTE
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/autonomics.Rcheck/00check.log’
for details.



Installation output

autonomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL autonomics
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* 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
** 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
* DONE (autonomics)

Tests output

autonomics.Rcheck/tests/testthat.Rout


R version 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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 103 ]
> 
> proc.time()
   user  system elapsed 
116.597   7.077 124.516 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS0.0000.0010.001
MAXQUANT_PATTERNS_PEPCOUNTS0.0000.0010.000
MAXQUANT_PATTERNS_QUANTITY0.0010.0000.001
TESTS000
add_smiles2.3270.2953.248
analysis1.6160.0851.772
analyze5.1750.3905.602
assert_is_valid_sumexp1.6870.3552.075
biplot3.5710.3193.933
biplot_corrections4.7120.3635.104
biplot_covariates7.5030.3427.886
center2.2160.1182.415
contrast_subgroup_cols0.8870.1971.092
contrastdefs2.6430.0992.760
counts1.5210.1701.745
counts2cpm1.2690.1821.463
counts2tpm0.6890.0440.737
cpm1.4280.1221.560
create_design2.2770.1512.448
create_sfile1.3200.0911.424
default_formula1.7260.3392.085
default_sfile0.1780.0270.209
download_data1.4250.2281.681
download_gtf000
dt2mat0.0050.0000.005
explore_imputations 9.687 0.33910.084
explore_transformations5.5130.3055.866
extract_features1.0730.0721.158
extract_rectangle0.8410.2231.078
fdata0.9360.0671.009
filter_exprs_replicated_in_some_subgroup1.6030.2831.953
filter_features1.0460.3071.372
filter_medoid11.186 0.91312.179
filter_replicated1.1900.0871.281
filter_samples1.0470.2371.294
fit_limma8.3930.2478.678
flevels0.9170.0560.982
fnames1.0160.0621.085
formula2str000
fvalues1.0680.0691.148
fvars1.0660.0601.132
guess_maxquant_quantity1.9380.1402.107
guess_sep0.0010.0010.001
halfnormimpute1.4600.0951.572
impute_systematic_nondetects2.4770.1582.654
invert1.4460.0951.557
is_imputed1.0220.0621.091
is_sig11.174 0.20211.431
limma1.7930.0801.879
log2counts1.4630.1281.598
log2countsratios1.4040.0971.510
log2cpm2.0920.1692.267
log2cpmratios1.4570.1051.573
log2tpm1.4990.1081.618
log2tpmratios1.5120.1071.630
log2transform4.6760.1934.903
make_volcano_dt1.7330.0951.838
matrix2sumexp1.7380.2692.023
merge_sdata0.8280.1630.998
merge_sfile1.5660.1681.889
message_df0.0020.0000.002
occupancies1.3600.0971.468
pca12.207 0.40712.689
plot_boxplots5.7830.3076.151
plot_contrastogram1.3160.2341.570
plot_data1.9130.2442.177
plot_densities2.5080.3412.869
plot_detections8.2690.4758.806
plot_features5.6370.2595.940
plot_venn5.1380.1635.341
plot_violins4.9890.3055.346
plot_volcano2.4920.1072.618
preprocess_rnaseq_counts2.1410.1532.320
proteingroups2.0160.1362.160
read_affymetrix0.8890.1671.077
read_metabolon7.1950.4817.724
read_proteingroups4.0190.1414.182
read_rectangles9.0550.5209.704
read_rnaseq_counts15.555 1.05216.715
read_somascan10.769 0.32811.177
rm_singleton_samples0.8590.0370.903
scaledlibsizes1.5530.1331.701
sdata1.1210.1041.240
slevels0.9730.0571.037
snames1.0960.1221.229
split_by_svar0.9280.0701.012
split_extract0.8420.2501.101
standardize_maxquant_snames0.0010.0000.002
subgroup_matrix0.9520.2271.190
subtract_baseline5.1320.3955.574
sumexp2mae2.0700.4002.494
sumexp_to_long_dt4.6320.4585.141
summarize_fit7.4710.4197.948
svalues1.0750.0871.171
svars1.0970.0961.201
tpm1.5450.1141.691
values1.1170.0741.203
venn_detects1.0390.1081.157
weights1.7710.1411.938
zero_to_na0.0220.0020.025