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This page was generated on 2021-09-22 15:05:37 -0400 (Wed, 22 Sep 2021).

CHECK results for autonomics on machv2

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: 2021-09-21 04:50:12 -0400 (Tue, 21 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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:autonomics.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings autonomics_1.0.1.tar.gz
StartedAt: 2021-09-21 16:27:57 -0400 (Tue, 21 Sep 2021)
EndedAt: 2021-09-21 16:41:37 -0400 (Tue, 21 Sep 2021)
EllapsedTime: 819.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: autonomics.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:autonomics.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings autonomics_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/autonomics.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘autonomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘autonomics’ version ‘1.0.1’
* 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 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 ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
read_rnaseq_counts      22.338  0.750  23.251
is_sig                  20.761  0.085  20.859
filter_medoid           18.711  0.632  19.357
pca                     16.991  0.144  17.151
explore_imputations     15.653  0.228  15.891
read_somascan           13.829  0.170  14.018
fit_limma               13.101  0.142  13.256
plot_detections         12.967  0.234  13.241
biplot_covariates       10.882  0.136  11.061
summarize_fit           10.711  0.222  10.940
read_rectangles         10.516  0.307  10.829
read_metabolon          10.236  0.168  10.419
plot_venn                9.279  0.158   9.450
plot_features            7.657  0.067   7.732
explore_transformations  7.183  0.215   7.403
analyze                  6.782  0.166   6.954
sumexp_to_long_dt        6.771  0.169   6.944
plot_boxplots            6.865  0.068   6.938
log2transform            6.721  0.122   6.853
subtract_baseline        6.560  0.087   6.650
read_proteingroups       6.548  0.080   6.649
plot_violins             6.215  0.125   6.352
biplot_corrections       5.016  0.139   5.158
* 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 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/autonomics.Rcheck/00check.log’
for details.



Installation output

autonomics.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 
170.730   3.770 174.725 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS0.0010.0010.001
MAXQUANT_PATTERNS_PEPCOUNTS0.0000.0000.001
MAXQUANT_PATTERNS_QUANTITY0.0000.0000.001
TESTS0.0000.0000.001
add_smiles3.0640.1343.517
analysis1.9330.1172.095
analyze6.7820.1666.954
assert_is_valid_sumexp2.1340.1272.266
biplot3.8500.0983.952
biplot_corrections5.0160.1395.158
biplot_covariates10.882 0.13611.061
center2.9790.0863.147
contrast_subgroup_cols1.1280.0471.176
contrastdefs3.2550.0643.355
counts2.6150.1062.748
counts2cpm2.6760.1132.790
counts2tpm1.1000.0151.118
cpm2.8520.1162.972
create_design3.7110.1123.829
create_sfile2.0590.0552.115
default_formula1.1160.0551.171
default_sfile0.3400.0040.345
download_data3.1990.1643.378
download_gtf000
dt2mat0.0050.0010.005
explore_imputations15.653 0.22815.891
explore_transformations7.1830.2157.403
extract_features1.7480.0521.801
extract_rectangle1.3100.0821.394
fdata1.6120.0431.656
filter_exprs_replicated_in_some_subgroup1.7480.0581.806
filter_features1.2320.0501.283
filter_medoid18.711 0.63219.357
filter_replicated2.2950.0542.352
filter_samples1.2540.0461.301
fit_limma13.101 0.14213.256
flevels1.7030.0371.740
fnames1.5550.0411.600
formula2str0.0000.0000.001
fvalues1.6120.0421.656
fvars1.7450.0441.791
guess_maxquant_quantity3.3840.0773.462
guess_sep0.0010.0010.001
halfnormimpute1.4840.0511.537
impute_systematic_nondetects4.1430.0974.242
invert3.2960.0733.370
is_imputed1.5090.0401.550
is_sig20.761 0.08520.859
limma3.4190.0573.478
log2counts2.4630.0552.520
log2countsratios2.6040.1462.751
log2cpm2.4280.2342.663
log2cpmratios2.2640.0662.333
log2tpm2.6110.1982.817
log2tpmratios3.2080.1563.388
log2transform6.7210.1226.853
make_volcano_dt3.6430.0603.709
matrix2sumexp2.3600.0712.443
merge_sdata1.2420.0451.290
merge_sfile3.3670.1693.620
message_df0.0040.0000.004
occupancies2.4790.0682.550
pca16.991 0.14417.151
plot_boxplots6.8650.0686.938
plot_contrastogram1.8490.0641.916
plot_data2.4780.0762.557
plot_densities3.7600.1163.880
plot_detections12.967 0.23413.241
plot_features7.6570.0677.732
plot_venn9.2790.1589.450
plot_violins6.2150.1256.352
plot_volcano3.9220.0714.079
preprocess_rnaseq_counts3.2980.1623.463
proteingroups2.0740.0392.115
read_affymetrix1.9660.1312.187
read_metabolon10.236 0.16810.419
read_proteingroups6.5480.0806.649
read_rectangles10.516 0.30710.829
read_rnaseq_counts22.338 0.75023.251
read_somascan13.829 0.17014.018
rm_singleton_samples1.2030.1221.325
scaledlibsizes2.2680.0662.337
sdata1.9090.0761.986
slevels1.8670.0441.912
snames1.9430.0531.996
split_by_svar1.5980.0881.687
split_extract1.1340.0511.185
standardize_maxquant_snames0.0030.0010.003
subgroup_matrix1.0800.0361.116
subtract_baseline6.5600.0876.650
sumexp2mae3.2710.0933.365
sumexp_to_long_dt6.7710.1696.944
summarize_fit10.711 0.22210.940
svalues1.9260.0712.005
svars1.6210.0601.680
tpm2.1200.0322.152
values1.6620.0861.748
venn_detects1.6230.0541.679
weights2.7290.1062.843
zero_to_na0.0220.0020.026