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This page was generated on 2021-10-26 14:06:16 -0400 (Tue, 26 Oct 2021).

CHECK results for autonomics on nebbiolo2

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 99/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
autonomics 1.1.7  (landing page)
Aditya Bhagwat
Snapshot Date: 2021-10-25 14:50:11 -0400 (Mon, 25 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
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  

Summary

Package: autonomics
Version: 1.1.7
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:autonomics.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings autonomics_1.1.7.tar.gz
StartedAt: 2021-10-25 19:10:25 -0400 (Mon, 25 Oct 2021)
EndedAt: 2021-10-25 19:19:25 -0400 (Mon, 25 Oct 2021)
EllapsedTime: 539.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: autonomics.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:autonomics.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings autonomics_1.1.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/autonomics.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (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 ‘1.1.7’
* 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 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 ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
read_rnaseq_counts      17.624  0.124  16.904
explore_imputations     12.087  0.317  11.784
is_sig                  12.227  0.052  11.783
filter_medoid           10.977  0.120  10.985
pca                      9.777  0.064   9.841
read_somascan            9.274  0.092   9.236
read_rectangles          8.809  0.172   8.965
plot_detections          8.714  0.140   8.299
fit_limma                8.501  0.092   8.347
read_metabolon           7.039  0.016   6.947
biplot_covariates        6.743  0.196   6.940
summarize_fit            6.543  0.116   5.998
explore_transformations  5.475  0.105   5.260
read_proteingroups       5.312  0.028   4.810
plot_venn                4.935  0.080   4.841
* 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
  ‘/home/biocbuild/bbs-3.14-bioc/meat/autonomics.Rcheck/00check.log’
for details.



Installation output

autonomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL autonomics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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-pc-linux-gnu (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 
108.770   2.442 105.646 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS000
MAXQUANT_PATTERNS_PEPCOUNTS000
MAXQUANT_PATTERNS_QUANTITY0.0000.0000.001
TESTS000
add_smiles2.3960.1642.953
analysis2.2020.1432.182
analyze4.3140.4594.672
assert_is_valid_sumexp1.5610.0881.649
biplot2.4790.1482.627
biplot_corrections3.6840.1043.789
biplot_covariates6.7430.1966.940
center3.0300.4413.260
contrast_subgroup_cols0.8140.0120.826
contrastdefs2.3480.1002.169
counts2.1890.0722.155
counts2cpm2.5580.1522.592
counts2tpm1.0470.0240.963
cpm2.0000.0371.923
create_design3.9710.0764.014
create_sfile1.7310.0641.511
default_formula0.9910.0121.003
default_sfile0.2840.0000.284
download_data2.3730.1242.575
download_gtf000
dt2mat0.0030.0000.003
explore_imputations12.087 0.31711.784
explore_transformations5.4750.1055.260
extract_features1.3760.0151.195
extract_rectangle0.9970.0041.002
fdata1.3130.0241.154
filter_exprs_replicated_in_some_subgroup1.5240.0401.477
filter_features0.9920.0040.996
filter_medoid10.977 0.12010.985
filter_replicated1.7430.0201.470
filter_samples0.9880.0040.991
fit_limma8.5010.0928.347
flevels1.4330.0321.276
fnames1.4560.0111.282
formula2str0.0010.0000.000
fvalues1.3980.0241.222
fvars1.3910.0241.224
guess_maxquant_quantity3.5240.0803.202
guess_sep0.0010.0000.000
halfnormimpute0.5480.0400.588
impute_systematic_nondetects3.9510.0763.724
invert2.0860.0161.804
is_imputed1.3790.0481.218
is_sig12.227 0.05211.783
limma2.2110.0201.974
log2counts1.9050.0241.808
log2countsratios1.7850.0161.700
log2cpm1.7220.0201.639
log2cpmratios1.7740.0081.676
log2tpm1.7510.0041.656
log2tpmratios2.4040.0562.362
log2transform4.4180.0324.152
make_volcano_dt3.0130.0802.675
matrix2sumexp1.4680.0281.494
merge_sdata0.7930.0000.793
merge_sfile1.8330.0641.591
message_df0.0020.0000.002
occupancies1.6130.0241.339
pca9.7770.0649.841
plot_boxplots3.6860.0003.651
plot_contrastogram1.2760.0081.256
plot_data1.5910.0321.623
plot_densities2.5900.0442.623
plot_detections8.7140.1408.299
plot_features4.1860.0124.198
plot_venn4.9350.0804.841
plot_violins4.0920.0284.100
plot_volcano3.1210.0202.653
preprocess_rnaseq_counts2.6990.0522.634
proteingroups1.7310.0121.434
read_affymetrix0.9420.0120.954
read_metabolon7.0390.0166.947
read_proteingroups5.3120.0284.810
read_rectangles8.8090.1728.965
read_rnaseq_counts17.624 0.12416.904
read_somascan9.2740.0929.236
rm_singleton_samples0.8010.0040.804
scaledlibsizes1.5740.0161.483
sdata2.1270.0161.949
slevels1.2570.0041.062
snames1.2210.0211.057
split_by_svar1.1410.0160.977
split_extract0.7730.0120.786
standardize_maxquant_snames0.0020.0000.002
subgroup_matrix0.7990.0040.803
subtract_baseline4.3340.0204.285
sumexp2mae1.9550.0201.975
sumexp_to_long_dt4.9500.0244.330
summarize_fit6.5430.1165.998
svalues1.4240.0231.251
svars1.2840.0161.115
tpm1.8010.0041.707
values1.2610.0201.091
venn_detects1.2090.0121.053
weights2.0670.0361.704
zero_to_na0.0160.0000.016