Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:05:04 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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

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? 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 1.2.0  (landing page)
Aditya Bhagwat
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/autonomics
git_branch: RELEASE_3_14
git_last_commit: f775f33
git_last_commit_date: 2021-10-26 13:07:36 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: autonomics
Version: 1.2.0
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_1.2.0.tar.gz
StartedAt: 2022-04-12 06:25:35 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 06:34:30 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 534.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: autonomics.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### 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_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/autonomics.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.2.0’
* 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  16.845  0.104  16.088
explore_imputations 12.235  0.311  11.897
is_sig              12.002  0.112  11.719
filter_medoid       10.765  0.100  10.763
read_rectangles     10.222  0.156  10.358
plot_detections      9.669  0.180   9.289
pca                  9.718  0.020   9.738
read_somascan        9.166  0.064   9.107
fit_limma            8.314  0.076   8.144
biplot_covariates    6.434  0.088   6.522
read_metabolon       6.478  0.032   6.402
summarize_fit        6.254  0.124   5.736
analyze              5.562  0.180   5.638
* 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 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 
108.822   1.859 105.275 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS000
MAXQUANT_PATTERNS_PEPCOUNTS000
MAXQUANT_PATTERNS_QUANTITY000
TESTS000
add_smiles2.4860.1413.016
analysis1.3430.0681.251
analyze5.5620.1805.638
assert_is_valid_sumexp1.5530.0881.641
biplot2.4290.1842.613
biplot_corrections3.3250.0283.353
biplot_covariates6.4340.0886.522
center2.3500.0802.226
contrast_subgroup_cols0.8320.0120.843
contrastdefs2.3250.0282.101
counts2.7790.1482.817
counts2cpm2.3620.0202.275
counts2tpm1.1480.0281.058
cpm1.7880.0041.682
create_design2.6480.0442.580
create_sfile1.5790.0241.343
default_formula0.9240.0120.937
default_sfile0.2710.0040.275
download_data2.5000.0762.666
download_gtf000
dt2mat0.0020.0000.003
explore_imputations12.235 0.31111.897
explore_transformations4.7030.1044.488
extract_features1.2880.0201.133
extract_rectangle0.9840.0160.999
fdata1.2610.0201.104
filter_exprs_replicated_in_some_subgroup1.3950.0041.305
filter_features0.9700.0080.979
filter_medoid10.765 0.10010.763
filter_replicated1.6680.0281.435
filter_samples1.0580.0121.071
fit_limma8.3140.0768.144
flevels1.3920.0361.234
fnames1.3690.0131.191
formula2str0.0010.0000.001
fvalues1.3550.0241.180
fvars1.3140.0091.147
guess_maxquant_quantity2.6900.0222.328
guess_sep0.0000.0000.001
halfnormimpute1.3860.0561.442
impute_systematic_nondetects3.7980.0283.461
invert1.9900.0231.703
is_imputed1.3110.0121.132
is_sig12.002 0.11211.719
limma2.1510.0291.937
log2counts1.7860.0161.700
log2countsratios1.7970.0201.712
log2cpm1.7940.0401.723
log2cpmratios2.4300.0122.345
log2tpm1.7390.0071.639
log2tpmratios2.4720.0042.372
log2transform4.3130.0134.009
make_volcano_dt2.3080.0071.925
matrix2sumexp1.5980.0281.623
merge_sdata0.9050.0000.904
merge_sfile1.8580.0841.649
message_df0.0020.0000.002
occupancies1.6990.0041.427
pca9.7180.0209.738
plot_boxplots3.6580.0683.706
plot_contrastogram1.2470.0201.239
plot_data1.5100.0041.514
plot_densities2.6030.0282.617
plot_detections9.6690.1809.289
plot_features4.0270.0044.032
plot_venn4.5610.0204.422
plot_violins4.1270.0204.111
plot_volcano3.4820.0523.152
preprocess_rnaseq_counts2.6520.0402.583
proteingroups1.7820.0321.501
read_affymetrix0.7390.0200.759
read_metabolon6.4780.0326.402
read_proteingroups4.7360.0844.315
read_rectangles10.222 0.15610.358
read_rnaseq_counts16.845 0.10416.088
read_somascan9.1660.0649.107
rm_singleton_samples0.8230.0080.832
scaledlibsizes2.8630.1122.861
sdata2.3080.0122.119
slevels1.2390.0201.077
snames1.2360.0081.066
split_by_svar1.1810.0081.022
split_extract0.8220.0200.842
standardize_maxquant_snames0.0010.0000.002
subgroup_matrix0.8180.0040.822
subtract_baseline4.3190.1004.346
sumexp2mae2.0640.0122.077
sumexp_to_long_dt4.8150.0644.267
summarize_fit6.2540.1245.736
svalues1.2470.0041.064
svars1.2250.0121.065
tpm1.8530.0001.745
values1.3220.0201.166
venn_detects1.2800.0241.131
weights2.0640.0201.731
zero_to_na0.0150.0000.015