Back to Multiple platform build/check report for BioC 3.14
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-10-23 14:05:53 -0400 (Sat, 23 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: 2021-10-22 14:50:11 -0400 (Fri, 22 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: /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: 2021-10-22 19:08:32 -0400 (Fri, 22 Oct 2021)
EndedAt: 2021-10-22 19:17:25 -0400 (Fri, 22 Oct 2021)
EllapsedTime: 533.2 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_1.1.7.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      17.221  0.192  16.534
explore_imputations     12.501  0.347  12.204
is_sig                  11.750  0.101  11.388
filter_medoid           10.766  0.180  10.834
read_somascan           10.036  0.116  10.027
pca                     10.049  0.032  10.082
plot_detections          8.813  0.143   8.367
fit_limma                8.363  0.048   8.170
read_rectangles          7.936  0.092   8.011
biplot_covariates        7.082  0.144   7.226
summarize_fit            6.670  0.044   6.030
read_metabolon           6.330  0.032   6.256
explore_transformations  5.775  0.104   5.576
plot_venn                5.625  0.096   5.555
sumexp_to_long_dt        5.113  0.040   4.542
* 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 
107.077   1.463 103.128 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS000
MAXQUANT_PATTERNS_PEPCOUNTS000
MAXQUANT_PATTERNS_QUANTITY0.0000.0000.001
TESTS000
add_smiles2.3670.1232.883
analysis2.3140.1242.224
analyze4.4690.4474.799
assert_is_valid_sumexp1.6880.1441.833
biplot2.7130.1522.865
biplot_corrections3.6120.1083.720
biplot_covariates7.0820.1447.226
center3.1780.4163.420
contrast_subgroup_cols0.7960.0080.804
contrastdefs2.4080.0482.162
counts2.1580.0602.129
counts2cpm2.4860.1402.518
counts2tpm1.0580.0120.952
cpm1.9380.0401.865
create_design3.4310.0803.401
create_sfile1.6280.0561.409
default_formula0.9270.0360.963
default_sfile0.3120.0000.312
download_data2.4210.1082.652
download_gtf000
dt2mat0.0030.0000.003
explore_imputations12.501 0.34712.204
explore_transformations5.7750.1045.576
extract_features1.2920.0201.136
extract_rectangle0.9520.0200.971
fdata1.2240.0161.069
filter_exprs_replicated_in_some_subgroup1.4730.0081.390
filter_features0.9860.0241.010
filter_medoid10.766 0.18010.834
filter_replicated1.6950.0401.425
filter_samples1.0030.0321.034
fit_limma8.3630.0488.170
flevels1.4180.0481.275
fnames1.3980.0241.228
formula2str0.0010.0000.000
fvalues1.3020.0161.123
fvars1.3200.0121.154
guess_maxquant_quantity3.5620.1123.219
guess_sep0.0010.0000.001
halfnormimpute0.5810.0270.609
impute_systematic_nondetects3.5990.0963.394
invert1.8880.0401.661
is_imputed1.2850.0191.109
is_sig11.750 0.10111.388
limma2.2900.0322.048
log2counts1.7950.0481.737
log2countsratios1.7640.0281.694
log2cpm1.6540.0041.558
log2cpmratios1.7220.0041.620
log2tpm1.7140.0031.618
log2tpmratios2.3500.0252.268
log2transform4.3320.0274.100
make_volcano_dt3.1830.0602.827
matrix2sumexp1.5050.0081.510
merge_sdata0.7870.0240.811
merge_sfile1.8300.0571.562
message_df0.0020.0000.002
occupancies1.6100.0161.345
pca10.049 0.03210.082
plot_boxplots4.0590.0604.088
plot_contrastogram1.4870.0241.482
plot_data1.6060.0081.615
plot_densities2.5000.0242.507
plot_detections8.8130.1438.367
plot_features4.5400.0044.544
plot_venn5.6250.0965.555
plot_violins3.8840.0483.911
plot_volcano2.8530.0202.465
preprocess_rnaseq_counts2.6860.0482.623
proteingroups1.5510.0161.283
read_affymetrix0.8510.0080.860
read_metabolon6.3300.0326.256
read_proteingroups4.8280.0244.321
read_rectangles7.9360.0928.011
read_rnaseq_counts17.221 0.19216.534
read_somascan10.036 0.11610.027
rm_singleton_samples0.770.000.77
scaledlibsizes1.5590.0481.499
sdata1.3350.0721.197
slevels1.2230.0241.061
snames1.2860.0001.112
split_by_svar1.1680.0121.013
split_extract0.7890.0120.802
standardize_maxquant_snames0.0020.0000.001
subgroup_matrix0.7920.0040.797
subtract_baseline4.6200.0084.553
sumexp2mae1.9740.0161.991
sumexp_to_long_dt5.1130.0404.542
summarize_fit6.6700.0446.030
svalues1.2900.0121.108
svars1.2290.0241.072
tpm1.8450.0081.746
values1.2970.0201.117
venn_detects1.2100.0241.045
weights2.0740.0321.748
zero_to_na0.0150.0000.015