Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-22 15:04:46 -0400 (Wed, 22 Sep 2021).

CHECK results for autonomics on nebbiolo1

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: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:autonomics.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings autonomics_1.0.1.tar.gz
StartedAt: 2021-09-21 08:53:43 -0400 (Tue, 21 Sep 2021)
EndedAt: 2021-09-21 09:02:53 -0400 (Tue, 21 Sep 2021)
EllapsedTime: 550.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: autonomics.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:autonomics.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings autonomics_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-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 ‘1.0.1’
* 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      16.983  0.191  16.307
explore_imputations     11.914  0.576  11.866
is_sig                  11.690  0.039  11.292
filter_medoid           11.502  0.196  11.589
summarize_fit           10.359  0.036   9.629
read_somascan           10.057  0.060   9.969
pca                      9.900  0.032   9.933
plot_detections          8.957  0.120   8.515
sumexp_to_long_dt        8.315  0.132   7.778
read_rectangles          8.177  0.188   8.349
biplot_covariates        7.571  0.488   8.061
fit_limma                7.742  0.052   7.549
subtract_baseline        6.991  0.076   6.973
read_metabolon           6.366  0.020   6.268
analyze                  5.022  0.212   5.129
explore_transformations  4.952  0.065   4.731
* 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-3.13-bioc/meat/autonomics.Rcheck/00check.log’
for details.



Installation output

autonomics.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL autonomics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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 
108.378   1.471 104.519 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS000
MAXQUANT_PATTERNS_PEPCOUNTS000
MAXQUANT_PATTERNS_QUANTITY000
TESTS000
add_smiles2.3850.0952.872
analysis1.2580.0651.253
analyze5.0220.2125.129
assert_is_valid_sumexp1.5340.0841.613
biplot2.5040.1882.692
biplot_corrections3.5880.0723.660
biplot_covariates7.5710.4888.061
center2.3170.1172.277
contrast_subgroup_cols0.7930.0640.856
contrastdefs2.2170.0271.989
counts2.3890.0882.373
counts2cpm2.7540.0602.702
counts2tpm1.1070.0281.015
cpm2.5070.0532.455
create_design2.5520.0762.523
create_sfile1.5810.0481.361
default_formula0.9020.0120.914
default_sfile0.2740.0000.274
download_data2.3290.1512.638
download_gtf000
dt2mat0.0030.0000.003
explore_imputations11.914 0.57611.866
explore_transformations4.9520.0654.731
extract_features1.4230.0441.270
extract_rectangle0.9470.0200.968
fdata1.4300.0121.237
filter_exprs_replicated_in_some_subgroup1.3920.0361.337
filter_features1.0050.0081.013
filter_medoid11.502 0.19611.589
filter_replicated1.5190.0191.281
filter_samples0.9320.0080.940
fit_limma7.7420.0527.549
flevels1.1800.0051.009
fnames1.2230.0121.055
formula2str0.0010.0000.001
fvalues1.2980.0361.142
fvars1.3050.0191.123
guess_maxquant_quantity2.6720.0332.291
guess_sep0.0010.0000.001
halfnormimpute1.2760.1401.416
impute_systematic_nondetects2.9180.0562.672
invert1.9120.0201.675
is_imputed1.3260.0121.136
is_sig11.690 0.03911.292
limma2.1700.0281.950
log2counts1.8610.0281.773
log2countsratios1.7310.0361.666
log2cpm2.5830.0472.523
log2cpmratios1.9190.0201.829
log2tpm1.7240.0161.636
log2tpmratios1.6470.0201.565
log2transform4.2100.0523.976
make_volcano_dt2.2150.0241.845
matrix2sumexp1.4760.0081.485
merge_sdata0.8620.0040.866
merge_sfile1.9990.0801.793
message_df0.0030.0000.003
occupancies1.6360.0201.341
pca9.9000.0329.933
plot_boxplots3.8480.0603.888
plot_contrastogram1.1900.0041.167
plot_data1.5530.0201.574
plot_densities2.4610.0962.540
plot_detections8.9570.1208.515
plot_features4.3280.0084.335
plot_venn4.9500.0084.791
plot_violins4.7650.0924.836
plot_volcano2.6260.0162.278
preprocess_rnaseq_counts2.6830.0602.629
proteingroups1.7080.0401.433
read_affymetrix0.9080.0320.940
read_metabolon6.3660.0206.268
read_proteingroups4.3530.1003.970
read_rectangles8.1770.1888.349
read_rnaseq_counts16.983 0.19116.307
read_somascan10.057 0.060 9.969
rm_singleton_samples1.1720.0081.179
scaledlibsizes2.1550.0002.041
sdata1.7890.0161.603
slevels1.4180.0081.229
snames1.5650.0201.376
split_by_svar1.4040.0721.253
split_extract1.2790.0281.319
standardize_maxquant_snames0.0040.0000.004
subgroup_matrix1.3760.0081.384
subtract_baseline6.9910.0766.973
sumexp2mae3.1090.0163.125
sumexp_to_long_dt8.3150.1327.778
summarize_fit10.359 0.036 9.629
svalues2.0650.0161.854
svars1.9250.0241.724
tpm1.9860.0041.871
values1.8500.0161.662
venn_detects1.3740.0161.288
weights2.7500.0842.434
zero_to_na0.0250.0000.024