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This page was generated on 2021-10-19 12:05:19 -0400 (Tue, 19 Oct 2021).

CHECK results for autonomics on merida1

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 99/2060HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
autonomics 1.1.7  (landing page)
Aditya Bhagwat
Snapshot Date: 2021-10-18 14:50:10 -0400 (Mon, 18 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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:autonomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings autonomics_1.1.7.tar.gz
StartedAt: 2021-10-19 00:44:07 -0400 (Tue, 19 Oct 2021)
EndedAt: 2021-10-19 00:58:46 -0400 (Tue, 19 Oct 2021)
EllapsedTime: 878.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: autonomics.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:autonomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings autonomics_1.1.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/autonomics.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* 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 ‘1.1.7’
* 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
is_sig                  23.233  0.121  23.384
read_rnaseq_counts      22.589  0.700  23.325
filter_medoid           20.538  0.498  21.068
pca                     16.773  0.149  16.957
fit_limma               15.680  0.108  15.812
explore_imputations     15.224  0.201  15.444
read_somascan           14.630  0.151  14.803
plot_detections         13.133  0.190  13.340
read_rectangles         11.557  0.337  11.915
biplot_covariates       10.874  0.150  11.042
read_metabolon          10.602  0.141  10.758
summarize_fit            9.776  0.180   9.966
plot_venn                8.970  0.116   9.104
explore_transformations  7.661  0.127   7.801
log2transform            7.238  0.117   7.377
plot_features            7.115  0.074   7.199
sumexp_to_long_dt        6.999  0.172   7.178
subtract_baseline        7.024  0.075   7.115
read_proteingroups       6.909  0.071   6.987
plot_violins             6.739  0.103   6.858
analyze                  6.386  0.215   6.611
plot_boxplots            6.119  0.075   6.205
biplot_corrections       5.583  0.114   5.705
add_smiles               3.444  0.144  10.055
* 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-3.14-bioc/meat/autonomics.Rcheck/00check.log’
for details.



Installation output

autonomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/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 Patched (2021-08-22 r80813) -- "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 
180.362   3.293 183.915 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS000
MAXQUANT_PATTERNS_PEPCOUNTS0.0010.0000.000
MAXQUANT_PATTERNS_QUANTITY0.0000.0000.001
TESTS000
add_smiles 3.444 0.14410.055
analysis2.4170.1252.605
analyze6.3860.2156.611
assert_is_valid_sumexp2.2860.1222.413
biplot4.0660.0924.165
biplot_corrections5.5830.1145.705
biplot_covariates10.874 0.15011.042
center4.0640.0874.198
contrast_subgroup_cols1.0270.0501.076
contrastdefs3.5380.0653.609
counts2.6920.0742.799
counts2cpm2.8990.0952.997
counts2tpm1.3970.0191.417
cpm3.0380.0923.133
create_design4.4180.0924.516
create_sfile2.3080.0562.366
default_formula1.1900.0501.242
default_sfile0.4600.0170.478
download_data3.5910.1593.768
download_gtf000
dt2mat0.0040.0000.004
explore_imputations15.224 0.20115.444
explore_transformations7.6610.1277.801
extract_features1.8890.0501.945
extract_rectangle1.3860.0711.459
fdata1.8350.0491.885
filter_exprs_replicated_in_some_subgroup1.9900.0652.057
filter_features1.3250.0501.377
filter_medoid20.538 0.49821.068
filter_replicated2.2600.0592.320
filter_samples1.5130.0521.567
fit_limma15.680 0.10815.812
flevels1.7920.0431.837
fnames1.9560.0512.008
formula2str0.0000.0010.001
fvalues1.9340.0531.989
fvars1.9640.0482.016
guess_maxquant_quantity3.7350.0803.819
guess_sep0.0010.0000.002
halfnormimpute2.3010.0722.378
impute_systematic_nondetects4.3280.0964.430
invert2.9110.0642.979
is_imputed1.8960.0481.946
is_sig23.233 0.12123.384
limma3.6830.0583.744
log2counts2.5090.0682.584
log2countsratios2.5400.0712.614
log2cpm3.1470.0893.239
log2cpmratios3.0100.0573.070
log2tpm2.4520.0572.511
log2tpmratios2.4850.0572.544
log2transform7.2380.1177.377
make_volcano_dt3.6040.0623.672
matrix2sumexp2.3510.0612.415
merge_sdata1.2540.0401.295
merge_sfile2.6780.1382.895
message_df0.0040.0000.005
occupancies2.9450.0683.016
pca16.773 0.14916.957
plot_boxplots6.1190.0756.205
plot_contrastogram1.8650.0501.920
plot_data3.1110.0623.183
plot_densities3.6100.0833.698
plot_detections13.133 0.19013.340
plot_features7.1150.0747.199
plot_venn8.9700.1169.104
plot_violins6.7390.1036.858
plot_volcano4.0660.0654.136
preprocess_rnaseq_counts4.4700.1324.612
proteingroups2.2920.0652.360
read_affymetrix1.2710.0941.367
read_metabolon10.602 0.14110.758
read_proteingroups6.9090.0716.987
read_rectangles11.557 0.33711.915
read_rnaseq_counts22.589 0.70023.325
read_somascan14.630 0.15114.803
rm_singleton_samples1.3370.0221.361
scaledlibsizes2.9750.0603.038
sdata1.8750.1041.980
slevels1.8400.0491.891
snames1.8800.0481.931
split_by_svar1.6270.0481.677
split_extract1.2120.0451.259
standardize_maxquant_snames0.0030.0000.004
subgroup_matrix1.1650.0561.222
subtract_baseline7.0240.0757.115
sumexp2mae3.0850.0703.163
sumexp_to_long_dt6.9990.1727.178
summarize_fit9.7760.1809.966
svalues1.7580.0571.817
svars1.7280.0501.779
tpm2.4390.0752.521
values1.9070.0451.958
venn_detects1.7340.0531.794
weights2.9370.1123.053
zero_to_na0.0250.0010.025