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This page was generated on 2021-10-22 12:04:50 -0400 (Fri, 22 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.
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raw results

Package 99/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
autonomics 1.1.7  (landing page)
Aditya Bhagwat
Snapshot Date: 2021-10-21 14:50:08 -0400 (Thu, 21 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: 2021-10-22 00:50:22 -0400 (Fri, 22 Oct 2021)
EndedAt: 2021-10-22 01:04:43 -0400 (Fri, 22 Oct 2021)
EllapsedTime: 861.6 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
read_rnaseq_counts      23.449  0.697  24.206
is_sig                  22.551  0.118  22.701
filter_medoid           18.847  0.529  19.404
pca                     17.040  0.163  17.235
explore_imputations     15.836  0.212  16.068
fit_limma               15.543  0.115  15.677
read_somascan           14.339  0.175  14.536
plot_detections         13.182  0.176  13.376
read_rectangles         11.691  0.340  12.054
biplot_covariates       10.818  0.156  10.991
read_metabolon          10.306  0.138  10.464
summarize_fit           10.046  0.166  10.229
plot_venn                8.976  0.081   9.068
explore_transformations  8.029  0.139   8.178
log2transform            7.155  0.099   7.267
plot_features            7.089  0.055   7.153
plot_violins             6.767  0.108   6.885
subtract_baseline        6.603  0.202   6.816
analyze                  6.554  0.206   6.772
read_proteingroups       6.661  0.075   6.773
sumexp_to_long_dt        6.478  0.193   6.679
plot_boxplots            6.454  0.078   6.544
biplot_corrections       5.617  0.118   5.743
* 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 
179.714   3.462 183.444 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS0.0010.0000.001
MAXQUANT_PATTERNS_PEPCOUNTS000
MAXQUANT_PATTERNS_QUANTITY0.0000.0000.001
TESTS000
add_smiles3.3110.1403.990
analysis2.4700.1312.642
analyze6.5540.2066.772
assert_is_valid_sumexp2.4340.1232.564
biplot4.1270.0974.232
biplot_corrections5.6170.1185.743
biplot_covariates10.818 0.15610.991
center4.1700.0924.311
contrast_subgroup_cols1.1940.0521.249
contrastdefs3.5680.0653.636
counts2.6990.0692.796
counts2cpm2.8920.0812.976
counts2tpm1.2940.0221.319
cpm2.9320.0733.007
create_design4.2680.0974.371
create_sfile2.1460.0582.208
default_formula1.1720.0421.215
default_sfile0.4330.0140.447
download_data3.4130.1673.597
download_gtf0.0000.0010.000
dt2mat0.0030.0000.004
explore_imputations15.836 0.21216.068
explore_transformations8.0290.1398.178
extract_features1.8180.0451.866
extract_rectangle1.3320.0671.402
fdata1.8590.0491.911
filter_exprs_replicated_in_some_subgroup1.9060.0551.962
filter_features1.1120.0531.166
filter_medoid18.847 0.52919.404
filter_replicated2.3250.0592.387
filter_samples1.4910.0491.542
fit_limma15.543 0.11515.677
flevels1.8450.0521.899
fnames1.6890.0401.730
formula2str0.0010.0000.001
fvalues1.8440.0451.891
fvars1.7500.0441.796
guess_maxquant_quantity3.5010.0843.589
guess_sep0.0010.0000.001
halfnormimpute2.1360.0592.198
impute_systematic_nondetects4.0620.0874.153
invert2.7630.0542.821
is_imputed1.7770.0421.822
is_sig22.551 0.11822.701
limma3.8380.0623.906
log2counts2.7120.0882.802
log2countsratios2.7050.0652.774
log2cpm3.2430.1243.370
log2cpmratios3.1080.0673.178
log2tpm2.5290.0812.613
log2tpmratios2.5770.0672.648
log2transform7.1550.0997.267
make_volcano_dt3.6270.0583.689
matrix2sumexp2.3540.0512.408
merge_sdata1.2750.0391.315
merge_sfile2.6400.1352.853
message_df0.0040.0000.004
occupancies2.8200.0592.881
pca17.040 0.16317.235
plot_boxplots6.4540.0786.544
plot_contrastogram1.9410.0662.014
plot_data3.2700.0833.375
plot_densities3.4370.0823.533
plot_detections13.182 0.17613.376
plot_features7.0890.0557.153
plot_venn8.9760.0819.068
plot_violins6.7670.1086.885
plot_volcano4.0570.0634.144
preprocess_rnaseq_counts4.4200.1434.615
proteingroups2.3120.0572.373
read_affymetrix1.1800.0871.270
read_metabolon10.306 0.13810.464
read_proteingroups6.6610.0756.773
read_rectangles11.691 0.34012.054
read_rnaseq_counts23.449 0.69724.206
read_somascan14.339 0.17514.536
rm_singleton_samples1.3270.0231.350
scaledlibsizes2.9850.0583.048
sdata1.8810.0931.978
slevels1.8180.0481.870
snames1.9130.0581.974
split_by_svar1.5830.0471.631
split_extract1.2800.0511.334
standardize_maxquant_snames0.0050.0000.005
subgroup_matrix1.1510.0411.195
subtract_baseline6.6030.2026.816
sumexp2mae3.1070.0603.173
sumexp_to_long_dt6.4780.1936.679
summarize_fit10.046 0.16610.229
svalues1.7440.0441.790
svars1.8630.0411.907
tpm2.5050.0642.572
values1.8870.0521.946
venn_detects1.7060.0481.758
weights2.9670.1173.089
zero_to_na0.0170.0010.018