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This page was generated on 2021-11-26 15:05:42 -0500 (Fri, 26 Nov 2021).

CHECK results for autonomics on machv2

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 1.2.0  (landing page)
Aditya Bhagwat
Snapshot Date: 2021-11-25 04:15:05 -0500 (Thu, 25 Nov 2021)
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 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 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: /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_1.2.0.tar.gz
StartedAt: 2021-11-25 13:55:51 -0500 (Thu, 25 Nov 2021)
EndedAt: 2021-11-25 14:10:50 -0500 (Thu, 25 Nov 2021)
EllapsedTime: 898.9 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_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/autonomics.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.2.0’
* 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           24.351  0.740  25.126
is_sig                       23.941  0.106  24.073
filter_medoid                20.463  0.556  21.042
pca                          18.340  0.142  18.512
explore_imputations          16.375  0.250  16.637
fit_limma                    16.137  0.199  16.354
read_somascan                15.270  0.203  15.489
plot_detections              14.530  0.237  14.787
read_rectangles              11.848  0.410  12.269
biplot_covariates            11.945  0.150  12.118
summarize_fit                11.603  0.306  11.918
read_metabolon               11.649  0.220  11.902
plot_venn                     9.358  0.130   9.661
explore_transformations       8.103  0.182   8.292
subtract_baseline             8.068  0.093   8.168
plot_features                 7.745  0.094   7.849
sumexp_to_long_dt             7.588  0.212   7.807
read_proteingroups            7.401  0.077   7.485
analyze                       7.180  0.239   7.429
plot_violins                  7.266  0.115   7.388
log2transform                 6.875  0.087   6.973
biplot_corrections            6.400  0.169   6.578
plot_boxplots                 6.440  0.064   6.512
impute_systematic_nondetects  5.470  0.138   5.611
* 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 4.1.2 (2021-11-01) -- "Bird Hippie"
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 
186.843   3.720 190.945 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS0.0000.0000.001
MAXQUANT_PATTERNS_PEPCOUNTS0.0000.0010.001
MAXQUANT_PATTERNS_QUANTITY0.0000.0000.001
TESTS0.0000.0000.001
add_smiles3.2980.1373.899
analysis1.8410.1332.010
analyze7.1800.2397.429
assert_is_valid_sumexp2.4690.1382.612
biplot3.9950.1124.112
biplot_corrections6.4000.1696.578
biplot_covariates11.945 0.15012.118
center3.6660.0953.811
contrast_subgroup_cols1.1780.0531.231
contrastdefs3.7020.0633.768
counts2.7840.1052.920
counts2cpm2.9810.2413.225
counts2tpm1.3460.0341.383
cpm2.5310.0882.620
create_design4.6630.1464.813
create_sfile2.5150.0882.604
default_formula1.4660.0891.556
default_sfile0.3970.0110.408
download_data3.6210.1843.822
download_gtf000
dt2mat0.0040.0010.005
explore_imputations16.375 0.25016.637
explore_transformations8.1030.1828.292
extract_features1.9910.0532.044
extract_rectangle1.4310.0721.504
fdata2.1220.0612.185
filter_exprs_replicated_in_some_subgroup2.0510.0782.132
filter_features1.5060.0781.585
filter_medoid20.463 0.55621.042
filter_replicated2.4640.0602.525
filter_samples1.3360.0631.400
fit_limma16.137 0.19916.354
flevels1.8750.0561.932
fnames2.0980.0502.149
formula2str0.0000.0000.001
fvalues2.7420.0762.820
fvars2.0410.0522.094
guess_maxquant_quantity3.6890.0713.762
guess_sep0.0010.0010.002
halfnormimpute0.9600.0701.032
impute_systematic_nondetects5.4700.1385.611
invert3.0280.0833.116
is_imputed1.7950.0441.840
is_sig23.941 0.10624.073
limma4.1320.0684.207
log2counts2.7010.0522.766
log2countsratios3.2540.1353.393
log2cpm2.5730.1022.685
log2cpmratios2.4830.0932.578
log2tpm2.5600.0962.657
log2tpmratios2.6030.1162.720
log2transform6.8750.0876.973
make_volcano_dt3.7960.0833.887
matrix2sumexp2.4870.0632.552
merge_sdata1.4240.0601.484
merge_sfile2.7960.1463.023
message_df0.0040.0010.004
occupancies2.4080.0522.460
pca18.340 0.14218.512
plot_boxplots6.4400.0646.512
plot_contrastogram1.6610.0521.718
plot_data2.5300.0572.591
plot_densities4.1930.1024.304
plot_detections14.530 0.23714.787
plot_features7.7450.0947.849
plot_venn9.3580.1309.661
plot_violins7.2660.1157.388
plot_volcano4.3430.0744.421
preprocess_rnaseq_counts3.8800.2104.092
proteingroups2.8120.0672.881
read_affymetrix1.4910.1121.603
read_metabolon11.649 0.22011.902
read_proteingroups7.4010.0777.485
read_rectangles11.848 0.41012.269
read_rnaseq_counts24.351 0.74025.126
read_somascan15.270 0.20315.489
rm_singleton_samples1.4630.0131.477
scaledlibsizes2.3520.0812.435
sdata2.1660.1622.329
slevels1.9930.0602.054
snames2.0440.0522.098
split_by_svar1.8510.0571.910
split_extract1.2680.0481.317
standardize_maxquant_snames0.0050.0010.006
subgroup_matrix1.3020.0501.353
subtract_baseline8.0680.0938.168
sumexp2mae3.2690.0903.361
sumexp_to_long_dt7.5880.2127.807
summarize_fit11.603 0.30611.918
svalues1.9200.0671.989
svars2.0710.0572.142
tpm2.6150.0492.697
values1.9490.0782.028
venn_detects1.8180.0641.883
weights3.1580.1353.296
zero_to_na0.0270.0020.029