Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-26 13:07:39 -0500 (Wed, 26 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

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: 2022-01-25 01:55:07 -0500 (Tue, 25 Jan 2022)
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 20.04.4 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: 2022-01-25 10:16:20 -0500 (Tue, 25 Jan 2022)
EndedAt: 2022-01-25 10:32:03 -0500 (Tue, 25 Jan 2022)
EllapsedTime: 943.4 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           24.936  0.875  25.835
is_sig                       25.038  0.109  25.174
filter_medoid                22.130  0.723  22.875
pca                          18.108  0.128  18.255
explore_imputations          16.971  0.240  17.237
fit_limma                    16.617  0.106  16.734
read_somascan                16.392  0.304  16.723
plot_detections              14.219  0.248  14.489
read_rectangles              12.923  0.377  13.316
biplot_covariates            11.953  0.171  12.134
read_metabolon               11.786  0.165  12.012
summarize_fit                11.569  0.243  11.825
plot_venn                    10.100  0.089  10.254
explore_transformations       8.552  0.163   8.720
subtract_baseline             8.327  0.103   8.472
plot_features                 8.240  0.103   8.470
sumexp_to_long_dt             7.865  0.221   8.091
log2transform                 7.839  0.116   7.967
analyze                       7.674  0.197   7.878
plot_violins                  7.739  0.130   7.957
read_proteingroups            7.600  0.082   7.698
plot_boxplots                 7.282  0.069   7.357
biplot_corrections            6.991  0.143   7.146
impute_systematic_nondetects  5.382  0.166   5.552
* 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 
198.872   4.020 203.298 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS0.0000.0010.001
MAXQUANT_PATTERNS_PEPCOUNTS0.0010.0000.001
MAXQUANT_PATTERNS_QUANTITY0.0010.0010.001
TESTS000
add_smiles3.6040.1344.500
analysis2.0020.1512.193
analyze7.6740.1977.878
assert_is_valid_sumexp2.5780.1632.759
biplot4.4460.1094.561
biplot_corrections6.9910.1437.146
biplot_covariates11.953 0.17112.134
center3.6880.0973.842
contrast_subgroup_cols1.2960.0581.376
contrastdefs3.9120.0894.002
counts3.0210.1343.183
counts2cpm3.2290.2353.465
counts2tpm1.4380.0341.473
cpm3.4530.1413.595
create_design3.9780.1154.095
create_sfile2.2700.0752.345
default_formula1.3510.0741.426
default_sfile0.4680.0080.477
download_data3.5000.1893.706
download_gtf0.0010.0000.000
dt2mat0.0030.0000.004
explore_imputations16.971 0.24017.237
explore_transformations8.5520.1638.720
extract_features2.0210.0382.062
extract_rectangle1.4340.0821.517
fdata2.0910.0562.149
filter_exprs_replicated_in_some_subgroup2.1200.0852.210
filter_features1.4310.0491.481
filter_medoid22.130 0.72322.875
filter_replicated2.6730.0662.741
filter_samples1.6510.0781.731
fit_limma16.617 0.10616.734
flevels2.0710.0452.116
fnames2.1730.0582.232
formula2str0.0010.0010.001
fvalues2.0110.0772.089
fvars2.1530.0482.202
guess_maxquant_quantity4.1760.0894.270
guess_sep0.0010.0010.003
halfnormimpute1.8150.1011.950
impute_systematic_nondetects5.3820.1665.552
invert3.2230.0883.327
is_imputed2.0160.0452.079
is_sig25.038 0.10925.174
limma3.9710.0624.036
log2counts2.9040.0802.987
log2countsratios2.6440.0802.726
log2cpm2.8090.0672.878
log2cpmratios3.3770.2643.644
log2tpm2.6450.0872.736
log2tpmratios2.7270.0972.827
log2transform7.8390.1167.967
make_volcano_dt4.5080.0914.607
matrix2sumexp2.5190.0682.589
merge_sdata1.3850.0601.445
merge_sfile2.6100.1252.817
message_df0.0040.0000.004
occupancies2.5320.0662.600
pca18.108 0.12818.255
plot_boxplots7.2820.0697.357
plot_contrastogram1.8680.0521.921
plot_data2.6340.0692.707
plot_densities4.2230.1014.331
plot_detections14.219 0.24814.489
plot_features8.2400.1038.470
plot_venn10.100 0.08910.254
plot_violins7.7390.1307.957
plot_volcano4.5820.0744.660
preprocess_rnaseq_counts4.6420.1654.811
proteingroups2.5040.0682.573
read_affymetrix1.4650.1141.581
read_metabolon11.786 0.16512.012
read_proteingroups7.6000.0827.698
read_rectangles12.923 0.37713.316
read_rnaseq_counts24.936 0.87525.835
read_somascan16.392 0.30416.723
rm_singleton_samples1.3140.0151.330
scaledlibsizes2.2540.0872.342
sdata2.1170.0822.200
slevels2.0420.0462.090
snames2.0200.0502.072
split_by_svar1.9140.0591.974
split_extract1.2960.0621.360
standardize_maxquant_snames0.0040.0010.004
subgroup_matrix1.3430.0501.393
subtract_baseline8.3270.1038.472
sumexp2mae3.4420.0803.524
sumexp_to_long_dt7.8650.2218.091
summarize_fit11.569 0.24311.825
svalues2.1550.0702.227
svars2.0770.0582.137
tpm2.8550.0742.932
values2.0300.0512.084
venn_detects1.9650.0932.153
weights3.1930.1323.332
zero_to_na0.0240.0020.026