Back to Multiple platform build/check report for BioC 3.15
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-10-19 13:19:59 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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 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? 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 98/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
autonomics 1.4.0  (landing page)
Aditya Bhagwat
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/autonomics
git_branch: RELEASE_3_15
git_last_commit: 7d33898
git_last_commit_date: 2022-04-26 12:13:35 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / 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: 1.4.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:autonomics.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings autonomics_1.4.0.tar.gz
StartedAt: 2022-10-18 18:36:42 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 18:45:34 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 531.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: autonomics.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:autonomics.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings autonomics_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/autonomics.Rcheck’
* using R version 4.2.1 (2022-06-23)
* 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 ‘1.4.0’
* 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      16.318  0.168  15.610
is_sig                  11.220  0.060  10.860
explore_imputations     10.675  0.289  10.321
read_somascan           10.540  0.124  10.532
filter_medoid           10.424  0.164  10.471
pca                      9.424  0.040   9.463
fit_limma                8.415  0.072   8.235
plot_detections          8.308  0.140   7.885
biplot_covariates        7.640  0.344   7.984
read_rectangles          7.422  0.228   7.634
read_metabolon           7.229  0.056   7.173
summarize_fit            6.363  0.032   5.725
analyze                  4.903  0.460   5.257
explore_transformations  5.242  0.087   5.030
plot_venn                4.989  0.028   4.847
log2transform            4.974  0.036   4.710
* 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-3.15-bioc/meat/autonomics.Rcheck/00check.log’
for details.



Installation output

autonomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL autonomics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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 
103.909   3.387 101.819 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS0.0010.0000.000
MAXQUANT_PATTERNS_PEPCOUNTS0.0010.0000.000
MAXQUANT_PATTERNS_QUANTITY0.0000.0000.001
TESTS0.0000.0000.001
add_smiles2.3970.2072.991
analysis1.1320.2031.242
analyze4.9030.4605.257
assert_is_valid_sumexp1.2770.0881.364
biplot2.8520.0922.944
biplot_corrections3.4850.1203.605
biplot_covariates7.6400.3447.984
center2.1620.1172.079
contrast_subgroup_cols0.6510.0320.684
contrastdefs2.050.041.83
counts1.6820.1161.679
counts2cpm2.2870.1002.279
counts2tpm0.8150.0040.705
cpm1.5070.0161.414
create_design3.0310.1083.034
create_sfile1.4990.0681.235
default_formula0.6920.0120.704
default_sfile0.1260.0000.127
download_data1.1170.1641.290
download_gtf0.0010.0000.000
dt2mat0.0010.0020.003
explore_imputations10.675 0.28910.321
explore_transformations5.2420.0875.030
extract_features1.0000.0280.853
extract_rectangle0.7710.0200.790
fdata1.0330.0540.910
filter_exprs_replicated_in_some_subgroup1.4100.0121.325
filter_features0.7530.0400.792
filter_medoid10.424 0.16410.471
filter_replicated1.3700.0281.115
filter_samples0.8890.0280.918
fit_limma8.4150.0728.235
flevels1.0090.0320.859
fnames1.1730.0481.031
formula2str0.0010.0010.001
fvalues1.0060.0150.845
fvars1.0780.0160.901
guess_maxquant_quantity2.7170.1552.471
guess_sep0.0010.0000.002
halfnormimpute0.5740.0360.611
impute_systematic_nondetects2.7000.0692.449
invert1.5740.0401.323
is_imputed0.9990.0110.836
is_sig11.22 0.0610.86
limma1.8440.0281.624
log2counts1.5210.0161.429
log2countsratios1.4160.0121.327
log2cpm1.4880.0681.456
log2cpmratios2.0330.0842.017
log2tpm1.3250.0001.224
log2tpmratios1.3740.0401.315
log2transform4.9740.0364.710
make_volcano_dt2.0180.0201.623
matrix2sumexp1.2440.0241.269
merge_sdata0.6250.0240.648
merge_sfile1.4870.2401.330
message_df0.0030.0000.003
occupancies1.3270.0201.072
pca9.4240.0409.463
plot_boxplots4.1970.0684.228
plot_contrastogram1.1940.0241.193
plot_data1.6300.0281.657
plot_densities2.3440.0522.384
plot_detections8.3080.1407.885
plot_features4.5030.0284.531
plot_venn4.9890.0284.847
plot_violins4.5120.0564.548
plot_volcano2.9120.0322.509
preprocess_rnaseq_counts2.6340.0522.569
proteingroups1.4890.0161.234
read_affymetrix0.9860.0401.026
read_metabolon7.2290.0567.173
read_proteingroups4.5470.0324.080
read_rectangles7.4220.2287.634
read_rnaseq_counts16.318 0.16815.610
read_somascan10.540 0.12410.532
rm_singleton_samples0.7480.0040.752
scaledlibsizes1.3650.0121.270
sdata1.1100.0160.924
slevels1.0180.0160.863
snames1.1470.0120.968
split_by_svar0.9660.0240.784
split_extract0.7030.0160.718
standardize_maxquant_snames0.0020.0000.002
subgroup_matrix0.6170.0120.629
subtract_baseline4.6900.0044.624
sumexp2mae1.6640.0481.711
sumexp_to_long_dt4.4930.0803.956
summarize_fit6.3630.0325.725
svalues1.0860.0120.919
svars1.1030.0280.933
tpm1.7890.0121.685
values1.1760.0160.989
venn_detects0.9930.0080.827
weights1.8990.0441.593
zero_to_na0.0180.0010.019