Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:21:07 -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 palomino3


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: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:autonomics.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings autonomics_1.4.0.tar.gz
StartedAt: 2022-10-18 22:04:36 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 22:15:12 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 636.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: autonomics.Rcheck
Warnings: 1

Command output

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


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/autonomics.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (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 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      20.24   0.65   20.72
is_sig                  13.80   0.28   13.97
pca                     13.06   0.13   13.41
filter_medoid           10.86   0.48   11.44
read_somascan           11.18   0.13   11.29
explore_imputations     10.65   0.50   11.04
read_rectangles         10.08   0.61   10.83
plot_detections          9.16   0.24    9.18
read_metabolon           8.91   0.22    9.12
biplot_covariates        8.95   0.06    9.02
fit_limma                8.67   0.23    8.92
summarize_fit            7.37   0.39    7.48
log2transform            6.11   0.31    6.31
analyze                  6.01   0.16    6.15
plot_features            5.93   0.17    6.11
explore_transformations  5.33   0.27    5.43
subtract_baseline        5.36   0.20    5.58
plot_venn                5.24   0.09    5.32
plot_violins             5.03   0.16    5.19
sumexp_to_long_dt        4.71   0.46    4.92
plot_boxplots            4.88   0.17    5.04
* 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
  'F:/biocbuild/bbs-3.15-bioc/meat/autonomics.Rcheck/00check.log'
for details.



Installation output

autonomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL autonomics
###
##############################################################################
##############################################################################


* installing to library 'F:/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 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
 123.35    5.70  128.31 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS000
MAXQUANT_PATTERNS_PEPCOUNTS000
MAXQUANT_PATTERNS_QUANTITY000
TESTS000
add_smiles2.780.203.61
analysis1.240.201.41
analyze6.010.166.15
assert_is_valid_sumexp1.410.231.64
biplot3.010.103.11
biplot_corrections3.790.123.91
biplot_covariates8.950.069.02
center2.300.162.40
contrast_subgroup_cols0.790.130.94
contrastdefs1.960.071.94
counts1.780.051.86
counts2cpm2.650.192.81
counts2tpm0.740.060.73
cpm1.430.241.63
create_design2.880.123.01
create_sfile1.660.091.63
default_formula0.840.130.97
default_sfile0.170.010.19
download_data1.500.252.09
download_gtf000
dt2mat000
explore_imputations10.65 0.5011.04
explore_transformations5.330.275.43
extract_features0.940.060.88
extract_rectangle0.780.060.85
fdata1.020.191.08
filter_exprs_replicated_in_some_subgroup1.460.111.60
filter_features1.080.131.23
filter_medoid10.86 0.4811.44
filter_replicated1.450.161.49
filter_samples0.880.141.01
fit_limma8.670.238.92
flevels1.110.141.13
fnames1.260.131.31
formula2str000
fvalues1.360.061.30
fvars1.210.161.23
guess_maxquant_quantity2.000.222.07
guess_sep000
halfnormimpute1.510.081.59
impute_systematic_nondetects2.640.152.66
invert1.640.141.62
is_imputed0.970.100.94
is_sig13.80 0.2813.97
limma1.760.081.72
log2counts1.430.121.53
log2countsratios1.850.081.87
log2cpm2.550.062.58
log2cpmratios1.550.081.58
log2tpm1.330.091.39
log2tpmratios1.610.131.67
log2transform6.110.316.31
make_volcano_dt1.810.191.83
matrix2sumexp1.190.151.35
merge_sdata0.790.251.04
merge_sfile1.580.321.74
message_df000
occupancies1.250.151.28
pca13.06 0.1313.41
plot_boxplots4.880.175.04
plot_contrastogram1.200.091.36
plot_data2.140.112.25
plot_densities3.560.173.75
plot_detections9.160.249.18
plot_features5.930.176.11
plot_venn5.240.095.32
plot_violins5.030.165.19
plot_volcano2.480.152.55
preprocess_rnaseq_counts3.410.243.53
proteingroups1.610.121.59
read_affymetrix0.970.141.24
read_metabolon8.910.229.12
read_proteingroups4.570.194.61
read_rectangles10.08 0.6110.83
read_rnaseq_counts20.24 0.6520.72
read_somascan11.18 0.1311.29
rm_singleton_samples0.810.030.84
scaledlibsizes1.380.061.42
sdata1.120.061.08
slevels1.220.101.20
snames1.060.151.08
split_by_svar1.720.171.78
split_extract0.810.130.94
standardize_maxquant_snames000
subgroup_matrix0.680.080.75
subtract_baseline5.360.205.58
sumexp2mae1.950.142.10
sumexp_to_long_dt4.710.464.92
summarize_fit7.370.397.48
svalues0.960.140.97
svars0.900.110.89
tpm1.720.071.75
values1.270.111.26
venn_detects1.180.131.21
weights1.930.341.94
zero_to_na0.010.020.03