Back to Multiple platform build/check report for BioC 3.18:   simplified   long
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-02-22 11:36:32 -0500 (Thu, 22 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4691
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4444
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4465
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

Package 111/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
autonomics 1.10.2  (landing page)
Aditya Bhagwat
Snapshot Date: 2024-02-21 14:05:05 -0500 (Wed, 21 Feb 2024)
git_url: https://git.bioconductor.org/packages/autonomics
git_branch: RELEASE_3_18
git_last_commit: 230045c
git_last_commit_date: 2023-11-08 04:08:57 -0500 (Wed, 08 Nov 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    ERROR  skipped
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for autonomics on palomino4


To the developers/maintainers of the autonomics package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: autonomics
Version: 1.10.2
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:autonomics.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings autonomics_1.10.2.tar.gz
StartedAt: 2024-02-21 23:06:55 -0500 (Wed, 21 Feb 2024)
EndedAt: 2024-02-21 23:16:14 -0500 (Wed, 21 Feb 2024)
EllapsedTime: 559.4 seconds
RetCode: 0
Status:   OK  
CheckDir: autonomics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:autonomics.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings autonomics_1.10.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/autonomics.Rcheck'
* using R version 4.3.2 (2023-10-31 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'autonomics/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'autonomics' version '1.10.2'
* 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 ... OK
* 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  17.20   0.33   17.44
filter_medoid       11.08   0.67   11.70
read_somascan       10.65   0.29   10.99
is_sig              10.68   0.25   10.85
pca                 10.40   0.20   10.65
explore_imputations  9.69   0.48   10.13
read_rectangles      8.18   0.41    8.70
read_metabolon       8.03   0.19    8.30
fit_limma            7.97   0.20    8.19
plot_detections      7.63   0.29    7.77
plot_boxplots        6.66   0.14    6.91
biplot_covariates    6.66   0.12    6.81
summarize_fit        5.88   0.26    5.94
plot_features        5.03   0.17    5.26
analyze              5.00   0.19    5.27
subtract_baseline    4.80   0.21    5.05
* 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 NOTE
See
  'F:/biocbuild/bbs-3.18-bioc/meat/autonomics.Rcheck/00check.log'
for details.



Installation output

autonomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL autonomics
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-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 4.3.2 (2023-10-31 ucrt) -- "Eye Holes"
Copyright (C) 2023 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 103 ]
> 
> proc.time()
   user  system elapsed 
 102.31    5.71  107.46 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS000
MAXQUANT_PATTERNS_PEPCOUNTS000
MAXQUANT_PATTERNS_QUANTITY000
TESTS000
add_smiles1.780.232.39
analysis1.940.112.04
analyze5.000.195.27
assert_is_valid_sumexp1.390.181.75
biplot3.090.183.34
biplot_corrections4.170.094.33
biplot_covariates6.660.126.81
center2.280.112.58
contrast_subgroup_cols0.710.130.87
contrastdefs1.810.091.82
counts2.400.062.43
counts2cpm1.250.111.33
counts2tpm0.660.040.67
cpm1.420.031.45
create_design2.890.092.97
create_sfile1.170.031.11
default_formula0.720.190.95
default_sfile0.140.030.17
download_data1.500.302.08
download_gtf000
dt2mat000
explore_imputations 9.69 0.4810.13
explore_transformations4.090.314.31
extract_features0.910.130.92
extract_rectangle0.640.220.91
fdata0.920.110.95
filter_exprs_replicated_in_some_subgroup1.410.091.55
filter_features0.760.170.98
filter_medoid11.08 0.6711.70
filter_replicated1.200.101.18
filter_samples0.800.171.05
fit_limma7.970.208.19
flevels0.940.110.92
fnames1.000.080.97
formula2str000
fvalues0.830.130.87
fvars0.840.120.91
guess_maxquant_quantity1.660.091.67
guess_sep000
halfnormimpute1.380.021.39
impute_systematic_nondetects2.390.122.43
invert1.340.051.37
is_imputed1.050.061.00
is_sig10.68 0.2510.85
limma1.750.131.76
log2counts1.520.151.57
log2countsratios2.040.142.13
log2cpm1.320.031.27
log2cpmratios1.350.011.33
log2tpm1.410.071.41
log2tpmratios1.300.061.32
log2transform4.110.124.11
make_volcano_dt1.670.101.72
matrix2sumexp1.300.091.47
merge_sdata0.840.171.08
merge_sfile1.500.291.81
message_df000
occupancies1.220.141.24
pca10.40 0.2010.65
plot_boxplots6.660.146.91
plot_contrastogram1.110.141.34
plot_data1.860.162.06
plot_densities2.140.112.36
plot_detections7.630.297.77
plot_features5.030.175.26
plot_venn4.690.134.78
plot_violins4.250.224.56
plot_volcano2.200.202.27
preprocess_rnaseq_counts2.600.172.70
proteingroups1.180.191.32
read_affymetrix0.860.090.95
read_metabolon8.030.198.30
read_proteingroups4.470.144.51
read_rectangles8.180.418.70
read_rnaseq_counts17.20 0.3317.44
read_somascan10.65 0.2910.99
rm_singleton_samples0.940.020.95
scaledlibsizes1.390.141.50
sdata0.960.090.96
slevels1.040.061.01
snames0.970.080.94
split_by_svar0.890.060.88
split_extract0.860.101.04
standardize_maxquant_snames000
subgroup_matrix0.670.150.89
subtract_baseline4.800.215.05
sumexp2mae1.860.212.11
sumexp_to_long_dt3.960.434.29
summarize_fit5.880.265.94
svalues1.140.031.06
svars1.090.071.06
tpm1.710.111.79
values0.980.141.01
venn_detects1.050.061.02
weights1.730.141.64
zero_to_na0.020.000.01