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This page was generated on 2023-01-02 09:00:19 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 4165
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CHECK results for autonomics on palomino5


To the developers/maintainers of the autonomics package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 98/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
autonomics 1.7.0  (landing page)
Aditya Bhagwat
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 2022)
git_url: https://git.bioconductor.org/packages/autonomics
git_branch: master
git_last_commit: 648ec51
git_last_commit_date: 2022-11-01 11:24:11 -0500 (Tue, 01 Nov 2022)
palomino5Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  

Summary

Package: autonomics
Version: 1.7.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:autonomics.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings autonomics_1.7.0.tar.gz
StartedAt: 2022-12-28 21:39:19 -0500 (Wed, 28 Dec 2022)
EndedAt: 2022-12-28 21:47:08 -0500 (Wed, 28 Dec 2022)
EllapsedTime: 469.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: autonomics.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:autonomics.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings autonomics_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/autonomics.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server 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 '1.7.0'
* 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 ... WARNING
'::' or ':::' imports not declared from:
  'bit64' 'dplyr'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
un_int64: no visible global function definition for 'where'
Undefined global functions or variables:
  where
* 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  15.21   0.60   15.65
pca                  9.17   0.14    9.31
is_sig               9.04   0.18    9.14
filter_medoid        8.67   0.37    9.00
explore_imputations  8.08   0.38    8.38
read_somascan        8.34   0.09    8.44
plot_detections      6.94   0.33    7.08
fit_limma            6.74   0.10    6.81
read_rectangles      6.19   0.40    9.44
biplot_covariates    6.34   0.14    6.63
read_metabolon       6.22   0.11    6.33
summarize_fit        5.33   0.16    5.43
* 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: 2 WARNINGs, 2 NOTEs
See
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/autonomics.Rcheck/00check.log'
for details.



Installation output

autonomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL autonomics
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-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 Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
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 
  82.46    4.21   85.76 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS000
MAXQUANT_PATTERNS_PEPCOUNTS000
MAXQUANT_PATTERNS_QUANTITY000
TESTS000
add_smiles1.980.172.67
analysis0.830.082.30
analyze4.220.124.34
assert_is_valid_sumexp1.080.251.42
biplot2.400.142.55
biplot_corrections2.990.103.31
biplot_covariates6.340.146.63
center1.610.111.73
contrast_subgroup_cols0.560.070.64
contrastdefs1.420.191.50
counts1.410.061.47
counts2cpm1.620.131.73
counts2tpm0.460.080.49
cpm1.220.121.33
create_design2.280.192.45
create_sfile0.970.080.95
default_formula0.620.120.75
default_sfile0.110.020.13
download_data1.110.313.83
download_gtf000
dt2mat000
explore_imputations8.080.388.38
explore_transformations3.900.153.98
extract_features0.740.100.74
extract_rectangle0.660.110.76
fdata0.760.090.77
filter_exprs_replicated_in_some_subgroup1.070.111.19
filter_features0.670.110.78
filter_medoid8.670.379.00
filter_replicated0.930.100.92
filter_samples0.650.120.78
fit_limma6.740.106.81
flevels0.890.040.80
fnames0.750.110.76
formula2str000
fvalues0.750.080.75
fvars0.810.090.82
guess_maxquant_quantity1.590.111.56
guess_sep0.020.000.02
halfnormimpute0.530.030.75
impute_systematic_nondetects2.440.142.45
invert1.110.061.08
is_imputed0.720.070.71
is_sig9.040.189.14
limma1.350.111.37
log2counts1.260.051.27
log2countsratios1.850.031.82
log2cpm1.170.061.20
log2cpmratios1.110.091.19
log2tpm1.180.021.17
log2tpmratios1.150.071.19
log2transform3.450.113.40
make_volcano_dt1.370.141.41
matrix2sumexp1.070.091.15
merge_sdata0.820.120.96
merge_sfile1.180.211.42
message_df000
occupancies0.980.080.97
pca9.170.149.31
plot_boxplots3.560.263.83
plot_contrastogram0.960.081.08
plot_data1.340.111.45
plot_densities1.920.061.98
plot_detections6.940.337.08
plot_features3.810.184.00
plot_venn4.160.054.19
plot_violins3.400.173.58
plot_volcano1.860.131.84
preprocess_rnaseq_counts2.030.142.14
proteingroups1.120.041.06
read_affymetrix0.610.130.78
read_metabolon6.220.116.33
read_proteingroups3.820.193.89
read_rectangles6.190.409.44
read_rnaseq_counts15.21 0.6015.65
read_somascan8.340.098.44
rm_singleton_samples0.560.030.59
scaledlibsizes1.220.031.25
sdata0.920.050.86
slevels0.780.050.74
snames0.830.060.79
split_by_svar0.660.070.62
split_extract0.510.110.63
standardize_maxquant_snames000
subgroup_matrix0.640.030.67
subtract_baseline3.500.123.63
sumexp2mae1.380.081.45
sumexp_to_long_dt3.160.253.25
summarize_fit5.330.165.43
svalues0.780.040.75
svars0.720.100.72
tpm1.310.081.32
values0.750.120.78
venn_detects0.690.080.68
weights1.230.231.25
zero_to_na0.020.000.01