Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-09-22 11:37:07 -0400 (Fri, 22 Sep 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4625
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4378
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4394
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 112/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
autonomics 1.8.0  (landing page)
Aditya Bhagwat
Snapshot Date: 2023-09-21 14:00:15 -0400 (Thu, 21 Sep 2023)
git_url: https://git.bioconductor.org/packages/autonomics
git_branch: RELEASE_3_17
git_last_commit: d84d5f1
git_last_commit_date: 2023-04-25 11:27:21 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 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 12.6.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for autonomics on merida1


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: 1.8.0
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_1.8.0.tar.gz
StartedAt: 2023-09-21 23:06:12 -0400 (Thu, 21 Sep 2023)
EndedAt: 2023-09-21 23:31:52 -0400 (Thu, 21 Sep 2023)
EllapsedTime: 1540.5 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_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/autonomics.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘autonomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘autonomics’ version ‘1.8.0’
* 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           30.247  1.265  41.770
is_sig                       29.120  0.363  39.935
filter_medoid                25.900  0.709  33.139
pca                          22.600  0.501  30.337
fit_limma                    21.647  0.423  28.022
explore_imputations          20.932  0.454  27.567
read_somascan                20.094  0.335  26.860
plot_detections              18.022  0.511  24.233
biplot_covariates            17.211  0.462  23.295
read_metabolon               16.832  0.620  23.082
summarize_fit                13.122  0.412  18.503
read_rectangles              12.481  0.742  17.464
plot_features                12.500  0.293  16.931
plot_venn                    12.289  0.205  16.958
analyze                      11.491  0.539  15.654
plot_boxplots                11.027  0.284  15.385
subtract_baseline            10.729  0.409  14.748
plot_violins                 10.562  0.345  14.933
log2transform                10.039  0.282  13.260
explore_transformations       9.975  0.277  13.385
read_proteingroups            9.165  0.193  12.719
biplot_corrections            8.775  0.402  11.902
sumexp_to_long_dt             8.328  0.581  12.304
biplot                        7.277  0.399  10.514
impute_systematic_nondetects  5.643  0.338   8.350
plot_densities                5.164  0.353   7.121
plot_volcano                  5.252  0.150   7.192
create_design                 4.737  0.158   6.420
center                        4.457  0.167   6.120
add_smiles                    3.997  0.530   5.598
contrastdefs                  4.283  0.169   6.177
limma                         4.172  0.149   5.739
preprocess_rnaseq_counts      3.998  0.173   5.597
make_volcano_dt               4.025  0.139   5.497
sumexp2mae                    3.689  0.365   5.414
* 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-3.17-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/4.3-x86_64/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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 
234.467   8.941 328.354 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS0.0000.0010.001
MAXQUANT_PATTERNS_PEPCOUNTS0.0000.0010.001
MAXQUANT_PATTERNS_QUANTITY0.0010.0010.002
TESTS0.0010.0010.001
add_smiles3.9970.5305.598
analysis2.1770.1842.991
analyze11.491 0.53915.654
assert_is_valid_sumexp3.0950.4834.811
biplot 7.277 0.39910.514
biplot_corrections 8.775 0.40211.902
biplot_covariates17.211 0.46223.295
center4.4570.1676.120
contrast_subgroup_cols1.5370.2272.367
contrastdefs4.2830.1696.177
counts2.8540.1534.036
counts2cpm3.0220.1134.161
counts2tpm1.1230.0431.539
cpm2.4300.1063.327
create_design4.7370.1586.420
create_sfile2.5670.1503.705
default_formula1.5670.3112.444
default_sfile0.2570.0190.355
download_data2.2060.3603.360
download_gtf0.0000.0000.001
dt2mat0.0060.0010.007
explore_imputations20.932 0.45427.567
explore_transformations 9.975 0.27713.385
extract_features1.9860.0902.613
extract_rectangle1.3430.2261.956
fdata2.0340.1332.718
filter_exprs_replicated_in_some_subgroup2.9700.4404.154
filter_features1.8180.4222.774
filter_medoid25.900 0.70933.139
filter_replicated2.5990.1513.561
filter_samples1.8720.2962.720
fit_limma21.647 0.42328.022
flevels1.9540.1202.684
fnames1.9610.0992.681
formula2str0.0000.0010.001
fvalues1.9290.0912.614
fvars1.9460.1062.658
guess_maxquant_quantity3.4000.2204.556
guess_sep0.0020.0020.006
halfnormimpute1.1570.1341.754
impute_systematic_nondetects5.6430.3388.350
invert2.7590.1854.101
is_imputed1.9590.1553.210
is_sig29.120 0.36339.935
limma4.1720.1495.739
log2counts2.4050.1873.900
log2countsratios2.3880.1103.340
log2cpm2.3680.1243.624
log2cpmratios2.4000.1053.372
log2tpm2.3740.1183.335
log2tpmratios2.3830.0953.307
log2transform10.039 0.28213.260
make_volcano_dt4.0250.1395.497
matrix2sumexp2.9130.3254.277
merge_sdata1.4630.2712.335
merge_sfile2.8580.2254.139
message_df0.0040.0010.005
occupancies2.6000.1213.599
pca22.600 0.50130.337
plot_boxplots11.027 0.28415.385
plot_contrastogram2.6150.2283.947
plot_data3.5620.2294.769
plot_densities5.1640.3537.121
plot_detections18.022 0.51124.233
plot_features12.500 0.29316.931
plot_venn12.289 0.20516.958
plot_violins10.562 0.34514.933
plot_volcano5.2520.1507.192
preprocess_rnaseq_counts3.9980.1735.597
proteingroups2.8390.1494.147
read_affymetrix1.8960.1682.815
read_metabolon16.832 0.62023.082
read_proteingroups 9.165 0.19312.719
read_rectangles12.481 0.74217.464
read_rnaseq_counts30.247 1.26541.770
read_somascan20.094 0.33526.860
rm_singleton_samples1.6250.0552.181
scaledlibsizes2.1240.0812.849
sdata2.0250.1092.886
slevels1.9180.1002.634
snames1.9980.1232.727
split_by_svar1.7360.1132.417
split_extract1.4400.2232.282
standardize_maxquant_snames0.0040.0020.010
subgroup_matrix1.4160.2172.203
subtract_baseline10.729 0.40914.748
sumexp2mae3.6890.3655.414
sumexp_to_long_dt 8.328 0.58112.304
summarize_fit13.122 0.41218.503
svalues1.9080.1002.615
svars1.9620.1202.668
tpm2.4260.1153.415
values1.9280.1042.968
venn_detects1.8110.1042.472
weights3.3120.2544.652
zero_to_na0.0310.0040.044