Aditya Bhagwat
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/autonomics |
| git_branch: master |
| git_last_commit: 8920c88 |
| git_last_commit_date: 2021-10-26 13:07:36 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:06:58 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 96/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| autonomics 1.3.0 (landing page) Aditya Bhagwat
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: autonomics |
| Version: 1.3.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:autonomics.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings autonomics_1.3.0.tar.gz |
| StartedAt: 2022-03-17 18:28:14 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:36:10 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 476.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: autonomics.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:autonomics.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings autonomics_1.3.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/autonomics.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'autonomics/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'autonomics' version '1.3.0'
* 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 13.86 1.08 14.78
filter_medoid 9.25 0.42 9.64
is_sig 9.41 0.11 9.40
explore_imputations 8.52 0.60 9.01
pca 8.50 0.19 8.69
read_somascan 7.64 0.06 7.99
fit_limma 7.17 0.07 7.19
plot_detections 6.21 0.39 6.37
biplot_covariates 6.22 0.11 6.34
read_rectangles 5.59 0.54 6.34
read_metabolon 5.61 0.13 5.73
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/autonomics.Rcheck/00check.log'
for details.
autonomics.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL autonomics
###
##############################################################################
##############################################################################
* installing to library 'D:/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
converting help for package 'autonomics'
finding HTML links ... done
AUTONOMICS_DATASETS html
MAXQUANT_PATTERNS_PEPCOUNTS html
MAXQUANT_PATTERNS_QUANTITY html
TESTS html
add_smiles html
analysis html
analyze html
assert_is_valid_sumexp html
biplot html
biplot_corrections html
biplot_covariates html
center html
contrast_subgroup_cols html
contrastdefs html
counts html
counts2cpm html
counts2tpm html
cpm html
create_design html
create_sfile html
default_formula html
default_sfile html
download_data html
download_gtf html
dt2mat html
explore_imputations html
explore_transformations html
extract_features html
extract_rectangle html
fdata html
filter_exprs_replicated_in_some_subgroup
html
filter_features html
filter_medoid html
filter_replicated html
filter_samples html
fit_limma html
flevels html
fnames html
formula2str html
fvalues html
fvars html
guess_maxquant_quantity html
guess_sep html
halfnormimpute html
impute_systematic_nondetects html
invert html
is_imputed html
is_sig html
limma html
log2counts html
log2countsratios html
log2cpm html
log2cpmratios html
log2tpm html
log2tpmratios html
log2transform html
make_volcano_dt html
matrix2sumexp html
merge_sdata html
merge_sfile html
message_df html
occupancies html
pca html
plot_boxplots html
plot_contrastogram html
plot_data html
plot_densities html
plot_detections html
plot_features html
plot_venn html
plot_violins html
plot_volcano html
preprocess_rnaseq_counts html
proteingroups html
read_affymetrix html
read_metabolon html
read_proteingroups html
read_rectangles html
read_rnaseq_counts html
read_somascan html
rm_singleton_samples html
scaledlibsizes html
sdata html
slevels html
snames html
split_by_svar html
split_extract html
standardize_maxquant_snames html
subgroup_matrix html
subtract_baseline html
sumexp2mae html
sumexp_to_long_dt html
summarize_fit html
svalues html
svars html
tpm html
values html
venn_detects html
weights html
zero_to_na html
** 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)
Making 'packages.html' ... done
autonomics.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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
97.93 5.12 101.60
autonomics.Rcheck/autonomics-Ex.timings
| name | user | system | elapsed | |
| AUTONOMICS_DATASETS | 0 | 0 | 0 | |
| MAXQUANT_PATTERNS_PEPCOUNTS | 0 | 0 | 0 | |
| MAXQUANT_PATTERNS_QUANTITY | 0 | 0 | 0 | |
| TESTS | 0 | 0 | 0 | |
| add_smiles | 1.73 | 0.15 | 2.40 | |
| analysis | 0.92 | 0.19 | 1.17 | |
| analyze | 3.72 | 0.28 | 4.00 | |
| assert_is_valid_sumexp | 0.98 | 0.16 | 1.16 | |
| biplot | 2.33 | 0.12 | 2.45 | |
| biplot_corrections | 2.61 | 0.16 | 2.77 | |
| biplot_covariates | 6.22 | 0.11 | 6.34 | |
| center | 2.27 | 0.08 | 2.27 | |
| contrast_subgroup_cols | 0.79 | 0.08 | 0.88 | |
| contrastdefs | 2.05 | 0.14 | 2.03 | |
| counts | 2.00 | 0.11 | 2.06 | |
| counts2cpm | 1.81 | 0.25 | 2.05 | |
| counts2tpm | 0.60 | 0.09 | 0.62 | |
| cpm | 1.25 | 0.20 | 1.42 | |
| create_design | 2.57 | 0.32 | 2.83 | |
| create_sfile | 1.04 | 0.11 | 1.03 | |
| default_formula | 0.78 | 0.09 | 0.88 | |
| default_sfile | 0.22 | 0.03 | 0.25 | |
| download_data | 1.51 | 0.20 | 2.28 | |
| download_gtf | 0 | 0 | 0 | |
| dt2mat | 0 | 0 | 0 | |
| explore_imputations | 8.52 | 0.60 | 9.01 | |
| explore_transformations | 4.12 | 0.34 | 4.36 | |
| extract_features | 0.72 | 0.10 | 0.74 | |
| extract_rectangle | 0.61 | 0.09 | 0.70 | |
| fdata | 0.72 | 0.12 | 0.75 | |
| filter_exprs_replicated_in_some_subgroup | 1.48 | 0.19 | 1.64 | |
| filter_features | 0.78 | 0.11 | 0.89 | |
| filter_medoid | 9.25 | 0.42 | 9.64 | |
| filter_replicated | 0.99 | 0.13 | 1.00 | |
| filter_samples | 0.92 | 0.08 | 1.00 | |
| fit_limma | 7.17 | 0.07 | 7.19 | |
| flevels | 0.77 | 0.11 | 0.81 | |
| fnames | 0.86 | 0.08 | 0.83 | |
| formula2str | 0 | 0 | 0 | |
| fvalues | 0.79 | 0.06 | 0.77 | |
| fvars | 1.00 | 0.18 | 1.06 | |
| guess_maxquant_quantity | 2.18 | 0.09 | 2.14 | |
| guess_sep | 0 | 0 | 0 | |
| halfnormimpute | 0.51 | 0.14 | 0.66 | |
| impute_systematic_nondetects | 1.92 | 0.16 | 1.98 | |
| invert | 1.38 | 0.18 | 1.45 | |
| is_imputed | 1.00 | 0.16 | 1.07 | |
| is_sig | 9.41 | 0.11 | 9.40 | |
| limma | 1.29 | 0.16 | 1.35 | |
| log2counts | 1.05 | 0.23 | 1.26 | |
| log2countsratios | 1.44 | 0.16 | 1.56 | |
| log2cpm | 1.16 | 0.06 | 1.20 | |
| log2cpmratios | 1.53 | 0.23 | 1.77 | |
| log2tpm | 1.11 | 0.11 | 1.19 | |
| log2tpmratios | 1.08 | 0.08 | 1.12 | |
| log2transform | 3.25 | 0.11 | 3.27 | |
| make_volcano_dt | 1.29 | 0.08 | 1.29 | |
| matrix2sumexp | 0.94 | 0.09 | 1.03 | |
| merge_sdata | 0.5 | 0.1 | 0.6 | |
| merge_sfile | 1.05 | 0.31 | 1.12 | |
| message_df | 0 | 0 | 0 | |
| occupancies | 0.92 | 0.06 | 0.86 | |
| pca | 8.50 | 0.19 | 8.69 | |
| plot_boxplots | 3.05 | 0.08 | 3.13 | |
| plot_contrastogram | 0.84 | 0.07 | 0.93 | |
| plot_data | 1.16 | 0.05 | 1.21 | |
| plot_densities | 2.43 | 0.16 | 2.59 | |
| plot_detections | 6.21 | 0.39 | 6.37 | |
| plot_features | 3.98 | 0.09 | 4.08 | |
| plot_venn | 3.88 | 0.00 | 3.85 | |
| plot_violins | 3.64 | 0.11 | 3.75 | |
| plot_volcano | 1.81 | 0.10 | 1.78 | |
| preprocess_rnaseq_counts | 2.30 | 0.15 | 2.56 | |
| proteingroups | 1.82 | 0.08 | 1.79 | |
| read_affymetrix | 0.56 | 0.08 | 0.64 | |
| read_metabolon | 5.61 | 0.13 | 5.73 | |
| read_proteingroups | 2.92 | 0.08 | 2.88 | |
| read_rectangles | 5.59 | 0.54 | 6.34 | |
| read_rnaseq_counts | 13.86 | 1.08 | 14.78 | |
| read_somascan | 7.64 | 0.06 | 7.99 | |
| rm_singleton_samples | 0.57 | 0.00 | 0.56 | |
| scaledlibsizes | 1.51 | 0.16 | 1.64 | |
| sdata | 0.67 | 0.06 | 0.63 | |
| slevels | 0.71 | 0.07 | 0.67 | |
| snames | 0.65 | 0.06 | 0.64 | |
| split_by_svar | 0.55 | 0.11 | 0.56 | |
| split_extract | 0.48 | 0.08 | 0.56 | |
| standardize_maxquant_snames | 0 | 0 | 0 | |
| subgroup_matrix | 0.44 | 0.09 | 0.53 | |
| subtract_baseline | 3.19 | 0.08 | 3.27 | |
| sumexp2mae | 1.30 | 0.08 | 1.38 | |
| sumexp_to_long_dt | 2.61 | 0.32 | 2.75 | |
| summarize_fit | 4.20 | 0.47 | 4.51 | |
| svalues | 0.69 | 0.11 | 0.70 | |
| svars | 0.67 | 0.06 | 0.68 | |
| tpm | 1.13 | 0.13 | 1.20 | |
| values | 0.67 | 0.11 | 0.67 | |
| venn_detects | 0.62 | 0.08 | 0.64 | |
| weights | 1.77 | 0.15 | 1.70 | |
| zero_to_na | 0.01 | 0.00 | 0.02 | |