Arne Smits
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/DEP |
| git_branch: master |
| git_last_commit: e24250e |
| git_last_commit_date: 2021-11-20 23:32:00 -0400 (Sat, 20 Nov 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:21 -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 DEP package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DEP.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 493/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DEP 1.17.1 (landing page) Arne Smits
| 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: DEP |
| Version: 1.17.1 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DEP.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings DEP_1.17.1.tar.gz |
| StartedAt: 2022-03-17 18:54:42 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:59:32 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 290.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: DEP.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:DEP.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings DEP_1.17.1.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/DEP.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 'DEP/DESCRIPTION' ... OK
* this is package 'DEP' version '1.17.1'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'DEP' 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 ... WARNING
Missing link or links in documentation object 'LFQ.Rd':
'[MSnbase:impute-methods]{impute}'
Missing link or links in documentation object 'TMT.Rd':
'[MSnbase:impute-methods]{impute}'
Missing link or links in documentation object 'impute.Rd':
'[MSnbase:impute-methods]{impute}'
Missing link or links in documentation object 'process.Rd':
'[MSnbase:impute-methods]{impute}'
See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* 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
See
'D:/biocbuild/bbs-3.15-bioc/meat/DEP.Rcheck/00check.log'
for details.
DEP.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL DEP
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'DEP' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'DEP'
finding HTML links ... done
DEP html
DiUbi html
DiUbi_ExpDesign html
LFQ html
TMT html
UbiLength html
UbiLength_ExpDesign html
add_rejections html
analyze_dep html
filter_missval html
filter_proteins html
get_df_long html
get_df_wide html
get_prefix html
get_results html
get_suffix html
import_IsobarQuant html
import_MaxQuant html
impute html
make_se html
make_se_parse html
make_unique html
manual_impute html
meanSdPlot html
normalize_vsn html
plot_all html
plot_cond html
plot_cond_freq html
plot_cond_overlap html
plot_cor html
plot_coverage html
plot_detect html
plot_dist html
plot_frequency html
plot_gsea html
plot_heatmap html
plot_imputation html
plot_missval html
plot_normalization html
plot_numbers html
plot_p_hist html
plot_pca html
plot_single html
plot_volcano html
process html
report html
run_app html
se2msn html
test_diff html
test_gsea html
theme_DEP1 html
theme_DEP2 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 (DEP)
Making 'packages.html' ... done
DEP.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(DEP)
>
> test_check("DEP")
[ FAIL 0 | WARN 12 | SKIP 0 | PASS 333 ]
[ FAIL 0 | WARN 12 | SKIP 0 | PASS 333 ]
>
> proc.time()
user system elapsed
39.51 1.06 56.90
DEP.Rcheck/DEP-Ex.timings
| name | user | system | elapsed | |
| LFQ | 1.17 | 0.09 | 1.26 | |
| TMT | 0 | 0 | 0 | |
| add_rejections | 1.17 | 0.03 | 1.21 | |
| analyze_dep | 1.66 | 0.00 | 1.65 | |
| filter_missval | 0.46 | 0.05 | 0.50 | |
| filter_proteins | 0.26 | 0.00 | 0.27 | |
| get_df_long | 0.78 | 0.00 | 0.78 | |
| get_df_wide | 0.68 | 0.05 | 0.72 | |
| get_prefix | 0 | 0 | 0 | |
| get_results | 0.92 | 0.00 | 0.92 | |
| get_suffix | 0 | 0 | 0 | |
| import_IsobarQuant | 0 | 0 | 0 | |
| import_MaxQuant | 0.05 | 0.00 | 0.05 | |
| impute | 1.58 | 0.00 | 1.59 | |
| make_se | 0.03 | 0.00 | 0.03 | |
| make_se_parse | 0.06 | 0.00 | 0.07 | |
| make_unique | 0.03 | 0.00 | 0.03 | |
| manual_impute | 0.85 | 0.09 | 0.94 | |
| meanSdPlot | 0.72 | 0.02 | 0.73 | |
| normalize_vsn | 0.45 | 0.01 | 0.47 | |
| plot_all | 1.58 | 0.00 | 1.58 | |
| plot_cond | 1.20 | 0.03 | 1.23 | |
| plot_cond_freq | 0.97 | 0.02 | 1.00 | |
| plot_cond_overlap | 1.14 | 0.00 | 1.14 | |
| plot_cor | 1.45 | 0.01 | 1.47 | |
| plot_coverage | 0.47 | 0.02 | 0.49 | |
| plot_detect | 1.45 | 0.00 | 1.45 | |
| plot_dist | 3.8 | 0.0 | 3.8 | |
| plot_frequency | 0.49 | 0.00 | 0.49 | |
| plot_gsea | 0.84 | 0.01 | 0.85 | |
| plot_heatmap | 2.59 | 0.00 | 2.60 | |
| plot_imputation | 1.02 | 0.02 | 1.03 | |
| plot_missval | 1.55 | 0.01 | 1.56 | |
| plot_normalization | 1.23 | 0.05 | 1.28 | |
| plot_numbers | 0.44 | 0.02 | 0.46 | |
| plot_p_hist | 1.67 | 0.00 | 1.68 | |
| plot_pca | 1.16 | 0.00 | 1.16 | |
| plot_single | 1.21 | 0.00 | 1.22 | |
| plot_volcano | 3.72 | 0.00 | 3.72 | |
| process | 1.13 | 0.00 | 1.14 | |
| report | 0 | 0 | 0 | |
| run_app | 0 | 0 | 0 | |
| se2msn | 0.09 | 0.00 | 0.09 | |
| test_diff | 0.81 | 0.00 | 0.81 | |
| test_gsea | 0.64 | 0.00 | 0.65 | |
| theme_DEP1 | 0.38 | 0.00 | 0.37 | |
| theme_DEP2 | 0.56 | 0.00 | 0.56 | |