Arne Smits
| Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/DEP |
| git_branch: RELEASE_3_18 |
| git_last_commit: 3eedbc9 |
| git_last_commit_date: 2023-10-24 10:58:53 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-04-17 11:36:42 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
| 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 540/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DEP 1.24.0 (landing page) Arne Smits
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the DEP package: - 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 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. |
| Package: DEP |
| Version: 1.24.0 |
| Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DEP.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings DEP_1.24.0.tar.gz |
| StartedAt: 2024-04-16 00:04:08 -0400 (Tue, 16 Apr 2024) |
| EndedAt: 2024-04-16 00:11:32 -0400 (Tue, 16 Apr 2024) |
| EllapsedTime: 444.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: DEP.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DEP.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings DEP_1.24.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/DEP.Rcheck'
* using R version 4.3.3 (2024-02-29 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 'DEP/DESCRIPTION' ... OK
* this is package 'DEP' version '1.24.0'
* 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 ... 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 startup messages can be suppressed ... 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
impute 53.72 0.05 53.83
plot_volcano 4.88 0.03 5.02
* 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
'F:/biocbuild/bbs-3.18-bioc/meat/DEP.Rcheck/00check.log'
for details.
DEP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL DEP ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.18-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 ** 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)
DEP.Rcheck/tests/testthat.Rout
R version 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"
Copyright (C) 2024 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")
!!! Error: Cannot call Ghostscript: `mgs' (No such file or directory/The system cannot find the file specified)!
pdfcrop: major issue: User/administrator updates are out-of-sync.
!!! Error: Cannot call Ghostscript: `mgs' (No such file or directory/The system cannot find the file specified)!
pdfcrop: major issue: User/administrator updates are out-of-sync.
!!! Error: Cannot call Ghostscript: `mgs' (No such file or directory/The system cannot find the file specified)!
pdfcrop: major issue: User/administrator updates are out-of-sync.
!!! Error: Cannot call Ghostscript: `mgs' (No such file or directory/The system cannot find the file specified)!
pdfcrop: major issue: User/administrator updates are out-of-sync.
!!! Error: Cannot call Ghostscript: `mgs' (No such file or directory/The system cannot find the file specified)!
pdfcrop: major issue: User/administrator updates are out-of-sync.
!!! Error: Cannot call Ghostscript: `mgs' (No such file or directory/The system cannot find the file specified)!
pdfcrop: major issue: User/administrator updates are out-of-sync.
!!! Error: Cannot call Ghostscript: `mgs' (No such file or directory/The system cannot find the file specified)!
pdfcrop: major issue: User/administrator updates are out-of-sync.
!!! Error: Cannot call Ghostscript: `mgs' (No such file or directory/The system cannot find the file specified)!
pdfcrop: major issue: User/administrator updates are out-of-sync.
!!! Error: Cannot call Ghostscript: `mgs' (No such file or directory/The system cannot find the file specified)!
pdfcrop: major issue: User/administrator updates are out-of-sync.
!!! Error: Cannot call Ghostscript: `mgs' (No such file or directory/The system cannot find the file specified)!
pdfcrop: major issue: User/administrator updates are out-of-sync.
[ FAIL 0 | WARN 14 | SKIP 0 | PASS 333 ]
[ FAIL 0 | WARN 14 | SKIP 0 | PASS 333 ]
>
> proc.time()
user system elapsed
53.92 2.71 70.70
DEP.Rcheck/DEP-Ex.timings
| name | user | system | elapsed | |
| LFQ | 1.84 | 0.03 | 1.89 | |
| TMT | 0 | 0 | 0 | |
| add_rejections | 0.65 | 0.05 | 0.70 | |
| analyze_dep | 3.03 | 0.03 | 3.07 | |
| filter_missval | 0.58 | 0.00 | 0.58 | |
| filter_proteins | 0.39 | 0.00 | 0.39 | |
| get_df_long | 0.89 | 0.00 | 0.89 | |
| get_df_wide | 1.42 | 0.00 | 1.42 | |
| get_prefix | 0 | 0 | 0 | |
| get_results | 1.16 | 0.08 | 1.23 | |
| get_suffix | 0 | 0 | 0 | |
| import_IsobarQuant | 0 | 0 | 0 | |
| import_MaxQuant | 0.03 | 0.01 | 0.05 | |
| impute | 53.72 | 0.05 | 53.83 | |
| make_se | 0.06 | 0.00 | 0.06 | |
| make_se_parse | 0.10 | 0.00 | 0.09 | |
| make_unique | 0.01 | 0.02 | 0.04 | |
| manual_impute | 0.88 | 0.01 | 0.89 | |
| meanSdPlot | 1.06 | 0.02 | 1.07 | |
| normalize_vsn | 0.52 | 0.00 | 0.52 | |
| plot_all | 1.95 | 0.01 | 1.97 | |
| plot_cond | 1.30 | 0.03 | 1.51 | |
| plot_cond_freq | 1.17 | 0.02 | 1.19 | |
| plot_cond_overlap | 0.93 | 0.02 | 0.95 | |
| plot_cor | 1.50 | 0.43 | 1.63 | |
| plot_coverage | 0.74 | 0.35 | 0.59 | |
| plot_detect | 0.87 | 0.06 | 0.83 | |
| plot_dist | 4.11 | 0.03 | 4.14 | |
| plot_frequency | 0.35 | 0.02 | 0.36 | |
| plot_gsea | 0.93 | 0.03 | 0.97 | |
| plot_heatmap | 3.13 | 0.04 | 3.17 | |
| plot_imputation | 1.36 | 0.07 | 1.44 | |
| plot_missval | 1.51 | 0.12 | 1.64 | |
| plot_normalization | 1.40 | 0.08 | 1.47 | |
| plot_numbers | 0.56 | 0.00 | 0.56 | |
| plot_p_hist | 1.34 | 0.03 | 1.39 | |
| plot_pca | 1.35 | 0.06 | 1.46 | |
| plot_single | 1.96 | 0.02 | 1.98 | |
| plot_volcano | 4.88 | 0.03 | 5.02 | |
| process | 1.78 | 0.03 | 1.81 | |
| report | 0 | 0 | 0 | |
| run_app | 0 | 0 | 0 | |
| se2msn | 0.11 | 0.00 | 0.11 | |
| test_diff | 1.11 | 0.02 | 1.12 | |
| test_gsea | 0.84 | 0.00 | 0.85 | |
| theme_DEP1 | 0.53 | 0.03 | 0.56 | |
| theme_DEP2 | 0.47 | 0.01 | 0.48 | |