Arkadiusz Gladki
| Snapshot Date: 2024-05-08 14:00:19 -0400 (Wed, 08 May 2024) |
| git_url: https://git.bioconductor.org/packages/gDR |
| git_branch: RELEASE_3_19 |
| git_last_commit: b86b89e |
| git_last_commit_date: 2024-04-30 11:50:18 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-09 11:40:52 -0400 (Thu, 09 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4748 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4484 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4514 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4480 |
| 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 787/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| gDR 1.2.0 (landing page) Arkadiusz Gladki
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the gDR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gDR.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: gDR |
| Version: 1.2.0 |
| Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:gDR.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings gDR_1.2.0.tar.gz |
| StartedAt: 2024-05-09 07:35:01 -0000 (Thu, 09 May 2024) |
| EndedAt: 2024-05-09 07:38:33 -0000 (Thu, 09 May 2024) |
| EllapsedTime: 212.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: gDR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:gDR.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings gDR_1.2.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/gDR.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gDR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gDR’ version ‘1.2.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘gDR’ 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 code 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 loading without being on the library search path ... 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 ... NOTE
checkRd: (-1) small_combo_data.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_combo_data.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_combo_data.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_combo_data.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_combo_data.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_combo_data.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_combo_data.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_combo_data.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_combo_data.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_combo_data.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_combo_data.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_combo_data.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_combo_data.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_combo_data.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_combo_data.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_data.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_data.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_data.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_data.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_data.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_data.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_data.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_data.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_data.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_data.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_data.Rd:21: Lost braces in \itemize; meant \describe ?
* 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 ... 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 data for ASCII and uncompressed saves ... 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.19-bioc/meat/gDR.Rcheck/00check.log’
for details.
gDR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL gDR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’ * installing *source* package ‘gDR’ ... ** using staged installation ** R ** data ** 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 (gDR)
gDR.Rcheck/tests/testthat.Rout
R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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(gDR)
Loading required package: gDRcore
Loading required package: gDRimport
Loading required package: gDRutils
>
> test_check("gDR")
INFO [2024-05-09 07:38:28] Manifest loaded successfully
INFO [2024-05-09 07:38:28] Reading Template_7daytreated.xlsx with load_templates_xlsx
INFO [2024-05-09 07:38:28] Loading Template_7daytreated.xlsx
INFO [2024-05-09 07:38:28] Loading Template_Untreated.xlsx
INFO [2024-05-09 07:38:29] Templates loaded successfully!
INFO [2024-05-09 07:38:29] Reading file /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/gDRimport/extdata/data1/RawData_day0.xlsx, sheet Readout_0077vs0068_day7
INFO [2024-05-09 07:38:29] Plate 201904190a read; 384 wells
INFO [2024-05-09 07:38:29] Plate 201904190b read; 384 wells
INFO [2024-05-09 07:38:29] Plate 201904190c read; 384 wells
INFO [2024-05-09 07:38:29] Plate 201904190d read; 384 wells
INFO [2024-05-09 07:38:29] Plate 201904190e read; 384 wells
INFO [2024-05-09 07:38:29] Plate 201904190f read; 384 wells
INFO [2024-05-09 07:38:29] File done
INFO [2024-05-09 07:38:29] Reading file /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/gDRimport/extdata/data1/RawData_day7.xlsx, sheet Readout_0077vs0068_day7
INFO [2024-05-09 07:38:30] Plate 201904197a read; 384 wells
INFO [2024-05-09 07:38:30] Plate 201904197b read; 384 wells
INFO [2024-05-09 07:38:30] Plate 201904197c read; 384 wells
INFO [2024-05-09 07:38:30] Plate 201904197d read; 384 wells
INFO [2024-05-09 07:38:30] Plate 201904197e read; 384 wells
INFO [2024-05-09 07:38:30] Plate 201904197f read; 384 wells
INFO [2024-05-09 07:38:30] File done
INFO [2024-05-09 07:38:30] Merging data
INFO [2024-05-09 07:38:30] Merging the metadata (manifest and treatment files)
WARN [2024-05-09 07:38:30] 4608 well loaded, 768 wells discarded for lack of annotation,
3840 data point selected
INFO [2024-05-09 07:38:30] Merge with Cell line info
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]
>
> proc.time()
user system elapsed
11.728 0.413 12.140
gDR.Rcheck/gDR-Ex.timings
| name | user | system | elapsed | |
| import_data | 1.838 | 0.156 | 1.991 | |