Xutao Wang
| Snapshot Date: 2024-10-17 07:30 -0400 (Thu, 17 Oct 2024) |
| git_url: https://git.bioconductor.org/packages/curatedTBData |
| git_branch: RELEASE_3_19 |
| git_last_commit: 629b8c2 |
| git_last_commit_date: 2024-04-30 11:09:46 -0400 (Tue, 30 Apr 2024) |
| Back to Build/check report for BioC 3.19 experimental data |
|
This page was generated on 2024-10-17 14:51 -0400 (Thu, 17 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
| 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 85/430 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
| curatedTBData 2.0.0 (landing page) Xutao Wang
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | |||||||
|
To the developers/maintainers of the curatedTBData package: - 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: curatedTBData |
| Version: 2.0.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:curatedTBData.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings curatedTBData_2.0.0.tar.gz |
| StartedAt: 2024-10-17 11:12:31 -0400 (Thu, 17 Oct 2024) |
| EndedAt: 2024-10-17 11:18:53 -0400 (Thu, 17 Oct 2024) |
| EllapsedTime: 382.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: curatedTBData.Rcheck |
| Warnings: 2 |
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### Running command:
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### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:curatedTBData.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings curatedTBData_2.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-data-experiment/meat/curatedTBData.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.5 LTS
* using session charset: UTF-8
* checking for file ‘curatedTBData/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘curatedTBData’ version ‘2.0.0’
* 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 ‘curatedTBData’ 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) DataSummary.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:31: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) DataSummary.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:54: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) DataSummary.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DataSummary.Rd:76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:18: Lost braces in \itemize; meant \describe ?
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checkRd: (-1) SignatureInfoTraining.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SignatureInfoTraining.Rd:47: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented data sets:
‘Clinical_Information’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Data codoc mismatches from Rd file 'DataSummary.Rd':
Variables in data frame 'DataSummary'
Code: Age Control Country/Region DiagnosisMethod GEOAccession
GeneralType HIVStatus LTBI Notes OD PTB Platform Tissue Total
Docs: Age Control DiagnosisMethod GeneralType GeographicalRegion
HIVStatus LTBI Notes OD PTB Platform Study Tissue Total
* 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 ... NOTE
Note: found 3 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
combine_objects 16.628 1.731 19.416
curatedTBData 10.853 1.241 12.997
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 2 NOTEs
See
‘/home/biocbuild/bbs-3.19-data-experiment/meat/curatedTBData.Rcheck/00check.log’
for details.
curatedTBData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL curatedTBData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘curatedTBData’ ... ** 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 (curatedTBData)
curatedTBData.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-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(curatedTBData)
>
> test_check("curatedTBData")
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[ FAIL 0 | WARN 2 | SKIP 0 | PASS 21 ]
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 21 ]
>
> proc.time()
user system elapsed
33.755 2.875 38.922
curatedTBData.Rcheck/curatedTBData-Ex.timings
| name | user | system | elapsed | |
| combine_objects | 16.628 | 1.731 | 19.416 | |
| curatedTBData | 10.853 | 1.241 | 12.997 | |
| subset_curatedTBData | 3.195 | 0.316 | 3.939 | |