| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-23 12:06 -0400 (Thu, 23 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4894 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4684 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4629 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4642 |
| 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 1799/2355 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RImmPort 1.37.0 (landing page) Zicheng Hu
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | NA | ||||||||||
|
To the developers/maintainers of the RImmPort package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RImmPort.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: RImmPort |
| Version: 1.37.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RImmPort.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RImmPort_1.37.0.tar.gz |
| StartedAt: 2025-10-22 21:39:46 -0400 (Wed, 22 Oct 2025) |
| EndedAt: 2025-10-22 21:40:07 -0400 (Wed, 22 Oct 2025) |
| EllapsedTime: 20.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RImmPort.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RImmPort.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RImmPort_1.37.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/RImmPort.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RImmPort/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RImmPort’ version ‘1.37.0’
* 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 ‘RImmPort’ 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 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 ... NOTE
buildNewSqliteDb: no visible global function definition for
‘dbListTables’
Undefined global functions or variables:
dbListTables
* checking Rd files ... NOTE
checkRd: (-1) SUPPDV.Rd:22-32: Lost braces
22 | The following table enumerates the values in QNAM and QLABEL variables {
| ^
checkRd: (-1) SUPPFA.Rd:23-28: Lost braces
23 | The following table enumerates the values in QNAM and QLABEL variables {
| ^
checkRd: (-1) SUPPLB.Rd:22-29: Lost braces
22 | The following table enumerates the values in QNAM and QLABEL variables {
| ^
checkRd: (-1) SUPPMH.Rd:23-30: Lost braces
23 | The following table enumerates the values in QNAM and QLABEL variables {
| ^
checkRd: (-1) SUPPPE.Rd:23-28: Lost braces
23 | The following table enumerates the values in QNAM and QLABEL variables {
| ^
checkRd: (-1) SUPPPF.Rd:22-38: Lost braces
22 | The following table enumerates the values in QNAM and QLABEL variables {
| ^
checkRd: (-1) SUPPVS.Rd:23-28: Lost braces
23 | The following table enumerates the values in QNAM and QLABEL variables {
| ^
checkRd: (-1) SUPPZA.Rd:22-39: Lost braces
22 | The following table enumerates the values in QNAM and QLABEL variables {
| ^
checkRd: (-1) SUPPZB.Rd:22-38: Lost braces
22 | The following table enumerates the values in QNAM and QLABEL variables {
| ^
checkRd: (-1) SUPPZC.Rd:22-37: Lost braces
22 | The following table enumerates the values in QNAM and QLABEL variables {
| ^
checkRd: (-1) SUPPZD.Rd:22-37: Lost braces
22 | The following table enumerates the values in QNAM and QLABEL variables {
| ^
checkRd: (-1) TS.Rd:20-41: Lost braces
20 | The following table enumerates the values in TSPARMCD and TSPARM variables {
| ^
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.22-bioc/meat/RImmPort.Rcheck/00check.log’
for details.
RImmPort.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RImmPort ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘RImmPort’ ... ** this is package ‘RImmPort’ version ‘1.37.0’ ** using staged installation ** R ** 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 (RImmPort)
RImmPort.Rcheck/RImmPort-Ex.timings
| name | user | system | elapsed | |
| Events-class | 0.179 | 0.031 | 0.286 | |
| Findings-class | 0.085 | 0.012 | 0.100 | |
| Interventions-class | 0.066 | 0.008 | 0.074 | |
| SpecialPurpose-class | 0.070 | 0.009 | 0.078 | |
| Study-class | 0.065 | 0.007 | 0.072 | |
| TrialDesign-class | 0.064 | 0.007 | 0.070 | |
| buildNewSqliteDb | 0.000 | 0.001 | 0.001 | |
| getAssayDataOfStudies | 0.051 | 0.004 | 0.055 | |
| getDomainCode | 0 | 0 | 0 | |
| getDomainDataOfStudies | 0.014 | 0.002 | 0.017 | |
| getListOfAssayTypes | 0 | 0 | 0 | |
| getListOfDomains | 0.000 | 0.001 | 0.000 | |
| getListOfStudies | 0.013 | 0.002 | 0.014 | |
| getStudiesWithSpecificAssayData | 0.017 | 0.002 | 0.019 | |
| getStudiesWithSpecificDomainData | 0.014 | 0.003 | 0.015 | |
| getStudy | 0.070 | 0.007 | 0.076 | |
| loadSerializedStudyData | 0.001 | 0.001 | 0.002 | |
| mergeDomainAndSupplemental | 0.047 | 0.005 | 0.059 | |
| serialzeStudyData | 0.119 | 0.027 | 0.159 | |
| setImmPortDataSource | 0.013 | 0.002 | 0.016 | |