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This page was generated on 2024-11-09 21:31 -0500 (Sat, 09 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4505
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4506
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4538
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4486
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 1757/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RImmPort 1.34.0  (landing page)
Zicheng Hu , Ravi Shankar
Snapshot Date: 2024-11-08 13:40 -0500 (Fri, 08 Nov 2024)
git_url: https://git.bioconductor.org/packages/RImmPort
git_branch: RELEASE_3_20
git_last_commit: 96364a3
git_last_commit_date: 2024-10-29 10:07:27 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  YES
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for RImmPort on kjohnson3

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.

raw results


Summary

Package: RImmPort
Version: 1.34.0
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_1.34.0.tar.gz
StartedAt: 2024-11-09 11:30:10 -0500 (Sat, 09 Nov 2024)
EndedAt: 2024-11-09 11:34:13 -0500 (Sat, 09 Nov 2024)
EllapsedTime: 242.3 seconds
RetCode: 0
Status:   OK  
CheckDir: RImmPort.Rcheck
Warnings: 0

Command output

##############################################################################
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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_1.34.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/RImmPort.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RImmPort/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RImmPort’ version ‘1.34.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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-3.20-bioc/meat/RImmPort.Rcheck/00check.log’
for details.


Installation output

RImmPort.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RImmPort
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘RImmPort’ ...
** 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)

Tests output


Example timings

RImmPort.Rcheck/RImmPort-Ex.timings

nameusersystemelapsed
Events-class0.1730.0280.208
Findings-class0.0820.0130.095
Interventions-class0.0690.0080.077
SpecialPurpose-class0.0740.0140.087
Study-class0.0690.0110.080
TrialDesign-class0.0890.0080.097
buildNewSqliteDb0.0010.0010.000
getAssayDataOfStudies0.0280.0030.032
getDomainCode000
getDomainDataOfStudies0.0170.0020.019
getListOfAssayTypes000
getListOfDomains000
getListOfStudies0.0150.0030.018
getStudiesWithSpecificAssayData0.0140.0020.017
getStudiesWithSpecificDomainData0.0160.0030.019
getStudy0.0720.0120.083
loadSerializedStudyData0.0010.0010.002
mergeDomainAndSupplemental0.0550.0070.063
serialzeStudyData0.1260.0260.157
setImmPortDataSource0.0150.0030.018