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This page was generated on 2022-04-13 12:07:13 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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

CHECK results for RImmPort on tokay2


To the developers/maintainers of the RImmPort package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/RImmPort.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1610/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RImmPort 1.22.0  (landing page)
Zicheng Hu , Ravi Shankar
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/RImmPort
git_branch: RELEASE_3_14
git_last_commit: 5cca829
git_last_commit_date: 2021-10-26 12:25:37 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: RImmPort
Version: 1.22.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RImmPort.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings RImmPort_1.22.0.tar.gz
StartedAt: 2022-04-13 01:43:56 -0400 (Wed, 13 Apr 2022)
EndedAt: 2022-04-13 01:45:20 -0400 (Wed, 13 Apr 2022)
EllapsedTime: 83.6 seconds
RetCode: 0
Status:   OK  
CheckDir: RImmPort.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RImmPort.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings RImmPort_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/RImmPort.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RImmPort/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RImmPort' version '1.22.0'
* 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 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... OK
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/RImmPort.Rcheck/00check.log'
for details.



Installation output

RImmPort.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/RImmPort_1.22.0.tar.gz && rm -rf RImmPort.buildbin-libdir && mkdir RImmPort.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RImmPort.buildbin-libdir RImmPort_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL RImmPort_1.22.0.zip && rm RImmPort_1.22.0.tar.gz RImmPort_1.22.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 19 1912k   19  371k    0     0   551k      0  0:00:03 --:--:--  0:00:03  551k
 89 1912k   89 1714k    0     0  1012k      0  0:00:01  0:00:01 --:--:-- 1011k
100 1912k  100 1912k    0     0  1059k      0  0:00:01  0:00:01 --:--:-- 1059k

install for i386

* installing *source* package 'RImmPort' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RImmPort'
    finding HTML links ... done
    AE                                      html  
    APMH                                    html  
    Adverse-Events-Domain                   html  
    Associated-Persons-Medical-History-Domain
                                            html  
    CM                                      html  
    Cellular-Quantification-Domain          html  
    Concomitant-Medications-Domain          html  
    DM                                      html  
    DV                                      html  
    Demographics-Domain                     html  
    EX                                      html  
    Events-class                            html  
    Exposure-Domain                         html  
    FA                                      html  
    Findings-About-Domain                   html  
    Findings-class                          html  
    Genetics-Findings-Domain                html  
    Interventions-class                     html  
    LB                                      html  
    Laboratory-Test-Results-Domain          html  
    MH                                      html  
    Medical-History-Domain                  html  
    Nucleic-Acid-Quantification-Domain      html  
    PE                                      html  
    PF                                      html  
    Physical-Examination-Domain             html  
    Protein-Quantification-Domain           html  
    Protocol-Deviations-Domain              html  
    QS                                      html  
    Questionnaires-Domain                   html  
    RImmPort                                html  
    SR                                      html  
    SU                                      html  
    SUPP                                    html  
    SUPPDV                                  html  
    SUPPFA                                  html  
    SUPPLB                                  html  
    SUPPMH                                  html  
    SUPPPE                                  html  
    SUPPPF                                  html  
    SUPPVS                                  html  
    SUPPZA                                  html  
    SUPPZB                                  html  
    SUPPZC                                  html  
    SUPPZD                                  html  
    SV                                      html  
    Skin-Response-Domain                    html  
    SpecialPurpose-class                    html  
    Study-class                             html  
    Subject-Visits-Domain                   html  
    Substance-Use-Domain                    html  
    TA                                      html  
    TI                                      html  
    TS                                      html  
    TV                                      html  
    Titer-Assay-Results-Domain              html  
    Trial-Arms-Domain                       html  
    Trial-Inclusion-Exclusion-Criteria-Domain
                                            html  
    Trial-Summary-Domain                    html  
    Trial-Visits-Domain                     html  
    TrialDesign-class                       html  
    VS                                      html  
    Vital-Signs-Domain                      html  
    ZA                                      html  
    ZB                                      html  
    ZC                                      html  
    ZD                                      html  
    buildNewSqliteDb                        html  
    getAssayDataOfStudies                   html  
    getDomainCode                           html  
    getDomainDataOfStudies                  html  
    getListOfAssayTypes                     html  
    getListOfDomains                        html  
    getListOfStudies                        html  
    getStudiesWithSpecificAssayData         html  
    getStudiesWithSpecificDomainData        html  
    getStudy                                html  
    loadSerializedStudyData                 html  
    mergeDomainAndSupplemental              html  
    serialzeStudyData                       html  
    setImmPortDataSource                    html  
** 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

install for x64

* installing *source* package 'RImmPort' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RImmPort' as RImmPort_1.22.0.zip
* DONE (RImmPort)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'RImmPort' successfully unpacked and MD5 sums checked

Tests output


Example timings

RImmPort.Rcheck/examples_i386/RImmPort-Ex.timings

nameusersystemelapsed
Events-class0.480.102.89
Findings-class0.430.030.45
Interventions-class0.280.000.28
SpecialPurpose-class0.270.010.28
Study-class0.230.000.24
TrialDesign-class0.220.000.22
buildNewSqliteDb000
getAssayDataOfStudies0.140.020.16
getDomainCode000
getDomainDataOfStudies0.080.000.08
getListOfAssayTypes000
getListOfDomains000
getListOfStudies0.060.000.06
getStudiesWithSpecificAssayData0.070.000.07
getStudiesWithSpecificDomainData0.060.000.06
getStudy0.250.010.27
loadSerializedStudyData0.020.000.02
mergeDomainAndSupplemental0.190.020.29
serialzeStudyData0.560.020.69
setImmPortDataSource0.030.030.06

RImmPort.Rcheck/examples_x64/RImmPort-Ex.timings

nameusersystemelapsed
Events-class0.320.050.35
Findings-class0.260.000.27
Interventions-class0.200.010.21
SpecialPurpose-class0.370.020.39
Study-class0.360.050.41
TrialDesign-class0.270.040.31
buildNewSqliteDb000
getAssayDataOfStudies0.140.000.14
getDomainCode000
getDomainDataOfStudies0.040.020.06
getListOfAssayTypes000
getListOfDomains000
getListOfStudies0.050.000.05
getStudiesWithSpecificAssayData0.050.010.06
getStudiesWithSpecificDomainData0.030.020.05
getStudy0.210.020.24
loadSerializedStudyData000
mergeDomainAndSupplemental0.140.000.15
serialzeStudyData0.450.000.45
setImmPortDataSource0.050.000.05