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CHECK report for RImmPort on tokay1

This page was generated on 2019-04-13 11:26:21 -0400 (Sat, 13 Apr 2019).

Package 1312/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RImmPort 1.10.0
Zicheng Hu , Ravi Shankar
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/RImmPort
Branch: RELEASE_3_8
Last Commit: abbe516
Last Changed Date: 2018-10-30 11:42:00 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RImmPort
Version: 1.10.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RImmPort.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings RImmPort_1.10.0.tar.gz
StartedAt: 2019-04-13 05:03:57 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 05:05:53 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 116.0 seconds
RetCode: 0
Status:  OK  
CheckDir: RImmPort.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RImmPort.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings RImmPort_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/RImmPort.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.10.0'
* 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 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-3.8-bioc/meat/RImmPort.Rcheck/00check.log'
for details.



Installation output

RImmPort.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/RImmPort_1.10.0.tar.gz && rm -rf RImmPort.buildbin-libdir && mkdir RImmPort.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RImmPort.buildbin-libdir RImmPort_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL RImmPort_1.10.0.zip && rm RImmPort_1.10.0.tar.gz RImmPort_1.10.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1911k  100 1911k    0     0  29.1M      0 --:--:-- --:--:-- --:--:-- 30.5M

install for i386

* installing *source* package 'RImmPort' ...
** 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
In R CMD INSTALL

install for x64

* installing *source* package 'RImmPort' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RImmPort' as RImmPort_1.10.0.zip
* DONE (RImmPort)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'RImmPort' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

RImmPort.Rcheck/examples_i386/RImmPort-Ex.timings

nameusersystemelapsed
Events-class0.390.081.51
Findings-class0.200.030.22
Interventions-class0.140.010.16
SpecialPurpose-class0.160.000.15
Study-class0.160.020.17
TrialDesign-class0.150.000.16
buildNewSqliteDb0.000.010.02
getAssayDataOfStudies0.080.000.07
getDomainCode000
getDomainDataOfStudies0.030.020.05
getListOfAssayTypes000
getListOfDomains000
getListOfStudies0.050.000.05
getStudiesWithSpecificAssayData0.030.020.04
getStudiesWithSpecificDomainData0.050.000.05
getStudy0.250.030.28
loadSerializedStudyData000
mergeDomainAndSupplemental0.070.000.08
serialzeStudyData0.250.010.28
setImmPortDataSource0.050.000.05

RImmPort.Rcheck/examples_x64/RImmPort-Ex.timings

nameusersystemelapsed
Events-class0.470.030.46
Findings-class0.220.000.22
Interventions-class0.140.030.17
SpecialPurpose-class0.140.020.15
Study-class0.150.000.16
TrialDesign-class0.160.030.16
buildNewSqliteDb000
getAssayDataOfStudies0.080.000.08
getDomainCode000
getDomainDataOfStudies0.030.000.03
getListOfAssayTypes000
getListOfDomains000
getListOfStudies0.050.000.04
getStudiesWithSpecificAssayData0.040.000.05
getStudiesWithSpecificDomainData0.030.000.03
getStudy0.20.00.2
loadSerializedStudyData000
mergeDomainAndSupplemental0.100.000.09
serialzeStudyData0.250.060.32
setImmPortDataSource0.040.000.04