Back to Multiple platform build/check report for BioC 3.12
ABCDE[F]GHIJKLMNOPQRSTUVWXYZ

CHECK report for FlowRepositoryR on tokay1

This page was generated on 2021-02-22 12:38:12 -0500 (Mon, 22 Feb 2021).

To the developers/maintainers of the FlowRepositoryR package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 630/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FlowRepositoryR 1.22.0
Josef Spidlen
Snapshot Date: 2021-02-21 14:52:07 -0500 (Sun, 21 Feb 2021)
URL: https://git.bioconductor.org/packages/FlowRepositoryR
Branch: RELEASE_3_12
Last Commit: be013a0
Last Changed Date: 2020-10-27 11:04:58 -0500 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    ERROR  
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: FlowRepositoryR
Version: 1.22.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FlowRepositoryR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings FlowRepositoryR_1.22.0.tar.gz
StartedAt: 2021-02-22 02:55:00 -0500 (Mon, 22 Feb 2021)
EndedAt: 2021-02-22 02:56:33 -0500 (Mon, 22 Feb 2021)
EllapsedTime: 93.3 seconds
RetCode: 0
Status:   OK   
CheckDir: FlowRepositoryR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FlowRepositoryR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings FlowRepositoryR_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/FlowRepositoryR.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'FlowRepositoryR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'FlowRepositoryR' 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 'FlowRepositoryR' 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
attachmentProxy: no visible global function definition for 'new'
fcsProxy: no visible global function definition for 'new'
flowRep.search: no visible global function definition for 'is'
flowRepData: no visible global function definition for 'new'
flowRepOrganization: no visible global function definition for 'new'
attachments<-,flowRepData: no visible global function definition for
  'is'
fcs.files<-,flowRepData: no visible global function definition for 'is'
impc.experiments<-,flowRepData: no visible global function definition
  for 'is'
Undefined global functions or variables:
  is new
Consider adding
  importFrom("methods", "is", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
flowRep.search 0.02      0    7.86
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 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-3.12-bioc/meat/FlowRepositoryR.Rcheck/00check.log'
for details.



Installation output

FlowRepositoryR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/FlowRepositoryR_1.22.0.tar.gz && rm -rf FlowRepositoryR.buildbin-libdir && mkdir FlowRepositoryR.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=FlowRepositoryR.buildbin-libdir FlowRepositoryR_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL FlowRepositoryR_1.22.0.zip && rm FlowRepositoryR_1.22.0.tar.gz FlowRepositoryR_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
100   98k  100   98k    0     0  2385k      0 --:--:-- --:--:-- --:--:-- 2601k

install for i386

* installing *source* package 'FlowRepositoryR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'FlowRepositoryR'
    finding HTML links ... done
    FlowRepositoryR-package                 html  
    attachmentProxy-class                   html  
    download-methods                        html  
    fcsProxy-class                          html  
    fileProxy-class                         html  
    flowRep.get                             html  
    flowRep.ls                              html  
    flowRep.search                          html  
    flowRep.submitGeneStatus                html  
    flowRep.submitImpcResults               html  
    flowRepData-class                       html  
    flowRepOrganization-class               html  
    forgetFlowRepositoryCredentials         html  
    getFlowRepositoryURL                    html  
    id-methods                              html  
    ilarCodeDescription                     html  
    impcCodeDescription                     html  
    impcResultsCopy-methods                 html  
    is.downloaded-methods                   html  
    listKnownIlarCodes                      html  
    setFlowRepositoryCredentials            html  
    setFlowRepositoryURL                    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 'FlowRepositoryR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'FlowRepositoryR' as FlowRepositoryR_1.22.0.zip
* DONE (FlowRepositoryR)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'FlowRepositoryR' successfully unpacked and MD5 sums checked

Tests output

FlowRepositoryR.Rcheck/tests_i386/runTests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

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.

> BiocGenerics:::testPackage("FlowRepositoryR")
File about.txt downloaded.
File GvHD2.fcs downloaded.
Downloading to C:/Users/biocbuild/bbs-3.12-bioc/meat/FlowRepositoryR.Rcheck/tests_i386/FR-FCM-ZZJ7 
File GvHD2.fcs is downloaded already.
File GvHD8.fcs downloaded.
File about.txt is downloaded already.
File ExampleGate.png downloaded.
Download finished.


RUNIT TEST PROTOCOL -- Mon Feb 22 02:56:15 2021 
*********************************************** 
Number of test functions: 16 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
FlowRepositoryR RUnit Tests - 16 test functions, 0 errors, 0 failures
Number of test functions: 16 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   1.40    0.15   19.59 

FlowRepositoryR.Rcheck/tests_x64/runTests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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.

> BiocGenerics:::testPackage("FlowRepositoryR")
File about.txt downloaded.
File GvHD2.fcs downloaded.
Downloading to C:/Users/biocbuild/bbs-3.12-bioc/meat/FlowRepositoryR.Rcheck/tests_x64/FR-FCM-ZZJ7 
File GvHD2.fcs is downloaded already.
File GvHD8.fcs downloaded.
File about.txt is downloaded already.
File ExampleGate.png downloaded.
Download finished.


RUNIT TEST PROTOCOL -- Mon Feb 22 02:56:27 2021 
*********************************************** 
Number of test functions: 16 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
FlowRepositoryR RUnit Tests - 16 test functions, 0 errors, 0 failures
Number of test functions: 16 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   1.31    0.01   11.43 

Example timings

FlowRepositoryR.Rcheck/examples_i386/FlowRepositoryR-Ex.timings

nameusersystemelapsed
attachmentProxy-class0.330.070.70
download-methods0.160.032.52
fcsProxy-class0.060.000.26
fileProxy-class0.060.000.27
flowRep.get0.070.000.26
flowRep.ls0.040.000.38
flowRep.search0.020.007.86
flowRep.submitGeneStatus000
flowRep.submitImpcResults000
flowRepData-class0.030.000.22
flowRepOrganization-class0.050.000.25
forgetFlowRepositoryCredentials000
getFlowRepositoryURL000
id-methods0.080.000.28
ilarCodeDescription000
impcCodeDescription000
impcResultsCopy-methods0.040.000.24
is.downloaded-methods0.040.000.25
listKnownIlarCodes000
setFlowRepositoryCredentials000
setFlowRepositoryURL000

FlowRepositoryR.Rcheck/examples_x64/FlowRepositoryR-Ex.timings

nameusersystemelapsed
attachmentProxy-class0.280.110.56
download-methods0.140.033.63
fcsProxy-class0.030.010.25
fileProxy-class0.030.000.22
flowRep.get0.020.000.20
flowRep.ls0.030.000.42
flowRep.search0.010.000.22
flowRep.submitGeneStatus000
flowRep.submitImpcResults000
flowRepData-class0.070.000.23
flowRepOrganization-class0.060.000.23
forgetFlowRepositoryCredentials000
getFlowRepositoryURL000
id-methods0.080.000.27
ilarCodeDescription000
impcCodeDescription000
impcResultsCopy-methods0.060.000.25
is.downloaded-methods0.030.000.23
listKnownIlarCodes000
setFlowRepositoryCredentials000
setFlowRepositoryURL000