Package: ImmuneSpaceR

Version: 1.8.2

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ImmuneSpaceR.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ImmuneSpaceR_1.8.2.tar.gz

StartedAt: 2018-10-10 02:57:35 -0400 (Wed, 10 Oct 2018)

EndedAt: 2018-10-10 02:59:16 -0400 (Wed, 10 Oct 2018)

EllapsedTime: 101.7 seconds

RetCode: 0

Status:  OK

CheckDir: ImmuneSpaceR.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ImmuneSpaceR.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ImmuneSpaceR_1.8.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/ImmuneSpaceR.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ImmuneSpaceR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ImmuneSpaceR' version '1.8.2'
* 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 'ImmuneSpaceR' 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 ... NOTE
Unexported objects imported by ':::' calls:
  'Rlabkey:::.lkdefaults' 'Rlabkey:::labkey.getRequestOptions'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.getDataToPlot: no visible binding for global variable 'value_reported'
Undefined global functions or variables:
  value_reported
* 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 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/ImmuneSpaceR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/ImmuneSpaceR_1.8.2.tar.gz && rm -rf ImmuneSpaceR.buildbin-libdir && mkdir ImmuneSpaceR.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ImmuneSpaceR.buildbin-libdir ImmuneSpaceR_1.8.2.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL ImmuneSpaceR_1.8.2.zip && rm ImmuneSpaceR_1.8.2.tar.gz ImmuneSpaceR_1.8.2.zip
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100 1785k  100 1785k    0     0  23.8M      0 --:--:-- --:--:-- --:--:-- 26.0M

install for i386

* installing *source* package 'ImmuneSpaceR' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ImmuneSpaceR'
    finding HTML links ... done
    CreateConnection                        html  
    ISpalette                               html  
    ImmuneSpaceConnection                   html  
    ImmuneSpaceR-package                    html  
    check_netrc                             html  
    loadConnection                          html  
    template_IS                             html  
    theme_IS                                html  
    write_netrc                             html  
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'ImmuneSpaceR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ImmuneSpaceR' as ImmuneSpaceR_1.8.2.zip
* DONE (ImmuneSpaceR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'ImmuneSpaceR' successfully unpacked and MD5 sums checked
In R CMD INSTALL

R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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.

> library(testthat)
> library(ImmuneSpaceR)
A .netrc file is required to connect to ImmuneSpace. For more information on how to create one, refer to the Configuration section of the introduction vignette.
> 
> if (Sys.info()["user"] != "biocbuild") test_check("ImmuneSpaceR")
> 
> proc.time()
   user  system elapsed 
   2.46    0.17    2.61 

R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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.

> library(testthat)
> library(ImmuneSpaceR)
A .netrc file is required to connect to ImmuneSpace. For more information on how to create one, refer to the Configuration section of the introduction vignette.
> 
> if (Sys.info()["user"] != "biocbuild") test_check("ImmuneSpaceR")
> 
> proc.time()
   user  system elapsed 
   2.54    0.23    2.76