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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HPAanalyze.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings HPAanalyze_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/HPAanalyze.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 'HPAanalyze/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HPAanalyze' version '1.12.0'
* package encoding: UTF-8
* 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 'HPAanalyze' 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
hpaDownload: no visible binding for global variable 'datasetnames'
hpaDownload: no visible binding for global variable
  'hpa_histology_data'
hpaDownload: no visible binding for global variable '.'
hpaSubset : subsetting: no visible binding for global variable 'gene'
hpaSubset : subsetting: no visible binding for global variable 'tissue'
hpaSubset : subsetting: no visible binding for global variable
  'cell_type'
hpaSubset : subsetting: no visible binding for global variable 'cancer'
hpaSubset : subsetting: no visible binding for global variable
  'cell_line'
hpaVis: no visible binding for global variable 'hpa_histology_data'
hpaVisPatho: no visible binding for global variable 'gene'
hpaVisPatho: no visible binding for global variable 'cancer'
hpaVisPatho: no visible binding for global variable 'high'
hpaVisPatho: no visible binding for global variable 'medium'
hpaVisPatho: no visible binding for global variable 'low'
hpaVisPatho: no visible binding for global variable 'not_detected'
hpaVisPatho: no visible binding for global variable 'patient_count'
hpaVisPatho: no visible binding for global variable 'level'
hpaVisSubcell: no visible binding for global variable 'gene'
hpaVisSubcell: no visible binding for global variable 'sub_location'
hpaVisTissue: no visible binding for global variable 'gene'
hpaVisTissue: no visible binding for global variable '.'
hpaVisTissue: no visible binding for global variable 'tissue'
hpaVisTissue: no visible binding for global variable 'cell_type'
hpaVisTissue: no visible binding for global variable 'level'
hpaVisTissue: no visible binding for global variable 'tissue_cell'
hpaXmlTissueExpr : <anonymous>: no visible binding for global variable
  'patientId'
hpaXmlTissueExpr : <anonymous>: no visible binding for global variable
  'age'
hpaXmlTissueExpr : <anonymous>: no visible binding for global variable
  'sex'
hpaXmlTissueExpr : <anonymous>: no visible binding for global variable
  'staining'
hpaXmlTissueExpr : <anonymous>: no visible binding for global variable
  'intensity'
hpaXmlTissueExpr : <anonymous>: no visible binding for global variable
  'quantity'
hpaXmlTissueExpr : <anonymous>: no visible binding for global variable
  'imageUrl'
hpaXmlTissueExprSum: no visible binding for global variable 'tissue'
hpaXmlTissueExprSum: no visible binding for global variable 'imageUrl'
is_null_data: no visible binding for global variable
  'hpa_histology_data'
named_vector_list_to_tibble: no visible binding for global variable
  'index'
Undefined global functions or variables:
  . age cancer cell_line cell_type datasetnames gene high
  hpa_histology_data imageUrl index intensity level low medium
  not_detected patientId patient_count quantity sex staining
  sub_location tissue tissue_cell
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... 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/HPAanalyze.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/HPAanalyze_1.12.0.tar.gz && rm -rf HPAanalyze.buildbin-libdir && mkdir HPAanalyze.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=HPAanalyze.buildbin-libdir HPAanalyze_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL HPAanalyze_1.12.0.zip && rm HPAanalyze_1.12.0.tar.gz HPAanalyze_1.12.0.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
  9 6382k    9  633k    0     0   670k      0  0:00:09 --:--:--  0:00:09  670k
 33 6382k   33 2146k    0     0  1105k      0  0:00:05  0:00:01  0:00:04 1105k
 72 6382k   72 4623k    0     0  1573k      0  0:00:04  0:00:02  0:00:02 1573k
100 6382k  100 6382k    0     0  1841k      0  0:00:03  0:00:03 --:--:-- 1841k

install for i386

* installing *source* package 'HPAanalyze' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'HPAanalyze'
    finding HTML links ... done
    hpaDownload                             html  
    hpaExport                               html  
    hpaListParam                            html  
    hpaVis                                  html  
    hpaVisPatho                             html  
    hpaVisSubcell                           html  
    hpaVisTissue                            html  
    hpaXml                                  html  
    hpaXmlAntibody                          html  
    hpaXmlGet                               html  
    hpaXmlProtClass                         html  
    hpaXmlTissueExpr                        html  
    hpaXmlTissueExprSum                     html  
    hpa_histology_data                      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 'HPAanalyze' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HPAanalyze' as HPAanalyze_1.12.0.zip
* DONE (HPAanalyze)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'HPAanalyze' successfully unpacked and MD5 sums checked