Package: HPAanalyze

Version: 1.2.1

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HPAanalyze.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings HPAanalyze_1.2.1.tar.gz

StartedAt: 2019-10-16 04:26:44 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:29:19 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 154.5 seconds

RetCode: 0

Status:  OK

CheckDir: HPAanalyze.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HPAanalyze.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings HPAanalyze_1.2.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/HPAanalyze.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.2.1'
* 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 'hpaNormalTissue'
hpaDownload: no visible binding for global variable 'hpaCancer'
hpaDownload: no visible binding for global variable 'Total.patients'
hpaDownload: no visible binding for global variable 'Level'
hpaDownload: no visible binding for global variable 'Count.patients'
hpaDownload: no visible binding for global variable 'hpaSubcellularLoc'
hpaDownload: no visible binding for global variable 'rnaGeneTissue'
hpaDownload: no visible binding for global variable 'rnaGeneCellLine'
hpaSubset: no visible binding for global variable 'gene'
hpaSubset: no visible binding for global variable 'tissue'
hpaSubset: no visible binding for global variable 'cell_type'
hpaSubset: no visible binding for global variable 'cancer'
hpaSubset: no visible binding for global variable 'cell_line'
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'
hpaVisSubcell: no visible binding for global variable 'enhanced'
hpaVisSubcell: no visible binding for global variable 'supported'
hpaVisSubcell: no visible binding for global variable 'approved'
hpaVisSubcell: no visible binding for global variable 'uncertain'
hpaVisTissue: no visible binding for global variable 'gene'
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 : : no visible binding for global variable
  'patientId'
hpaXmlTissueExpr : : no visible binding for global variable
  'age'
hpaXmlTissueExpr : : no visible binding for global variable
  'sex'
hpaXmlTissueExpr : : no visible binding for global variable
  'staining'
hpaXmlTissueExpr : : no visible binding for global variable
  'intensity'
hpaXmlTissueExpr : : no visible binding for global variable
  'quantity'
hpaXmlTissueExpr : : no visible binding for global variable
  'imageUrl'
hpaXmlTissueExprSum: no visible binding for global variable 'tissue'
hpaXmlTissueExprSum: no visible binding for global variable 'imageUrl'
named_vector_list_to_tibble: no visible binding for global variable
  'index'
named_vector_list_to_tibble: no visible binding for global variable
  'value'
Undefined global functions or variables:
  Count.patients Level Total.patients age approved cancer cell_line
  cell_type enhanced gene high hpaCancer hpaNormalTissue
  hpaSubcellularLoc imageUrl index intensity level low medium
  not_detected patientId patient_count quantity rnaGeneCellLine
  rnaGeneTissue sex staining sub_location supported tissue tissue_cell
  uncertain value
* 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 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
Examples with CPU or elapsed time > 5s
          user system elapsed
hpaExport 0.53   0.08    5.02
** 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-3.9-bioc/meat/HPAanalyze.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/HPAanalyze_1.2.1.tar.gz && rm -rf HPAanalyze.buildbin-libdir && mkdir HPAanalyze.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=HPAanalyze.buildbin-libdir HPAanalyze_1.2.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL HPAanalyze_1.2.1.zip && rm HPAanalyze_1.2.1.tar.gz HPAanalyze_1.2.1.zip
###
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100 3089k  100 3089k    0     0  33.7M      0 --:--:-- --:--:-- --:--:-- 36.3M

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_downloaded_histology_v18            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_1.2.1.zip
* DONE (HPAanalyze)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'HPAanalyze' successfully unpacked and MD5 sums checked