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CHECK report for HPAanalyze on tokay1

This page was generated on 2019-04-13 11:29:36 -0400 (Sat, 13 Apr 2019).

Package 733/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HPAanalyze 1.0.0
Anh Nhat Tran
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/HPAanalyze
Branch: RELEASE_3_8
Last Commit: 2d7785a
Last Changed Date: 2018-10-30 11:42:10 -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: HPAanalyze
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HPAanalyze.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings HPAanalyze_1.0.0.tar.gz
StartedAt: 2019-04-13 03:03:58 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 03:06:52 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 173.5 seconds
RetCode: 0
Status:  OK  
CheckDir: HPAanalyze.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:HPAanalyze.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings HPAanalyze_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/HPAanalyze.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 'HPAanalyze/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HPAanalyze' version '1.0.0'
* 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 '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 'go_id'
hpaVisSubcell: no visible binding for global variable 'sub_location'
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 : <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'
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 cancer cell_line cell_type
  gene go_id high hpaCancer hpaNormalTissue hpaSubcellularLoc imageUrl
  index intensity level low medium not_detected patientId patient_count
  quantity rnaGeneCellLine rnaGeneTissue sex staining sub_location
  tissue tissue_cell 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
hpaXmlTissueExpr 5.49   0.09    5.70
hpaExport        1.41   0.17   10.01
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
hpaXmlTissueExpr 5.91   0.05    6.07
* 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/HPAanalyze.Rcheck/00check.log'
for details.



Installation output

HPAanalyze.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/HPAanalyze_1.0.0.tar.gz && rm -rf HPAanalyze.buildbin-libdir && mkdir HPAanalyze.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=HPAanalyze.buildbin-libdir HPAanalyze_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL HPAanalyze_1.0.0.zip && rm HPAanalyze_1.0.0.tar.gz HPAanalyze_1.0.0.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
 50 1451k   50  736k    0     0  16.0M      0 --:--:-- --:--:-- --:--:-- 17.1M
100 1451k  100 1451k    0     0  26.0M      0 --:--:-- --:--:-- --:--:-- 27.2M

install for i386

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

install for x64

* installing *source* package 'HPAanalyze' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HPAanalyze' as HPAanalyze_1.0.0.zip
* DONE (HPAanalyze)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'HPAanalyze' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

HPAanalyze.Rcheck/examples_i386/HPAanalyze-Ex.timings

nameusersystemelapsed
hpaDownload1.940.112.05
hpaExport 1.41 0.1710.01
hpaListParam0.110.050.15
hpaVis1.160.031.19
hpaVisPatho2.630.122.75
hpaVisSubcell1.420.161.58
hpaVisTissue1.700.221.92
hpaXml0.350.021.04
hpaXmlAntibody0.050.000.19
hpaXmlGet0.000.000.13
hpaXmlProtClass0.040.000.17
hpaXmlTissueExpr5.490.095.70
hpaXmlTissueExprSum0.040.000.70
hpa_downloaded_histology_v181.570.161.72

HPAanalyze.Rcheck/examples_x64/HPAanalyze-Ex.timings

nameusersystemelapsed
hpaDownload1.220.101.31
hpaExport1.900.191.14
hpaListParam0.090.010.11
hpaVis1.300.061.36
hpaVisPatho3.480.103.58
hpaVisSubcell1.780.252.03
hpaVisTissue1.970.202.17
hpaXml0.250.030.92
hpaXmlAntibody0.070.000.30
hpaXmlGet0.020.000.14
hpaXmlProtClass0.040.000.18
hpaXmlTissueExpr5.910.056.07
hpaXmlTissueExprSum0.030.000.69
hpa_downloaded_histology_v180.940.111.05