Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-07-23 15:06:15 -0400 (Fri, 23 Jul 2021).

CHECK results for pogos on tokay2

To the developers/maintainers of the pogos package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pogos.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1411/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pogos 1.12.0  (landing page)
VJ Carey
Snapshot Date: 2021-07-22 04:50:13 -0400 (Thu, 22 Jul 2021)
URL: https://git.bioconductor.org/packages/pogos
Branch: RELEASE_3_13
Last Commit: 9ddc3d7
Last Changed Date: 2021-05-19 12:32:46 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: pogos
Version: 1.12.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pogos.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings pogos_1.12.0.tar.gz
StartedAt: 2021-07-23 03:53:28 -0400 (Fri, 23 Jul 2021)
EndedAt: 2021-07-23 03:56:48 -0400 (Fri, 23 Jul 2021)
EllapsedTime: 200.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: pogos.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pogos.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings pogos_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/pogos.Rcheck'
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pogos/DESCRIPTION' ... OK
* this is package 'pogos' version '1.12.0'
* 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 'pogos' 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
compoundsByCell: no visible binding for global variable 'cell_lines_v1'
compoundsByCell: no visible binding for global variable 'compounds_v1'
compoundsByCell: no visible binding for global variable 'datasets_v1'
lkc: no visible binding for global variable 'cell_lines_v1'
lkc: no visible binding for global variable 'compounds_v1'
lkc: no visible binding for global variable 'datasets_v1'
plot,DRProfSet-missing: no visible binding for global variable 'dose'
plot,DRProfSet-missing: no visible binding for global variable
  'response'
plot,DRProfSet-missing: no visible binding for global variable 'drug'
plot,DRTraceSet-missing: no visible binding for global variable 'dose'
plot,DRTraceSet-missing: no visible binding for global variable
  'response'
plot,DRTraceSet-missing: no visible binding for global variable
  'cell_line'
Undefined global functions or variables:
  cell_line cell_lines_v1 compounds_v1 datasets_v1 dose drug response
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'DRProfSet,character,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 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: 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/pogos.Rcheck/00check.log'
for details.



Installation output

pogos.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/pogos_1.12.0.tar.gz && rm -rf pogos.buildbin-libdir && mkdir pogos.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pogos.buildbin-libdir pogos_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL pogos_1.12.0.zip && rm pogos_1.12.0.tar.gz pogos_1.12.0.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 27565  100 27565    0     0   295k      0 --:--:-- --:--:-- --:--:--  299k

install for i386

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  failed to copy 'pogos/vignettes/pogos.Rmd' to 'pogos/README.md'
* installing *source* package 'pogos' ...
** 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 'pogos'
    finding HTML links ... done
    DRProfSet                               html  
    DRTraceSet                              html  
    basicDecoder                            html  
    compoundsByCell                         html  
    compounds_v1                            html  
    iriCCLE                                 html  
    rxdbQuery_v1                            html  
    sub-DRProfSet-character-method          html  
    topEndpoints_v1                         html  
    traces                                  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

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  failed to copy 'pogos/vignettes/pogos.Rmd' to 'pogos/README.md'
* installing *source* package 'pogos' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pogos' as pogos_1.12.0.zip
* DONE (pogos)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'pogos' successfully unpacked and MD5 sums checked

Tests output

pogos.Rcheck/tests_i386/testthat.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 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(pogos)
Loading required package: rjson
Loading required package: httr
> 
> test_check("pogos")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 5 ]
> 
> proc.time()
   user  system elapsed 
   6.59    0.60    7.56 

pogos.Rcheck/tests_x64/testthat.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 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(pogos)
Loading required package: rjson
Loading required package: httr
> 
> test_check("pogos")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 5 ]
> 
> proc.time()
   user  system elapsed 
   6.60    0.42    7.40 

Example timings

pogos.Rcheck/examples_i386/pogos-Ex.timings

nameusersystemelapsed
DRProfSet000
DRTraceSet0.440.081.25
basicDecoder0.020.000.06
compoundsByCell000
compounds_v10.090.000.09
iriCCLE0.720.000.72
rxdbQuery_v10.010.000.06
topEndpoints_v1000
traces0.040.000.03

pogos.Rcheck/examples_x64/pogos-Ex.timings

nameusersystemelapsed
DRProfSet000
DRTraceSet0.710.021.40
basicDecoder0.000.000.05
compoundsByCell000
compounds_v10.080.010.10
iriCCLE0.950.020.96
rxdbQuery_v10.000.000.05
topEndpoints_v1000
traces0.020.010.03