Back to Multiple platform build/check report for BioC 3.14
ABCDEFGH[I]JKLMNOPQRSTUVWXYZ

This page was generated on 2022-01-14 13:06:35 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for iPAC on tokay2


To the developers/maintainers of the iPAC package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/iPAC.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 950/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iPAC 1.38.0  (landing page)
Gregory Ryslik
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/iPAC
git_branch: RELEASE_3_14
git_last_commit: e34e9ed
git_last_commit_date: 2021-10-26 12:03:56 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: iPAC
Version: 1.38.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:iPAC.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings iPAC_1.38.0.tar.gz
StartedAt: 2022-01-13 21:20:55 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 21:27:40 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 405.0 seconds
RetCode: 0
Status:   OK  
CheckDir: iPAC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:iPAC.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings iPAC_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/iPAC.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'iPAC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'iPAC' version '1.38.0'
* 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 'iPAC' 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
Package in Depends field not imported from: 'gdata'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Plot.Protein.Linear: no visible global function definition for
  'heat.colors'
Plot.Protein.Linear: no visible global function definition for 'gray'
Plot.Protein.Linear: no visible global function definition for
  'topo.colors'
Plot.Protein.Linear: no visible global function definition for
  'cm.colors'
Plot.Protein.Linear: no visible global function definition for 'par'
Plot.Protein.Linear: no visible global function definition for 'rect'
Plot.Protein.Linear: no visible global function definition for 'text'
SetTextContrastColor: no visible global function definition for
  'col2rgb'
calcorder: no visible global function definition for 'dist'
calcorder: no visible global function definition for 'cmdscale'
difforder0: no visible global function definition for 'pbinom'
difforder0: no visible global function definition for 'dmultinom'
difforder1: no visible global function definition for 'dmultinom'
nmc: no visible global function definition for 'pbeta'
plotLinear: no visible global function definition for 'pdf'
plotLinear: no visible global function definition for 'dev.off'
plotLinear: no visible global function definition for 'dev.copy2pdf'
plotMDS: no visible global function definition for 'pdf'
plotMDS: no visible global function definition for 'dev.off'
plotMDS: no visible global function definition for 'dev.copy2pdf'
Undefined global functions or variables:
  cm.colors cmdscale col2rgb dev.copy2pdf dev.off dist dmultinom gray
  heat.colors par pbeta pbinom pdf rect text topo.colors
Consider adding
  importFrom("grDevices", "cm.colors", "col2rgb", "dev.copy2pdf",
             "dev.off", "gray", "heat.colors", "pdf", "topo.colors")
  importFrom("graphics", "par", "rect", "text")
  importFrom("stats", "cmdscale", "dist", "dmultinom", "pbeta", "pbinom")
to your NAMESPACE file.
* 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 (user + system) or elapsed time > 5s
               user system elapsed
ClusterFind   68.00   0.62   69.20
get.Positions 14.14   0.67   16.06
nmc           14.05   0.02   14.08
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
ClusterFind   73.58   0.79   74.94
get.Positions 22.74   1.83   25.61
nmc           16.15   0.02   16.18
* 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-3.14-bioc/meat/iPAC.Rcheck/00check.log'
for details.



Installation output

iPAC.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/iPAC_1.38.0.tar.gz && rm -rf iPAC.buildbin-libdir && mkdir iPAC.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=iPAC.buildbin-libdir iPAC_1.38.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL iPAC_1.38.0.zip && rm iPAC_1.38.0.tar.gz iPAC_1.38.0.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  162k  100  162k    0     0  1037k      0 --:--:-- --:--:-- --:--:-- 1043k

install for i386

* installing *source* package 'iPAC' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'iPAC'
    finding HTML links ... done
    ClusterFind                             html  
    KRAS.Mutations                          html  
    PIK3CA.Mutations                        html  
    Plot.Protein.Linear                     html  
    get.AASeq                               html  
    get.AlignedPositions                    html  
    get.Positions                           html  
    get.Remapped.Order                      html  
    get.SingleLetterCode                    html  
    iPAC-package                            html  
    nmc                                     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 'iPAC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'iPAC' as iPAC_1.38.0.zip
* DONE (iPAC)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'iPAC' successfully unpacked and MD5 sums checked

Tests output


Example timings

iPAC.Rcheck/examples_i386/iPAC-Ex.timings

nameusersystemelapsed
ClusterFind68.00 0.6269.20
KRAS.Mutations000
PIK3CA.Mutations0.020.020.03
Plot.Protein.Linear3.220.143.88
get.AASeq0.010.000.11
get.AlignedPositions3.270.033.45
get.Positions14.14 0.6716.06
get.Remapped.Order2.890.033.09
get.SingleLetterCode000
iPAC-package000
nmc14.05 0.0214.08

iPAC.Rcheck/examples_x64/iPAC-Ex.timings

nameusersystemelapsed
ClusterFind73.58 0.7974.94
KRAS.Mutations000
PIK3CA.Mutations0.000.030.03
Plot.Protein.Linear3.270.294.05
get.AASeq0.000.000.09
get.AlignedPositions3.400.033.58
get.Positions22.74 1.8325.61
get.Remapped.Order3.080.103.37
get.SingleLetterCode000
iPAC-package000
nmc16.15 0.0216.18