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CHECK report for QuartPAC on tokay1

This page was generated on 2020-04-15 12:24:09 -0400 (Wed, 15 Apr 2020).

Package 1351/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
QuartPAC 1.18.0
Gregory Ryslik
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/QuartPAC
Branch: RELEASE_3_10
Last Commit: c5fcfd7
Last Changed Date: 2019-10-29 13:09:07 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ ERROR ] OK 
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: QuartPAC
Version: 1.18.0
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:QuartPAC.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings QuartPAC_1.18.0.tar.gz
StartedAt: 2020-04-15 05:49:21 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 05:54:06 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 285.4 seconds
RetCode: 1
Status:  ERROR  
CheckDir: QuartPAC.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:QuartPAC.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings QuartPAC_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/QuartPAC.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'QuartPAC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'QuartPAC' version '1.18.0'
* 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 'QuartPAC' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
alignPositions: no visible global function definition for
  'PhredQuality'
alignPositions: no visible global function definition for
  'pairwiseAlignment'
constructCanonicalNumbering: no visible global function definition for
  'pattern'
constructCanonicalNumbering: no visible global function definition for
  'subject'
constructCanonicalNumbering: no visible global function definition for
  'start'
getMutations : <anonymous>: no visible global function definition for
  'read.table'
getRangeLocInfo: no visible global function definition for 'aggregate'
quartCluster: no visible global function definition for
  'capture.output'
Undefined global functions or variables:
  PhredQuality aggregate capture.output pairwiseAlignment pattern
  read.table start subject
Consider adding
  importFrom("stats", "aggregate", "start")
  importFrom("utils", "capture.output", "read.table")
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'QuartPAC-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: QuartPAC-package
> ### Title: Identifying mutational clusters while incorporating protein
> ###   quaternary structure.
> ### Aliases: QuartPAC-package QuartPAC
> ### Keywords: protein quaternary clustering
> 
> ### ** Examples
> 
> 
> #read the mutational data
> mutation_files <- list(
+         system.file("extdata","HFE_Q30201_MutationOutput.txt", package = "QuartPAC"),
+         system.file("extdata","B2M_P61769_MutationOutput.txt", package = "QuartPAC")
+ 					)
> uniprots <- list("Q30201","P61769")
> mutation.data <- getMutations(mutation_files = mutation_files, uniprots = uniprots)
Warning in file(con, "r") :
  InternetOpenUrl failed: 'An error occurred in the secure channel support'
Error in file(con, "r") : cannot open the connection
Calls: getMutations -> lapply -> FUN -> get.AASeq -> readLines -> file
Execution halted
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
QuartPAC-package          50.02   4.34   49.67
makeAlignedSuperStructure 24.62   4.73   24.41
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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 ERROR, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/QuartPAC.Rcheck/00check.log'
for details.


Installation output

QuartPAC.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/QuartPAC_1.18.0.tar.gz && rm -rf QuartPAC.buildbin-libdir && mkdir QuartPAC.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=QuartPAC.buildbin-libdir QuartPAC_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL QuartPAC_1.18.0.zip && rm QuartPAC_1.18.0.tar.gz QuartPAC_1.18.0.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  331k  100  331k    0     0  4758k      0 --:--:-- --:--:-- --:--:-- 5017k

install for i386

* installing *source* package 'QuartPAC' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'QuartPAC'
    finding HTML links ... done
    QuartPAC-package                        html  
    getMutations                            html  
    makeAlignedSuperStructure               html  
    quartCluster                            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 'QuartPAC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'QuartPAC' as QuartPAC_1.18.0.zip
* DONE (QuartPAC)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'QuartPAC' successfully unpacked and MD5 sums checked

Tests output

QuartPAC.Rcheck/tests_i386/runTests.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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.

> BiocGenerics:::testPackage("QuartPAC")
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.

gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.

Attaching package: 'gdata'

The following object is masked from 'package:stats':

    nobs

The following object is masked from 'package:utils':

    object.size

The following object is masked from 'package:base':

    startsWith


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from 'package:gdata':

    combine

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min


Attaching package: 'S4Vectors'

The following objects are masked from 'package:gdata':

    first, first<-

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'IRanges'

The following object is masked from 'package:gdata':

    trim

The following object is masked from 'package:grDevices':

    windows


Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'igraph'

The following object is masked from 'package:Biostrings':

    union

The following object is masked from 'package:IRanges':

    union

The following object is masked from 'package:S4Vectors':

    union

The following objects are masked from 'package:BiocGenerics':

    normalize, path, union

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union


Attaching package: 'combinat'

The following object is masked from 'package:utils':

    combn


Attaching package: 'data.table'

The following object is masked from 'package:IRanges':

    shift

The following objects are masked from 'package:S4Vectors':

    first, second

The following objects are masked from 'package:gdata':

    first, last

Performing SpacePAC calculations
Processing radius # 1 : radius length = 1.00 : Percentage complete 0.00 
Processing radius # 2 : radius length = 2.00 : Percentage complete 0.50 
Performing iPAC Calculations
[1] "Running Remapped"
Performing GraphPAC Calculations
Calculating Remapped Clusters.

RUNIT TEST PROTOCOL -- Wed Apr 15 05:53:12 2020 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
QuartPAC RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  40.68    4.43   41.79 

QuartPAC.Rcheck/tests_x64/runTests.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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.

> BiocGenerics:::testPackage("QuartPAC")
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.

gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.

Attaching package: 'gdata'

The following object is masked from 'package:stats':

    nobs

The following object is masked from 'package:utils':

    object.size

The following object is masked from 'package:base':

    startsWith


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from 'package:gdata':

    combine

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min


Attaching package: 'S4Vectors'

The following objects are masked from 'package:gdata':

    first, first<-

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'IRanges'

The following object is masked from 'package:gdata':

    trim

The following object is masked from 'package:grDevices':

    windows


Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'igraph'

The following object is masked from 'package:Biostrings':

    union

The following object is masked from 'package:IRanges':

    union

The following object is masked from 'package:S4Vectors':

    union

The following objects are masked from 'package:BiocGenerics':

    normalize, path, union

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union


Attaching package: 'combinat'

The following object is masked from 'package:utils':

    combn


Attaching package: 'data.table'

The following object is masked from 'package:IRanges':

    shift

The following objects are masked from 'package:S4Vectors':

    first, second

The following objects are masked from 'package:gdata':

    first, last

Performing SpacePAC calculations
Processing radius # 1 : radius length = 1.00 : Percentage complete 0.00 
Processing radius # 2 : radius length = 2.00 : Percentage complete 0.50 
Performing iPAC Calculations
[1] "Running Remapped"
Performing GraphPAC Calculations
Calculating Remapped Clusters.

RUNIT TEST PROTOCOL -- Wed Apr 15 05:53:58 2020 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
QuartPAC RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  45.56    5.31   45.53 

Example timings

QuartPAC.Rcheck/examples_i386/QuartPAC-Ex.timings

nameusersystemelapsed

QuartPAC.Rcheck/examples_x64/QuartPAC-Ex.timings

nameusersystemelapsed
QuartPAC-package50.02 4.3449.67
getMutations0.060.020.20
makeAlignedSuperStructure24.62 4.7324.41
quartCluster000