Back to Multiple platform build/check report for BioC 3.8
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

CHECK report for riboSeqR on tokay1

This page was generated on 2019-04-13 11:24:00 -0400 (Sat, 13 Apr 2019).

Package 1311/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
riboSeqR 1.16.0
Thomas J. Hardcastle
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/riboSeqR
Branch: RELEASE_3_8
Last Commit: 231a1bf
Last Changed Date: 2018-10-30 11:41:54 -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: riboSeqR
Version: 1.16.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:riboSeqR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings riboSeqR_1.16.0.tar.gz
StartedAt: 2019-04-13 05:03:47 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 05:07:26 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 218.7 seconds
RetCode: 0
Status:  OK  
CheckDir: riboSeqR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:riboSeqR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings riboSeqR_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/riboSeqR.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 'riboSeqR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'riboSeqR' version '1.16.0'
* 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 'riboSeqR' 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
.readAlignments : <anonymous>: no visible global function definition
  for 'read.delim'
filterHits : <anonymous> : <anonymous>: no visible global function
  definition for 'chisq.test'
frameCounting : getHits: no visible global function definition for
  'queryHits'
frameCounting : getHits: no visible global function definition for
  'subjectHits'
lengthDist: no visible global function definition for 'modifyList'
lengthDist: no visible global function definition for 'rainbow'
lengthDist: no visible binding for global variable 'lines'
plotCDS: no visible global function definition for 'dev.list'
plotCDS: no visible global function definition for 'par'
plotCDS : <anonymous> : <anonymous> : makeMatz: no visible binding for
  global variable 'weighted.mean'
plotCDS : <anonymous> : <anonymous>: no visible global function
  definition for 'barplot'
plotCDS : <anonymous> : <anonymous>: no visible global function
  definition for 'rainbow'
plotCDS : <anonymous> : <anonymous>: no visible global function
  definition for 'axis'
plotFS: no visible global function definition for 'barplot'
plotFS: no visible global function definition for 'rainbow'
plotTranscript: no visible global function definition for 'dev.list'
plotTranscript: no visible global function definition for 'par'
plotTranscript: no visible global function definition for 'plot'
plotTranscript: no visible global function definition for 'barplot'
plotTranscript: no visible global function definition for 'axis'
plotTranscript: no visible global function definition for 'rect'
plotTranscript: no visible global function definition for 'text'
plotTranscript: no visible global function definition for 'rgb'
plotTranscript: no visible global function definition for 'segments'
rnaCounts : <anonymous>: no visible global function definition for
  'subjectHits'
Undefined global functions or variables:
  axis barplot chisq.test dev.list lines modifyList par plot queryHits
  rainbow read.delim rect rgb segments subjectHits text weighted.mean
Consider adding
  importFrom("grDevices", "dev.list", "rainbow", "rgb")
  importFrom("graphics", "axis", "barplot", "lines", "par", "plot",
             "rect", "segments", "text")
  importFrom("stats", "chisq.test", "weighted.mean")
  importFrom("utils", "modifyList", "read.delim")
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' ... OK
** running examples for arch 'x64' ... OK
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/riboSeqR.Rcheck/00check.log'
for details.



Installation output

riboSeqR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/riboSeqR_1.16.0.tar.gz && rm -rf riboSeqR.buildbin-libdir && mkdir riboSeqR.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=riboSeqR.buildbin-libdir riboSeqR_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL riboSeqR_1.16.0.zip && rm riboSeqR_1.16.0.tar.gz riboSeqR_1.16.0.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 3546k  100 3546k    0     0  35.7M      0 --:--:-- --:--:-- --:--:-- 37.2M

install for i386

* installing *source* package 'riboSeqR' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'riboSeqR'
    finding HTML links ... done
    filterHits                              html  
    findCDS                                 html  
    frameCounting                           html  
    frameShift                              html  
    lengthDist                              html  
    libScales                               html  
    logoContext                             html  
    plotCDS                                 html  
    plotTranscript                          html  
    readRibodata                            html  
    riboCoding-class                        html  
    riboData-class                          html  
    riboSeqR-package                        html  
    rnaCounts                               html  
    sliceCounts                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'riboSeqR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'riboSeqR' as riboSeqR_1.16.0.zip
* DONE (riboSeqR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'riboSeqR' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

riboSeqR.Rcheck/tests_i386/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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("riboSeqR")

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 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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min


Attaching package: 'S4Vectors'

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

    expand.grid


Attaching package: 'IRanges'

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

    windows



RUNIT TEST PROTOCOL -- Sat Apr 13 05:07:16 2019 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
riboSeqR RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   5.50    0.46    5.95 

riboSeqR.Rcheck/tests_x64/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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("riboSeqR")

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 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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min


Attaching package: 'S4Vectors'

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

    expand.grid


Attaching package: 'IRanges'

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

    windows



RUNIT TEST PROTOCOL -- Sat Apr 13 05:07:21 2019 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
riboSeqR RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   5.04    0.20    5.23 

Example timings

riboSeqR.Rcheck/examples_i386/riboSeqR-Ex.timings

nameusersystemelapsed
filterHits1.470.112.37
findCDS0.200.000.21
frameCounting1.410.001.40
frameShift1.670.021.69
lengthDist0.890.000.89
plotCDS1.610.001.61
plotTranscript1.730.011.75
readRibodata0.890.000.89
rnaCounts1.500.021.51
sliceCounts1.740.021.75

riboSeqR.Rcheck/examples_x64/riboSeqR-Ex.timings

nameusersystemelapsed
filterHits1.900.031.94
findCDS0.220.000.22
frameCounting1.50.01.5
frameShift2.300.012.31
lengthDist0.920.040.96
plotCDS2.030.002.03
plotTranscript1.890.001.89
readRibodata1.020.001.01
rnaCounts1.860.001.86
sliceCounts2.330.012.34