Back to Multiple platform build/check report for BioC 3.8
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for cellscape on tokay1

This page was generated on 2019-04-13 11:27:33 -0400 (Sat, 13 Apr 2019).

Package 220/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellscape 1.6.0
Maia Smith
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/cellscape
Branch: RELEASE_3_8
Last Commit: 56305f7
Last Changed Date: 2018-10-30 11:42:04 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: cellscape
Version: 1.6.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cellscape.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings cellscape_1.6.0.tar.gz
StartedAt: 2019-04-13 01:04:24 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 01:06:03 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 98.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: cellscape.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cellscape.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings cellscape_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/cellscape.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 'cellscape/DESCRIPTION' ... OK
* this is package 'cellscape' version '1.6.0'
* 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 'cellscape' 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
Namespace in Imports field not imported from: 'plyr'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
cellscape: no visible global function definition for 'setNames'
cellscape: no visible global function definition for 'melt'
cellscape: no visible global function definition for 'na.omit'
cellscape: no visible global function definition for 'combn'
cellscape: no visible binding for global variable 'site'
cellscape: no visible binding for global variable 'genotype'
cellscape: no visible binding for global variable 'VAF'
cellscape: no visible global function definition for 'n'
cellscape: no visible binding for global variable 'n_gt'
cellscape: no visible binding for global variable 'n'
cellscape: no visible binding for global variable 'timepoint'
cellscape: no visible binding for global variable 'single_cell_id'
getCNVHeatmapForEachSC: no visible binding for global variable
  'single_cell_id'
getCNVHeatmapForEachSC: no visible binding for global variable 'px'
getCNVHeatmapForEachSC: no visible binding for global variable
  'px_width'
getCNVHeatmapForEachSC: no visible binding for global variable 'chr'
getCNVHeatmapForEachSC: no visible binding for global variable
  'chrom_index'
getCNVHeatmapForEachSC: no visible binding for global variable
  'copy_number'
getCNVHeatmapForEachSC: no visible binding for global variable 'sc_id'
getCNVHeatmapForEachSC: no visible binding for global variable
  'mode_cnv'
getCNVHeatmapForEachSC: no visible binding for global variable
  'cumsum_values'
getMutOrder: no visible global function definition for 'dist'
getMutOrder: no visible global function definition for 'hclust'
getMutOrder: no visible binding for global variable 'site'
getMutOrder: no visible binding for global variable 'VAF'
getMutOrder: no visible global function definition for 'lm'
getMutOrder: no visible binding for global variable 'na.omit'
getMutOrder: no visible global function definition for 'coef'
getMutationsData: no visible binding for global variable
  'show_warnings'
getTargetedHeatmapForEachSC: no visible binding for global variable
  'single_cell_id'
getTargetedHeatmapForEachSC: no visible binding for global variable
  'chr'
getTargetedHeatmapForEachSC: no visible binding for global variable
  'coord'
Undefined global functions or variables:
  VAF chr chrom_index coef combn coord copy_number cumsum_values dist
  genotype hclust lm melt mode_cnv n n_gt na.omit px px_width sc_id
  setNames show_warnings single_cell_id site timepoint
Consider adding
  importFrom("stats", "coef", "dist", "hclust", "lm", "na.omit",
             "setNames")
  importFrom("utils", "combn")
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 ... WARNING
Duplicated \argument entries in documentation object 'dfs_tree':
  'chrom_bounds' 'ncols' 'chrom_bounds' 'cnv_data' 'chrom_bounds'
  'n_bp_per_pixel' 'mut_data' 'width' 'height' 'mutations' 'height'
  'width' 'clonal_prev' 'tree_edges' 'alpha' 'clonal_prev' 'tree_edges'
  'genotype_position' 'clone_colours' 'perturbations' 'mutations'
  'tree_edges' 'clonal_prev' 'clonal_prev' 'tree_edges' 'clone_colours'
  'mutations'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 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, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/cellscape.Rcheck/00check.log'
for details.



Installation output

cellscape.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/cellscape_1.6.0.tar.gz && rm -rf cellscape.buildbin-libdir && mkdir cellscape.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cellscape.buildbin-libdir cellscape_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL cellscape_1.6.0.zip && rm cellscape_1.6.0.tar.gz cellscape_1.6.0.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  698k  100  698k    0     0  17.6M      0 --:--:-- --:--:-- --:--:-- 19.4M

install for i386

* installing *source* package 'cellscape' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'cellscape'
    finding HTML links ... done
    cellscape                               html  
    helpers                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'cellscape' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cellscape' as cellscape_1.6.0.zip
* DONE (cellscape)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'cellscape' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

cellscape.Rcheck/examples_i386/cellscape-Ex.timings

nameusersystemelapsed
cellscape1.880.423.95
helpers0.090.000.09

cellscape.Rcheck/examples_x64/cellscape-Ex.timings

nameusersystemelapsed
cellscape1.990.322.32
helpers0.080.000.08